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(-) Description

Title :  PAB0955 CRYSTAL STRUCTURE : A GTPASE IN GDP AND PO4 BOUND FORM FROM PYROCOCCUS ABYSSI
 
Authors :  S. Gras, P. Carpentier, J. Armengaud, D. Housset
Date :  03 Feb 05  (Deposition) - 14 Feb 06  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gtp Binding Protein, Gtpase, P-Loop, Rossmann Fold, Gdp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gras, V. Chaumont, B. Fernandez, P. Carpentier, F. Charrier-Savournin, S. Schmitt, C. Pineau, D. Flament, A. Hecker, P. Forterre, J. Armengaud, D. Housset
Structural Insights Into A New Homodimeric Self-Activated Gtpase Family.
Embo Rep. V. 8 569 2007
PubMed-ID: 17468740  |  Reference-DOI: 10.1038/SJ.EMBOR.7400958
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP(GTP)BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCRT7/NT-TOPO
    Expression System Strain: ROSETTA(DE3)PLYS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-248
    Gene: PAB0955
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: PAB0955 GENE PRODUCT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:38 , VAL A:39 , LYS A:40 , ASN A:67 , GLY A:68BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWARETHR A:8 , GLY A:10 , SER A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , ASN A:165 , LYS A:166 , ASP A:168 , SER A:223 , ALA A:224 , HOH A:509BINDING SITE FOR RESIDUE GDP A 401

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:143 -A:207

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YR9)

(-) Exons   (0, 0)

(no "Exon" information available for 1YR9)

(-) 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:246
 aligned with GPN_PYRAB | Q9UYR9 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                              1                                                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      
            GPN_PYRAB     - --MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLDTGVKELPYEPSIDVREFVTVEEIMREGYGPNGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETFLFHEFGVRLMENLPYPLVVYISDPEILKKPNDYCFVRFFALLIDLRLGATTIPALNKVDLLSEEEKERHRKYFEDIDYLTARLKLDPSMQGLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETLAYEHYCTC 244
               SCOP domains d1yr9a_ A: ATP(GTP)-binding protein PAB0955                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh....eeeee.............ee.....hhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhh...hhhhhhhhh...hhhhhhhhhhh............ee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yr9 A 499 ASMIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLDTGVKELPYEPSIDVREFVTVEEIMREGYGPNGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETFLFHEFGVRLMENLPYPLVVYISDPEILKKPNDYCFVRFFALLIDLRLGATTIPALNKVDLLSEEEKERHRKYFEDIDYLTARLKLDPSMQGLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETLAYEHYCTC 244
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      
                             ||                                                                                                                                                                                                                                                   
                           500|                                                                                                                                                                                                                                                   
                              1
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  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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YR9)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (GPN_PYRAB | Q9UYR9)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GPN_PYRAB | Q9UYR9: 1yr6 1yr7 1yr8 1yra 1yrb 2oxr

(-) Related Entries Specified in the PDB File

1yr6 THE SAME PROTEIN IN APO FORM
1yr7 THE SAME PROTEIN IN GTP-GAMMA-S BOUND FORM
1yr8 THE SAME PROTEIN IN GTP BOUND FORM
1yra THE SAME PROTEIN IN GDP BOUND FORM
1yrb THE SAME PROTEIN IN GDP AND MG BOUND FORM