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Title :  CRYSTAL STRUCTURE OF AMINOMETHYLTRANSFERASE (T PROTEIN; TETRAHYDROFOLATE-DEPENDENT) OF GLYCINE CLEAVAGE SYSTEM (NP417381) FROM ESCHERICHIA COLI K12 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Aug 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Np417381, Aminomethyltransferase (T Protein; Tetrahydrofolate- Dependent) Of Glycine Cleavage System, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Aminomethyltransferase (T Protein; Tetrahydrofolate-Dependent) Of Glycine Cleavage System (Np417381) From Escherichia Coli K12 At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOMETHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GCVT
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Other Details: T PROTEIN, TETRAHYDROFOLATE-DEPENDENT
    Strain: K12
    Synonym: GLYCINE CLEAVAGE SYSTEM T PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric/Biological Unit (1, 13)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VLO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:258 -Pro A:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VLO)

(-) Sequences/Alignments

Asymmetric/Biological 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:364
 aligned with GCST_ECOLI | P27248 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:364
                                                                                                                                                                                                                                                                                                                                                                                                  364   
                                    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|   
           GCST_ECOLI     4 QTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA---   -
               SCOP domains d1vloa2 A:4-277 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                           d1vloa1 A:278-367 Glycine cleavage system T protein, GcvT                                  SCOP domains
               CATH domains 1vloA01 A:4-50,A:139-231                       ----------------------------------------------------------------------------------------1vloA01 A:4-50,A:139-231 Probable tRNA modification gtpase trme; domain 1                    ---------------------------------------------1vloA04 A:277-367 Aminomethyltransferase beta-barrel domains                                CATH domains
               Pfam domains ------------------------------------------GCV_T-1vloA01 A:46-254                                                                                                                                                                                           -------GCV_T_C-1vloA02 A:262-354                                                                    ------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..hhhhh.....eeeeeee.....eeeeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh.eeee...eeeeeee..hhhhhhhh..hhhhhhhhh......eeee..eeee........eeeeeeehhhhhhhhhhhhhh..ee.hhhhhhhhhhhh.............hhhhh.hhhhh..........hhhhhhhhhhhh..eeeeeee..........eeeee.....eeeeeeeeeeee....eeeeeeee......eeeeee..eeeeeeee....ee..ee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlo A   4 QTPLYEQHTLCGARmVDFHGWmmPLHYGSQIDEHHAVRTDAGmFDVSHmTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGmLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSmIAVQGPNAQAKAATLFNDAQRQAVEGmKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGmNLYGQEmDETISPLAANmGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVmTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREmPVKVTKPVFVRNGKAVAGLC 367
                                    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    
                                         18-MSE 25-MSE               46-MSE |                                  88-MSE                                                 144-MSE                    171-MSE                                                       233-MSE  |        251-MSE                            286-MSE                                                      347-MSE                
                                                 26-MSE                    52-MSE                                                                                                                                                                                     240-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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FBD (14)
(-)
Clan: no clan defined [family: GCV_T_C] (10)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

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    Glu A:258 - Pro A:259   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCST_ECOLI | P27248: 3a8i 3a8j 3a8k

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