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(-) Description

Title :  CRYSTAL STRUCTURE OF T-PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM
 
Authors :  H. H. Lee, D. J. Kim, H. J. Ahn, J. Y. Ha, S. W. Suh
Date :  24 Aug 04  (Deposition) - 07 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Aminomethyltransferase, T-Protein, Folinic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Lee, D. J. Kim, H. J. Ahn, J. Y. Ha, S. W. Suh
Crystal Structure Of T-Protein Of The Glycine Cleavage System: Cofactor Binding, Insights Into H-Protein Recognition, And Molecular Basis For Understanding Nonketotic Hyperglycinemia
J. Biol. Chem. V. 279 50514 2004
PubMed-ID: 15355973  |  Reference-DOI: 10.1074/JBC.M409672200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOMETHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    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, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FFO2Ligand/Ion5-FORMYL-6-HYDROFOLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:51 , TYR A:83 , ASP A:96 , VAL A:98 , TYR A:100 , VAL A:110 , ASN A:112 , TYR A:168 , TYR A:169 , GLY A:187 , TYR A:188 , GLU A:195 , ARG A:227 , TYR A:236 , TRP A:256 , ARG A:362 , HOH A:2909 , HOH A:2931 , HOH A:2941 , HOH A:2983 , HOH A:3138BINDING SITE FOR RESIDUE FFO A 2887
2AC2SOFTWARELEU A:55 , GLU A:106 , LEU A:108 , ILE A:137 , GLU A:160 , LYS A:173 , SER A:174 , ILE A:175 , GLU A:180 , THR A:181 , LEU A:182 , MET A:197 , HOH A:2910 , HOH A:2950 , HOH A:2960BINDING SITE FOR RESIDUE FFO A 2888

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:353 -Pro A:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WOP)

(-) 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:362
 aligned with GCST_THEMA | Q9WY54 from UniProtKB/Swiss-Prot  Length:364

    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_THEMA     1 MKRTPLFEKHVELGAKMVDFAGWEMPLYYTSIFEEVMAVRKSVGMFDVSHMGEFLVKGPEAVSFIDFLITNDFSSLPDGKAIYSVMCNENGGIIDDLVVYKVSPDEALMVVNAANIEKDFNWIKSHSKNFDVEVSNISDTTALIAFQGPKAQETLQELVEDGLEEIAYYSFRKSIVAGVETLVSRTGYTGEDGFELMLEAKNAPKVWDALMNLLRKIDGRPAGLGARDVCRLEATYLLYGQDMDENTNPFEVGLSWVVKLNKDFVGKEALLKAKEKVERKLVALELSGKRIARKGYEVLKNGERVGEITSGNFSPTLGKSIALALVSKSVKIGDQLGVVFPGGKLVEALVVKKPFYRGSVRR 362
               SCOP domains d1wopa2 A:1-278 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                               d1wopa1 A:279-362 Glycine cleavage system T protein, GcvT                            SCOP domains
               CATH domains 1wopA01 A:1-49,A:137-234                         ---------------------------------------------------------------------------------------1wopA01 A:1-49,A:137-234 Probable tRNA modification gtpase trme; domain 1                         -----------------------------------------1wopA04 A:276-362 Aminomethyltransferase beta-barrel domains                            CATH domains
               Pfam domains --------------------------------------------GCV_T-1wopA01 A:45-257                                                                                                                                                                                               ----GCV_T_C-1wopA02 A:262-353                                                                   --------- Pfam domains
         Sec.struct. author .....hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..........eeeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhh.......eeee....eeeeeee..hhhhhhhhhh..hhhhh....eeeeee..eeeeee........eeeeeee..hhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhh.............hhhhhhhhhhh.......hhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeeee....eeeeeeeee.......eeeeee...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wop A   1 MKRTPLFEKHVELGAKMVDFAGWEMPLYYTSIFEEVMAVRKSVGMFDVSHMGEFLVKGPEAVSFIDFLITNDFSSLPDGKAIYSVMCNENGGIIDDLVVYKVSPDEALMVVNAANIEKDFNWIKSHSKNFDVEVSNISDTTALIAFQGPKAQETLQELVEDGLEEIAYYSFRKSIVAGVETLVSRTGYTGEDGFELMLEAKNAPKVWDALMNLLRKIDGRPAGLGARDVCRLEATYLLYGQDMDENTNPFEVGLSWVVKLNKDFVGKEALLKAKEKVERKLVALELSGKRIARKGYEVLKNGERVGEITSGNFSPTLGKSIALALVSKSVKIGDQLGVVFPGGKLVEALVVKKPFYRGSVRR 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
   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  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GCST_THEMA | Q9WY54)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        GCST_THEMA | Q9WY54: 1woo 1wor 1wos

(-) Related Entries Specified in the PDB File

1woo THE SAME PROTEIN COMPLEXED WITH TETRAHYDROFOLATE
1wor THE SAME PROTEIN COMPLEXED WITH DIHYDROLIPOIC ACID
1wos THE SAME PROTEIN OF NATIVE FORM