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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPONENT OF GLYCINE CLEAVAGE SYSTEM: T-PROTEIN FROM PYROCOCCUS HORIKOSHII OT3 AT 1.5 A RESOLUTION
 
Authors :  N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomic Initiative (Rsgi)
Date :  26 Nov 03  (Deposition) - 26 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycine-Cleavage Sytem, Aminomethyl Transferase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, C. Kuroishi, N. Okazaki, N. Kunishima
Crystal Structure Of A Component Of Glycine Cleavage System T-Protein From Pyrococcus Horikoshii Ot3 At 1. 5 A Resolutio
Proteins V. 58 769 2004
PubMed-ID: 15609340  |  Reference-DOI: 10.1002/PROT.20345

(-) Compounds

Molecule 1 - AMINOMETHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GCS
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: GLYCINE CLEAVAGE SYSTEM T PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:316 , HIS A:317 , ALA A:365 , PRO A:367 , VAL A:385 , HOH A:1070 , HOH A:1110 , HOH A:1113BINDING SITE FOR RESIDUE GOL A 901
2AC2SOFTWAREVAL B:316 , HIS B:317 , ALA B:365 , LYS B:366 , PRO B:367 , VAL B:385 , HOH B:1728BINDING SITE FOR RESIDUE GOL B 902
3AC3SOFTWAREPHE A:398 , LYS B:79 , TRP B:177BINDING SITE FOR RESIDUE PEG B 1503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V5V)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:82 -Ile A:83
2Glu A:279 -Val A:280
3Pro A:387 -Pro A:388
4Ala B:82 -Ile B:83
5Glu B:279 -Val B:280
6Pro B:387 -Pro B:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V5V)

(-) Exons   (0, 0)

(no "Exon" information available for 1V5V)

(-) 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:399
 aligned with GCST_PYRHO | O58888 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:399
                             1                                                                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389         
           GCST_PYRHO     - -MVKRVHIFDWHKEHARKIEEFAGWEMPIWYSSIKEEHLAVRNAVGIFDVSHMGEIVFRGKDALKFLQYVTTNDISKPPAISGTYTLVLNERGAIKDETLVFNMGNNEYLMICDSDAFEKLYAWFTYLKRTIEQFTKLDLEIELKTYDIAMFAVQGPKARDLAKDLFGIDINEMWWFQARWVELDGIKMLLSRSGYTGENGFEVYIEDANPYHPDESKRGEPEKALHVWERILEEGKKYGIKPCGLGARDTLRLEAGYTLYGNETKELQLLSTDIDEVTPLQANLEFAIYWDKDFIGKDALLKQKERGVGRKLVHFKMIDKGIPREGYKVYANGEMIGEVTSGTLSPLLNVGIGIAFVKEEYAKPGIEIEVEIRGQRKKAVTVTPPFYDPKKYGLFRET 398
               SCOP domains d1v5va2 A:3-312 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                                                               d1v5va1 A:313-401 Glycine cleavage system T protein, GcvT                                 SCOP domains
               CATH domains 1v5vA01 A:3-54,A:147-258                            --------------------------------------------------------------------------------------------1v5vA01 A:3-54,A:147-258 Probable tRNA modification gtpase trme; domain 1                                       -----------------------------------------------------1v5vA03 A:312-386 Aminomethyltransferase beta-barrel domains               --------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..........eeeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhhh......eeee....eeeeeee..hhhhhhhhhhh.hhhhh....eeeeee..eeeeee........eeeeeee.......hhhhh..hhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhh...........................hhhhh.......hhhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeee......eeeeeeee.hhh....eeeeee..eeeeeeee................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v5v A   3 QMVKRVHIFDWHKEHARKIEEFAGWEMPIWYSSIKEEHLAVRNAVGIFDVSHMGEIVFRGKDALKFLQYVTTNDISKPPAISGTYTLVLNERGAIKDETLVFNMGNNEYLMICDSDAFEKLYAWFTYLKRTIEQFTKLDLEIELKTYDIAMFAVQGPKARDLAKDLFGIDINEMWWFQARWVELDGIKMLLSRSGYTGENGFEVYIEDANPYHPDESKRGEPEKALHVWERILEEGKKYGIKPCGLGARDTLRLEAGYTLYGNETKELQLLSTDIDEVTPLQANLEFAIYWDKDFIGKDALLKQKERGVGRKLVHFKMIDKGIPREGYKVYANGEMIGEVTSGTLSPLLNVGIGIAFVKEEYAKPGIEIEVEIRGQRKKAVTVTPPFYDPKKYGLFRET 401
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392         


