Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ET-EHRED COMPLEX
 
Authors :  K. Okamura-Ikeda, H. Hosaka
Date :  06 Oct 09  (Deposition) - 07 Apr 10  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Glycine Cleavage System, Aminotransferase, Transferase, Lipoyl, Transferase-Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okamura-Ikeda, H. Hosaka, N. Maita, K. Fujiwara, A. C. Yoshizawa, A. Nakagawa, H. Taniguchi
Crystal Structure Of Aminomethyltransferase In Complex With Dihydrolipoyl-H-Protein Of The Glycine Cleavage System: Implications For Recognition Of Lipoyl Protein Substrate, Disease-Related Mutations, And Reaction Mechanism
J. Biol. Chem. V. 285 18684 2010
PubMed-ID: 20375021  |  Reference-DOI: 10.1074/JBC.M110.110718

(-) Compounds

Molecule 1 - AMINOMETHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12 SUBSTR. W3110
    Synonym: GLYCINE CLEAVAGE SYSTEM T PROTEIN
 
Molecule 2 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12 SUBSTR. W3110

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A   E 
Biological Unit 2 (1x):  B   F
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1LA22Mod. Amino AcidN~6~-[(6R)-6,8-DISULFANYLOCTANOYL]-L-LYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1LA21Mod. Amino AcidN~6~-[(6R)-6,8-DISULFANYLOCTANOYL]-L-LYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1LA21Mod. Amino AcidN~6~-[(6R)-6,8-DISULFANYLOCTANOYL]-L-LYSINE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1LA2-1Mod. Amino AcidN~6~-[(6R)-6,8-DISULFANYLOCTANOYL]-L-LYSINE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1LA2-1Mod. Amino AcidN~6~-[(6R)-6,8-DISULFANYLOCTANOYL]-L-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 3A8J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A8J)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:257 -Pro A:258
2Glu B:257 -Pro B:258
3Glu C:257 -Pro C:258
4Glu D:257 -Pro D:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A8J)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_ECOLI24-106
 		  2E:23-105
F:23-105
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_ECOLI49-78
 		  2E:48-77
F:48-77
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_ECOLI24-106
 		  1E:23-105
-
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_ECOLI49-78
 		  1E:48-77
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_ECOLI24-106
 		  1-
F:23-105
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_ECOLI49-78
 		  1-
F:48-77
Biological Unit 3 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_ECOLI24-106
 		  0-
-
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_ECOLI49-78
 		  0-
-
Biological Unit 4 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.GCSH_ECOLI24-106
 		  0-
-
2LIPOYLPS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.GCSH_ECOLI49-78
 		  0-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3A8J)

(-) 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:363
 aligned with GCST_ECOLI | P27248 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
           GCST_ECOLI     2 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 364
               SCOP domains d3a8ja1 A:1-276 automated matches                                                                                                                                                                                                                                                   d3a8ja2 A:277-363 automated matches                                                     SCOP domains
               CATH domains 3a8jA01 A:1-49,A:138-230                         ----------------------------------------------------------------------------------------3a8jA01 A:1-49,A:138-230 Probable tRNA modification gtpase trme; domain 1                    ---------------------------------------------3a8jA04 A:276-363 Aminomethyltransferase beta-barrel domains                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..hhhhh.....eeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.eeeee..eeeeeee..hhhhhhhh..hhhhhhhhh......eeee..eeee........eeeeeeehhhhhhhhhhhhhh..ee.hhhhhhhhhhhh.............hhhhh.hhhhh..........hhhhhhhhhhhh..eeeeeee..........eeeee.....eeeeeeeeeee......eeeeeee......eeeeee..eeeeeeee....ee..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8j A   1 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with GCST_ECOLI | P27248 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
           GCST_ECOLI     2 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 364
               SCOP domains d3a8jb1 B:1-276 automated matches                                                                                                                                                                                                                                                   d3a8jb2 B:277-363 automated matches                                                     SCOP domains
               CATH domains 3a8jB01 B:1-49,B:138-230                         ----------------------------------------------------------------------------------------3a8jB01 B:1-49,B:138-230 Probable tRNA modification gtpase trme; domain 1                    ---------------------------------------------3a8jB04 B:276-363 Aminomethyltransferase beta-barrel domains                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..hhhhh.....eeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.eeeee..eeeeeee..hhhhhhhh..hhhhhhhh.......eeee..eeee........eeeeeeehhhhhhhhhhhhhh..ee.hhhhhhhhhhhh.............hhhhh.hhhhh..........hhhhhhhhhhh...eeeeeee..........eeeee.....eeeeeeeeeee......eeeeeee......eeeeee..eeeeeeee....ee..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8j B   1 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   


