Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) 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 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycine Cleavage System, Tetrahydrofolate, T-Protein, Transferase (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

(-) 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, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1THG1Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
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:2907 , HOH A:2909 , HOH A:2935 , HOH A:2960BINDING SITE FOR RESIDUE THG A 2887

(-) SS Bonds  (0, 0)

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

(-) 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 1WOO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WOO)

(-) 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 d1wooa2 A:1-278 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                               d1wooa1 A:279-362 Glycine cleavage system T protein, GcvT                            SCOP domains
               CATH domains 1wooA01 A:1-49,A:137-234                         ---------------------------------------------------------------------------------------1wooA01 A:1-49,A:137-234 Probable tRNA modification gtpase trme; domain 1                         -----------------------------------------1wooA04 A:276-362 Aminomethyltransferase beta-barrel domains                            CATH domains
               Pfam domains --------------------------------------------GCV_T-1wooA01 A:45-257                                                                                                                                                                                               ----GCV_T_C-1wooA02 A:262-353                                                                   --------- Pfam domains
         Sec.struct. author .....hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..........eeeeeeee.....eeeeeeeeeee..eeeeeehhhhhhhhhhhhhh.......eeee....eeeeeee..hhhhhhhhhh..hhhhh....eeeeee..eeeeee........eeeeeee..hhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhh............hhhhhhhhhhh.......hhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeeee....eeeeeeeee.......eeeeee...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1woo 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    THG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:353 - Pro A:354   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1woo
    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
  GCST_THEMA | Q9WY54
    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
  GCST_THEMA | Q9WY54
    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
        GCST_THEMA | Q9WY54: 1wop 1wor 1wos

(-) Related Entries Specified in the PDB File

1wop THE SAME PROTEIN COMPLEXED WITH FOLINIC ACID
1wor THE SAME PROTEIN COMPLEXED WITH DIHYDROLIPOIC ACID
1wos THE SAME PROTEIN OF NATIVE FORM