Chain B from PDB  Type:PROTEIN  Length:399
 aligned with GCST_PYRHO | O58888 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:399
                             1                                                                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389         
           GCST_PYRHO     - -MVKRVHIFDWHKEHARKIEEFAGWEMPIWYSSIKEEHLAVRNAVGIFDVSHMGEIVFRGKDALKFLQYVTTNDISKPPAISGTYTLVLNERGAIKDETLVFNMGNNEYLMICDSDAFEKLYAWFTYLKRTIEQFTKLDLEIELKTYDIAMFAVQGPKARDLAKDLFGIDINEMWWFQARWVELDGIKMLLSRSGYTGENGFEVYIEDANPYHPDESKRGEPEKALHVWERILEEGKKYGIKPCGLGARDTLRLEAGYTLYGNETKELQLLSTDIDEVTPLQANLEFAIYWDKDFIGKDALLKQKERGVGRKLVHFKMIDKGIPREGYKVYANGEMIGEVTSGTLSPLLNVGIGIAFVKEEYAKPGIEIEVEIRGQRKKAVTVTPPFYDPKKYGLFRET 398
               SCOP domains d1v5vb2 B:3-312 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                                                               d1v5vb1 B:313-401 Glycine cleavage system T protein, GcvT                                 SCOP domains
               CATH domains 1v5vB01 B:3-54,B:147-258                            --------------------------------------------------------------------------------------------1v5vB01 B:3-54,B:147-258 Probable tRNA modification gtpase trme; domain 1                                       -----------------------------------------------------1v5vB03 B:312-386 Aminomethyltransferase beta-barrel domains               --------------- CATH domains
           Pfam domains (1) ----------------------------------------------GCV_T-1v5vB01 B:49-290                                                                                                                                                                                                                            ----GCV_T_C-1v5vB03 B:295-387                                                                    -------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------GCV_T-1v5vB02 B:49-290                                                                                                                                                                                                                            ----GCV_T_C-1v5vB04 B:295-387                                                                    -------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhh.eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..........eeeeeeee.....eeeeeeeee....eeeeee...hhhhhhhhhhhhhhhhh.......eeee....eeeeeee..hhhhhhhhhhh.hhhhh....eeeeee..eeeeee........eeeeeee.......hhhhh..hhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhh...........................hhhhh.......hhhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeee......eeeeeeee.hhh....eeeeee..eeeeeeee................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v5v B   3 QMVKRVHIFDWHKEHARKIEEFAGWEMPIWYSSIKEEHLAVRNAVGIFDVSHMGEIVFRGKDALKFLQYVTTNDISKPPAISGTYTLVLNERGAIKDETLVFNMGNNEYLMICDSDAFEKLYAWFTYLKRTIEQFTKLDLEIELKTYDIAMFAVQGPKARDLAKDLFGIDINEMWWFQARWVELDGIKMLLSRSGYTGENGFEVYIEDANPYHPDESKRGEPEKALHVWERILEEGKKYGIKPCGLGARDTLRLEAGYTLYGNETKELQLLSTDIDEVTPLQANLEFAIYWDKDFIGKDALLKQKERGVGRKLVHFKMIDKGIPREGYKVYANGEMIGEVTSGTLSPLLNVGIGIAFVKEEYAKPGIEIEVEIRGQRKKAVTVTPPFYDPKKYGLFRET 401
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
   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/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

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,B   (GCST_PYRHO | O58888)
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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