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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROBABLE AMINOMETHYLTRANSFERASE FROM BACILLUS SUBTILIS
 
Authors :  Midwest Center For Structural Genomics (Mcsg)
Date :  19 Feb 05  (Deposition) - 05 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aminomethyltransferase, Glycine Cleavage System T Protein, Alpha-Beta, Beta-Barrel, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, P. Quartey, L. Lezondra, F. Collart, A. Joachimiak
Crystal Structure Of The Probable Aminomethyltransferase From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOMETHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GCVT
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: GLYCINE CLEAVAGE SYSTEM T PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE13Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:27 , ASP B:48 , CYS B:223 , LEU B:225BINDING SITE FOR RESIDUE EDO B 1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YX2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:357 -Pro A:358
2Thr B:357 -Pro B:358

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YX2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YX2)

(-) Exons   (0, 0)

(no "Exon" information available for 1YX2)

(-) 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:358
 aligned with GCST_BACSU | P54378 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:358
                                    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        
           GCST_BACSU     2 LKRTPLFDLYKEYGGKTIDFGGWELPVQFSSIKKEHEAVRTAAGLFDVSHMGEVEVSGNDSLSFLQRLMTNDVSALTPGRAQYTAMCYPDGGTVDDLLIYQKGENRYLLVINASNIDKDLAWMKEHAAGDVQIDNQSDQIALLAVQGPKAEAILKNLTDADVSALKPFAFIDEADISGRKALISRTGYTGEDGYEIYCRSDDAMHIWKKIIDAGDAYGLIPCGLGARDTLRFEAKLPLYGQELTRDITPIEAGIGFAVKHKKESDFFGKSVLSEQKENGAKRKLVGLEMIEKGIPRHGYEVFQNGKSVGKVTTGTQSPTLGKNVGLALIDSETSEIGTVVDVEIRKKLVKAKVVKTPF 359
               SCOP domains d1yx2a1 A:2-282 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                                  d1yx2a2 A:283-359 Glycine cleavage system T protein, GcvT                     SCOP domains
               CATH domains 1yx2A01 A:2-50,A:137-235                         1yx2A02 A:51-136 Aminomethyltransferase beta-barrel domains                           1yx2A01 A:2-50,A:137-235 Probable tRNA modification gtpase trme; domain 1                          --------------------------------------------1yx2A04 A:280-359 Aminomethyltransferase beta-barrel domains                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh.eeeee..eeeeee..hhhhhhhhhhhheeeee....eeeeee..hhhhhhhhhh..hhhhh....eeeeeee.....eeeeeeeeeee..eeeeeehhhhhhhhhhhhhhh.....eeee....eeeeeee..hhhhhhhh....hhhhh....eeeeeee..eeeeee........eeeeeee..hhhhhhhhhhhhhh...eeeehhhhhhhhhhhh...................hhhhh.........hhhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeeee....eeeeeeeee.hhh....eeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yx2 A   2 LKRTPLFDLYKEYGGKTIDFGGWELPVQFSSIKKEHEAVRTAAGLFDVSHmGEVEVSGNDSLSFLQRLmTNDVSALTPGRAQYTAmCYPDGGTVDDLLIYQKGENRYLLVINASNIDKDLAWmKEHAAGDVQIDNQSDQIALLAVQGPKAEAILKNLTDADVSALKPFAFIDEADISGRKALISRTGYTGEDGYEIYCRSDDAmHIWKKIIDAGDAYGLIPCGLGARDTLRFEANIPLYGQELTRDITPIEAGIGFAVKHKKESDFFGKSVLSEQKENGAKRKLVGLEmIEKGIPRHGYEVFQNGKSVGKVTTGTQSPTLGKNVGLALIDSETSEIGTVVDVEIRKKLVKAKVVKTPF 359
                                    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        
                                                                             52-MSE            70-MSE           87-MSE                              124-MSE                                                                          205-MSE                                                                              290-MSE                                                                 


Chain B from PDB  Type:PROTEIN  Length:362
 aligned with GCST_BACSU | P54378 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:362
                                    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  
           GCST_BACSU     1 MLKRTPLFDLYKEYGGKTIDFGGWELPVQFSSIKKEHEAVRTAAGLFDVSHMGEVEVSGNDSLSFLQRLMTNDVSALTPGRAQYTAMCYPDGGTVDDLLIYQKGENRYLLVINASNIDKDLAWMKEHAAGDVQIDNQSDQIALLAVQGPKAEAILKNLTDADVSALKPFAFIDEADISGRKALISRTGYTGEDGYEIYCRSDDAMHIWKKIIDAGDAYGLIPCGLGARDTLRFEAKLPLYGQELTRDITPIEAGIGFAVKHKKESDFFGKSVLSEQKENGAKRKLVGLEMIEKGIPRHGYEVFQNGKSVGKVTTGTQSPTLGKNVGLALIDSETSEIGTVVDVEIRKKLVKAKVVKTPFYKR 362
               SCOP domains d1yx2b1 B:1-282 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                                   d1yx2b2 B:283-362 Glycine cleavage system T protein, GcvT                        SCOP domains
               CATH domains -1yx2B01 B:2-50,B:137-235                         1yx2B02 B:51-136 Aminomethyltransferase beta-barrel domains                           1yx2B01 B:2-50,B:137-235 Probable tRNA modification gtpase trme; domain 1                          --------------------------------------------1yx2B04 B:280-362 Aminomethyltransferase beta-barrel domains                        CATH domains
           Pfam domains (1) ---------------------------------------------GCV_T-1yx2B01 B:46-258                                                                                                                                                                                               ------GCV_T_C-1yx2B03 B:265-357                                                                    ----- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------GCV_T-1yx2B02 B:46-258                                                                                                                                                                                               ------GCV_T_C-1yx2B04 B:265-357                                                                    ----- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhh.eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..hhhhh...eeeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhhhh....eeee....eeeeeee..hhhhhhhhhh...........eeeeeee..eeeeee........eeeeeee..hhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhh...................hhhhh.........hhhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeeee....eeeeeeeee.hhh....eeeeee..eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yx2 B   1 mLKRTPLFDLYKEYGGKTIDFGGWELPVQFSSIKKEHEAVRTAAGLFDVSHmGEVEVSGNDSLSFLQRLmTNDVSALTPGRAQYTAmCYPDGGTVDDLLIYQKGENRYLLVINASNIDKDLAWmKEHAAGDVQIDNQSDQIALLAVQGPKAEAILKNLTDADVSALKPFAFIDEADISGRKALISRTGYTGEDGYEIYCRSDDAmHIWKKIIDAGDAYGLIPCGLGARDTLRFEANIPLYGQELTRDITPIEAGIGFAVKHKKESDFFGKSVLSEQKENGAKRKLVGLEmIEKGIPRHGYEVFQNGKSVGKVTTGTQSPTLGKNVGLALIDSETSEIGTVVDVEIRKKLVKAKVVKTPFYKR 362
                            |       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  
                            1-MSE                                             52-MSE            70-MSE           87-MSE                              124-MSE                                                                          205-MSE                                                                              290-MSE
   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  (2, 4)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: FBD (14)
(-)
Family: GCV_T (12)
(-)
Clan: no clan defined [family: GCV_T_C] (10)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GCST_BACSU | P54378)
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.

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