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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ADP-RIBOSE PYROPHOSPHATASE IN COMPLEX WITH GD+3
 
Authors :  S. B. Gabelli, M. A. Bianchet, M. J. Bessman, L. M. Amzel
Date :  29 Nov 00  (Deposition) - 02 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix Hydrolase, Gd Binding, Mg Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Gabelli, M. A. Bianchet, M. J. Bessman, L. M. Amzel
The Structure Of Adp-Ribose Pyrophosphatase Reveals The Structural Basis For The Versatility Of The Nudix Family.
Nat. Struct. Biol. V. 8 467 2001
PubMed-ID: 11323725  |  Reference-DOI: 10.1038/87647
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
    Chains: A, B
    EC Number: 3.6.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ORF209
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ADP-RIBOSE PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GD32Ligand/IonGADOLINIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:35 , GLU A:48 , GLU A:112 , GLU A:115BINDING SITE FOR RESIDUE GD3 A 302
2AC2SOFTWAREGLU B:112 , GLU B:115 , GLU B:164 , HOH B:304 , HOH B:305BINDING SITE FOR RESIDUE GD3 B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GA7)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.ADPP_ECOLI55-193
 		  2A:55-193
B:55-193
2NUDIX_BOXPS00893 Nudix box signature.ADPP_ECOLI97-118
 		  2A:97-118
B:97-118

(-) Exons   (0, 0)

(no "Exon" information available for 1GA7)

(-) 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:204
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           ADPP_ECOLI     1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
               SCOP domains d1ga7a_ A: ADP-ribose pyrophosphatase                                                                                                                                                                             SCOP domains
               CATH domains 1ga7A00 A:1-209 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeeeee...eeeeeeeee..........eeeeeee...eeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhhh......eeeeeeee........eeeeeeee.hhhhh.-----.......eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------NUDIX  PDB: A:55-193 UniProt: 55-193                                                                                                       ---------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ga7 A   1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTAS-----ADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200         
                                                                                                                                                                                   154   160                                                 


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with ADPP_ECOLI | Q93K97 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:202
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  
           ADPP_ECOLI     8 PVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
               SCOP domains d1ga7b_ B: ADP-ribose pyrophosphatase                                                                                                                                                                      SCOP domains
               CATH domains 1ga7B00 B:8-209 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee...eeeeeeeee..........eeeeeee...eeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhhhh.....eeeeeeee........eeeeeeee.hhhhh.............eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------NUDIX  PDB: B:55-193 UniProt: 55-193                                                                                                       ---------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ga7 B   8 PVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GA7)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ADPP_ECOLI | Q93K97)
molecular function
    GO:0047631    ADP-ribose diphosphatase activity    Catalysis of the reaction: ADP-ribose + H2O = AMP + D-ribose 5-phosphate.
    GO:0019144    ADP-sugar diphosphatase activity    Catalysis of the reaction: ADP-sugar + H2O = AMP + sugar 1-phosphate.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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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  1ga7
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  3.6.1.13
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 Related Entries

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

UniProtKB/Swiss-Prot
        ADPP_ECOLI | Q93K97: 1g0s 1g9q 1khz 1viq

(-) Related Entries Specified in the PDB File

1g0s 1G0S IS APO ADP-RIBOSE PYROPHOSPHATASE
1g9q 1G9Q IS COMPLEX ADP-RIBOSE PYROPHOSPHATASE WITH ITS SUBSTRATE, ADP-RIBOSE