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(-) Description

Title :  STRUCTURE OF THE ADPR-ASE IN COMPLEX WITH AMPCPR AND MG
 
Authors :  S. B. Gabelli, M. A. Bianchet, M. J. Bessman, L. M. Amzel
Date :  01 Dec 01  (Deposition) - 09 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix, Adp-Ribose Pyrophosphatase, Ampcpr, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. B. Gabelli, M. A. Bianchet, Y. Ohnishi, Y. Ichikawa, M. J. Bessman, L. M. Amzel
Mechanism Of The Escherichia Coli Adp-Ribose Pyrophosphatase, A Nudix Hydrolase.
Biochemistry V. 41 9279 2002
PubMed-ID: 12135348  |  Reference-DOI: 10.1021/BI0259296
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-RIBOSE PYROPHOSPHATASE
    ChainsA, B
    EC Number3.6.1.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneORF209
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymADP-RIBOSE DIPHOSPHATASE, ADENOSINE DIPHOSPHORIBOSE PYROPHOSPHATASE, ADPR-PPASE, ADP-RIBOSE PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ADV1Ligand/IonALPHA-BETA METHYLENE ADP-RIBOSE
2CL1Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:50 , GLU B:207BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREGLU B:112 , GLU B:116 , GLU B:164 , MG B:304 , MG B:310 , ADV B:402 , HOH B:403 , HOH B:407BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWAREGLU B:112 , GLU B:162 , MG B:301 , ADV B:402 , HOH B:404 , HOH B:405 , HOH B:406 , HOH B:407BINDING SITE FOR RESIDUE MG B 304
4AC4SOFTWAREALA B:96 , GLU B:116 , MG B:301 , ADV B:402 , HOH B:409 , HOH B:410BINDING SITE FOR RESIDUE MG B 310
5AC5SOFTWAREARG A:51 , GLU A:52 , SER A:133 , PRO A:134 , GLY A:135 , PHE B:28 , PHE B:29 , ARG B:56 , ARG B:79 , ALA B:96 , GLY B:97 , MET B:98 , GLU B:112 , GLU B:116 , GLU B:139 , GLU B:162 , GLU B:164 , MG B:301 , MG B:304 , MG B:310 , HOH B:405 , HOH B:407 , HOH B:408 , HOH B:409 , HOH B:436 , HOH B:489 , HOH B:501BINDING SITE FOR RESIDUE ADV B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1KHZ)

(-) 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:205
 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 d1khza_ A: ADP-ribose pyrophosphatase                                                                                                                                                                             SCOP domains
               CATH domains 1khzA00 A:1-209 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeeee....eeeeeeeee..........eeeeeee..eeeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhhhh.....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
                 1khz A   1 MLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTAS----LADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200         
                                                                                                                                                                                   154  159                                                  

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 d1khzb_ B: ADP-ribose pyrophosphatase                                                                                                                                                                      SCOP domains
               CATH domains 1khzB00 B:8-209 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                                               CATH domains
           Pfam domains (1) ------------------------------------------------NUDIX-1khzB01 B:56-198                                                                                                                         ----------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------NUDIX-1khzB02 B:56-198                                                                                                                         ----------- Pfam domains (2)
         Sec.struct. author ....hhh.eeeeeeeeeee...eeeeeeeee..........eeeeeee...eeeeeeee....eeeeeeee.hhhhhhh...eeee.eeee.....hhhhhhhhhhhhhhh.....eeeeeeee........eeeeeeee.hhhhh..ee........eeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh 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
                 1khz 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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NUDIX (85)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        ADPP_ECOLI | Q93K971g0s 1g9q 1ga7 1viq

(-) Related Entries Specified in the PDB File

1g0s THE CRYSTAL STRUCTURE OF THE E.COLI ADP-RIBOSE PYROPHOSPHATASE
1g9q COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP- RIBOSE
1ga7 CRYSTAL STRUCTURE OF THE ADP-RIBOSE PYROPHOSPHATASE IN COMPLEX WITH GD+3