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(-) Description

Title :  CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Aug 08  (Deposition) - 09 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Ssgcid, Decode, Bupsa00008A, One-Carbon Metabolism, Pyridoxal Phosphate, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Serine Hydroxymethyltransferase From Burkholderia Pseudomallei
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE 2
    Chains: A, B, C, D
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Vector Type: AVA0421
    Gene: GLYA2, BPSS0547
    Organism Common: PSEUDOMONAS PSEUDOMALLEI
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Strain: 1710B
    Synonym: SERINE METHYLASE 2, SHMT 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:237 , ASP A:286 , TYR A:290 , THR A:374 , HOH A:677 , HOH A:682 , ASN D:5 , PHE D:7BINDING SITE FOR RESIDUE GOL A 425
2AC2SOFTWAREARG B:237 , ASP B:286 , TYR B:290 , THR B:374 , HOH B:565 , HOH B:747 , HOH B:748 , ASN C:5 , PHE C:7BINDING SITE FOR RESIDUE GOL B 425
3AC3SOFTWAREASN B:5 , PHE B:7 , ARG C:237 , ASP C:286 , TYR C:290 , THR C:374 , HOH C:888 , HOH C:990BINDING SITE FOR RESIDUE GOL C 425
4AC4SOFTWAREASN A:5 , PHE A:7 , ARG D:237 , ASP D:286 , TYR D:290 , THR D:374 , HOH D:513 , HOH D:543 , HOH D:654BINDING SITE FOR RESIDUE GOL D 425

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ECD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly C:266 -Pro C:267
2Gly D:266 -Pro D:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ECD)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYA2_BURP1226-242
 
 
 		  4A:226-242
B:226-242
C:226-242
D:226-242
GLYA2_BURPS226-242
 
 
 		  4A:226-242
B:226-242
C:226-242
D:226-242
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYA2_BURP1226-242
 
 
 		  2A:226-242
-
-
D:226-242
GLYA2_BURPS226-242
 
 
 		  2A:226-242
-
-
D:226-242
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYA2_BURP1226-242
 
 
 		  2-
B:226-242
C:226-242
-
GLYA2_BURPS226-242
 
 
 		  2-
B:226-242
C:226-242
-

(-) Exons   (0, 0)

(no "Exon" information available for 3ECD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:387
 aligned with GLYA2_BURP1 | Q3JGP5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:422
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
          GLYA2_BURP1     3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -----------------------------------------3ecdA01 A:44-283 Ty            pe I PLP-dependent aspartate aminotransferase-like                   (Major domain)                                                                                                                              3ecdA02 A:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh.....------------.hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhhh-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd A   3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEG------------ADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVF-----GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    12        22        32        42        52        62         -  |     82        92       102       112       122  |      -         - |     152       162       172       182       192       202       212       222       232       242       252       | -   |   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                      62           75                                               125                144                                                                                                                 260   266                                                                                                                                                              


Chain A from PDB  Type:PROTEIN  Length:387
 aligned with GLYA2_BURPS | Q63MV1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:422
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
          GLYA2_BURPS     3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -----------------------------------------3ecdA01 A:44-283 Ty            pe I PLP-dependent aspartate aminotransferase-like                   (Major domain)                                                                                                                              3ecdA02 A:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh.....------------.hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhhh-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd A   3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEG------------ADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVF-----GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    12        22        32        42        52        62         -  |     82        92       102       112       122  |      -         - |     152       162       172       182       192       202       212       222       232       242       252       | -   |   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                      62           75                                               125                144                                                                                                                 260   266                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with GLYA2_BURP1 | Q3JGP5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:422
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
          GLYA2_BURP1     3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecdb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -----------------------------------------3ecdB01 B:44-283 Typ           e I PLP-dependent aspartate aminotransferase-like (                  Major domain)                                                                                                                               3ecdB02 B:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh......-----------.hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd B   3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGY-----------ADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFP----GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    12        22        32        42        52        62|        -  |     82        92       102       112       122  |      -         - |     152       162       172       182       192       202       212       222       232       242       252        |-   |   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                       63          75                                               125                144                                                                                                                  261  266                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with GLYA2_BURPS | Q63MV1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:422
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
          GLYA2_BURPS     3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecdb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -----------------------------------------3ecdB01 B:44-283 Typ           e I PLP-dependent aspartate aminotransferase-like (                  Major domain)                                                                                                                               3ecdB02 B:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh......-----------.hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd B   3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGY-----------ADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFP----GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    12        22        32        42        52        62|        -  |     82        92       102       112       122  |      -         - |     152       162       172       182       192       202       212       222       232       242       252        |-   |   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                       63          75                                               125                144                                                                                                                  261  266                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:386
 aligned with GLYA2_BURP1 | Q3JGP5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:422
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
          GLYA2_BURP1     3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecdc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -----------------------------------------3ecdC01 C:44-283 Typ            e I PLP-dependent aspartate aminotransferase-like                   (Major domain)                                                                                                                              3ecdC02 C:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh......------------hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhh------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd C   3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGY------------DEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAV------GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    12        22        32        42        52        62|        -   |    82        92       102       112       122  |      -         - |     152       162       172       182       192       202       212       222       232       242       252      |  -   |   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                       63           76                                              125                144                                                                                                                259    266                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:386
 aligned with GLYA2_BURPS | Q63MV1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:422
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
          GLYA2_BURPS     3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecdc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -----------------------------------------3ecdC01 C:44-283 Typ            e I PLP-dependent aspartate aminotransferase-like                   (Major domain)                                                                                                                              3ecdC02 C:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh......------------hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhh------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd C   3 NANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGY------------DEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAV------GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    12        22        32        42        52        62|        -   |    82        92       102       112       122  |      -         - |     152       162       172       182       192       202       212       222       232       242       252      |  -   |   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                       63           76                                              125                144                                                                                                                259    266                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:382
 aligned with GLYA2_BURP1 | Q3JGP5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
          GLYA2_BURP1     4 ANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecdd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------3ecdD01 D:44-283                Type I PLP-dependent aspartate aminotransferase-li                  ke (Major domain)                                                                                                                           3ecdD02 D:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh...---------------hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhh------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd D   4 ANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA---------------DEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAV------GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    13        23        33        43        53      |  -         -  |     83        93       103       113       123 |       -         -|      153       163       173       183       193       203       213       223       233       243       253     |   -  |    273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
                                                                                   60              76                                              125                144                                                                                                                259    266                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:382
 aligned with GLYA2_BURPS | Q63MV1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
          GLYA2_BURPS     4 ANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
               SCOP domains d3ecdd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------3ecdD01 D:44-283                Type I PLP-dependent aspartate aminotransferase-li                  ke (Major domain)                                                                                                                           3ecdD02 D:284-424 Aspartate Aminotransferase, domain 1                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh...---------------hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh....eeeee..------------------.eeeee.........hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeee.hhhhhhhhhhhh------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ecd D   4 ANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA---------------DEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSL------------------FNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLTNDEEIAKKINSAV------GPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
                                    13        23        33        43        53      |  -         -  |     83        93       103       113       123 |       -         -|      153       163       173       183       193       203       213       223       233       243       253     |   -  |    273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
                                                                                   60              76                                              125                144                                                                                                                259    266
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ECD)

(-) Gene Ontology  (12, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GLYA2_BURPS | Q63MV1)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004372    glycine hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0019264    glycine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B,C,D   (GLYA2_BURP1 | Q3JGP5)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004372    glycine hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0019264    glycine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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