Chain C from PDB  Type:PROTEIN  Length:363
 aligned with GCST_ECOLI | P27248 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
           GCST_ECOLI     2 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 364
               SCOP domains d3a8jc1 C:1-276 automated matches                                                                                                                                                                                                                                                   d3a8jc2 C:277-363 automated matches                                                     SCOP domains
               CATH domains 3a8jC01 C:1-49,C:138-230                         ----------------------------------------------------------------------------------------3a8jC01 C:1-49,C:138-230 Probable tRNA modification gtpase trme; domain 1                    ---------------------------------------------3a8jC04 C:276-363 Aminomethyltransferase beta-barrel domains                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..hhhhh.....eeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.eeeee..eeeeeee..hhhhhhhh..hhhhhhhhh......eeee..eeee........eeeeeee..hhhhhhhhhhhh..ee.hhhhhhhhhhhh.............hhhhhhhhhhh..........hhhhhhhhhhhh..eeeeeee..........eeeee.....eeeeeeeeeee......eeeeeee......eeeeee..eeeeeeee....ee..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8j C   1 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   


Chain D from PDB  Type:PROTEIN  Length:363
 aligned with GCST_ECOLI | P27248 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
           GCST_ECOLI     2 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 364
               SCOP domains d3a8jd1 D:1-276 automated matches                                                                                                                                                                                                                                                   d3a8jd2 D:277-363 automated matches                                                     SCOP domains
               CATH domains 3a8jD01 D:1-49,D:138-230                         ----------------------------------------------------------------------------------------3a8jD01 D:1-49,D:138-230 Probable tRNA modification gtpase trme; domain 1                    ---------------------------------------------3a8jD04 D:276-363 Aminomethyltransferase beta-barrel domains                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..hhhhh.....eeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.eeeee..eeeeeee..hhhhhhhh..hhhhhhhh.......eeee..eeee........eeeeeee..hhhhhhhhhhhh..ee.hhhhhhhhhhhh.............hhhhhhhhhhh..........hhhhhhhhhhhh..eeeeeee..........eeeee.....eeeeeeeeeeee....eeeeeeee......eeeeee..eeeeeeee....ee..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8j D   1 AQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   


Chain E from PDB  Type:PROTEIN  Length:127
 aligned with GCSH_ECOLI | P0A6T9 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           GCSH_ECOLI     2 SNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLED 128
               SCOP domains d3a8je_ E: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 3a8jE00 E:1-127  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....eeeee.....eeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhhhhhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------BIOTINYL_LIPOYL  PDB: E:23-105 UniProt: 24-106                                     ---------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------LIPOYL  PDB: E:48-77          -------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8j E   1 SNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVkAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLED 127
                                    10        20        30        40        50        60   |    70        80        90       100       110       120       
                                                                                          64-LA2                                                           


Chain F from PDB  Type:PROTEIN  Length:128
 aligned with GCSH_ECOLI | P0A6T9 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
           GCSH_ECOLI     2 SNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 129
               SCOP domains d3a8jf_ F: Protein H of glycine cleavage system                                                                                  SCOP domains
               CATH domains 3a8jF00 F:1-128  [code=2.40.50.100, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...eeeee.....eeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhhhhhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------BIOTINYL_LIPOYL  PDB: F:23-105 UniProt: 24-106                                     ----------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------LIPOYL  PDB: F:48-77          --------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8j F   1 SNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVkAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 128
                                    10        20        30        40        50        60   |    70        80        90       100       110       120        
                                                                                          64-LA2
   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  (3, 10)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 10)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A8J)

(-) Gene Ontology  (10, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GCST_ECOLI | P27248)
molecular function
    GO:0004047    aminomethyltransferase activity    Catalysis of the reaction: (6S)-tetrahydrofolate + S-aminomethyldihydrolipoylprotein = (6R)-5,10-methylenetetrahydrofolate + NH3 + dihydrolipoylprotein.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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:0006546    glycine catabolic process    The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.
    GO:0019464    glycine decarboxylation via glycine cleavage system    The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain E,F   (GCSH_ECOLI | P0A6T9)
molecular function
    GO:0031405    lipoic acid binding    Interacting selectively and non-covalently with lipoic acid, 1,2-dithiolane-3-pentanoic acid.
biological process
    GO:0019464    glycine decarboxylation via glycine cleavage system    The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005960    glycine cleavage complex    A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    LA2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3a8j)
 
  Cis Peptide Bonds
    Glu A:257 - Pro A:258   [ RasMol ]  
    Glu B:257 - Pro B:258   [ RasMol ]  
    Glu C:257 - Pro C:258   [ RasMol ]  
    Glu D:257 - Pro D:258   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3a8j
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GCSH_ECOLI | P0A6T9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  GCST_ECOLI | P27248
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.2.10
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GCSH_ECOLI | P0A6T9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GCST_ECOLI | P27248
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GCSH_ECOLI | P0A6T9: 3a7a 3a7l 3a8i 3a8k 3ab9
        GCST_ECOLI | P27248: 1vlo 3a8i 3a8k

(-) Related Entries Specified in the PDB File

1wsr HUMAN T-PROTEIN IN COMPLEX WITH 5-CH3-THF
1wsv UNLIGANDED HUMAN T-PROTEIN
3a8i
3a8k