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(-) Description

Title :  STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH ADP-RIBOSE
 
Authors :  S. Yoshiba, T. Ooga, N. Nakagawa, T. Shibata, Y. Inoue, S. Yokoyama, S. K R. Masui, Riken Structural Genomics/Proteomics Initiative (Rs
Date :  10 Jan 04  (Deposition) - 19 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nudix Motif, Loop-Helix-Loop, Mutt Family, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yoshiba, T. Ooga, N. Nakagawa, T. Shibata, Y. Inoue, S. Yokoyama, S. Kuramitsu, R. Masui
Structural Insights Into The Thermus Thermophilus Adp-Ribos Pyrophosphatase Mechanism Via Crystal Structures With The Bound Substrate And Metal
J. Biol. Chem. V. 279 37163 2004
PubMed-ID: 15210687  |  Reference-DOI: 10.1074/JBC.M403817200

(-) Compounds

Molecule 1 - ADP-RIBOSE PYROPHOSPHATASE
    Chains: A
    EC Number: 3.6.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:18 , ILE A:19 , ARG A:27 , TYR A:28 , GLU A:29 , GLN A:52 , ARG A:54 , ALA A:66 , GLY A:67 , LEU A:68 , SER A:102 , PRO A:103 , GLY A:104 , GLU A:108 , HOH A:624 , HOH A:627 , HOH A:629 , HOH A:630 , HOH A:635 , HOH A:643BINDING SITE FOR RESIDUE APR A 619

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V8L)

(-) Exons   (0, 0)

(no "Exon" information available for 1V8L)

(-) Sequences/Alignments

Asymmetric Unit
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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:157
 aligned with Q84CU3_THETH | Q84CU3 from UniProtKB/TrEMBL  Length:170

    Alignment length:159
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         
         Q84CU3_THETH    11 RTYLYRGRILNLALEGRYEIVEHKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLIEPGEDPLEAARRELAEETGLSGDLTYLFSYFVSPGFTDEKTHVFLAENLKEVEAHPDEDEAIEVVWMRPEEALERHQRGEVEFSATGLVGVLYYHAFLRG 169
               SCOP domains d1v8la_ A: ADP-ribose pyrophosphatase                                                                                                                           SCOP domains
               CATH domains 1v8lA00 A:11-169 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                   CATH domains
               Pfam domains ----------------------NUDIX-1v8lA01 A:33-158                                                                                                        ----------- Pfam domains
         Sec.struct. author .eeeee...eeeeee..eeeeee..eeeeeeee..eeeeee..............eee.....hhhhhhhhhhhhhhheeeeeeeeeeee........eeeeeeeeeeee...--......eeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8l A  11 RTYLYRGRILNLALEGRYEIVEHKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLIEPGEDPLEAARRELAEETGLSGDLTYLFSYFVSPGFTDEKTHVFLAENLKEVEA--DEDEAIEVVWMRPEEALERHQRGEVEFSATGLVGVLYYHAFLRG 169
                                    20        30        40        50        60        70        80        90       100       110       120  |  | 130       140       150       160         
                                                                                                                                          123  |                                           
                                                                                                                                             126
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  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) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q84CU3_THETH | Q84CU3)
molecular function
    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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  1v8l
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  Q84CU3_THETH | Q84CU3
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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
        Q84CU3_THETH | Q84CU3: 3x0i 3x0j
UniProtKB/TrEMBL
        Q84CU3_THETH | Q84CU3: 1v8i 1v8m 1v8n 1v8r 1v8s 1v8t 1v8u 1v8v 1v8w 1v8y

(-) Related Entries Specified in the PDB File

1v8i THE SAME PROTEIN
1v8m THE SAME PROTEIN WITH ADP-RIBOSE AND GD
1v8n THE SAME PROTEIN WITH ZN
1v8r THE SAME PROTEIN WITH ADP-RIBOSE AND ZN
1v8s THE SAME PROTEIN WITH AMP AND MG
1v8t THE SAME PROTEIN WITH RIBOSE-5'-PHOSPHATE AND ZN
1v8u E82Q MUTANT, WITH SO4 AND MG
1v8v E86Q MUTANT, WITH ADP-RIBOSE AND MG
1v8w E82Q MUTANT, WITH SO4 AND ZN
1v8y E86Q MUTANT, WITH ADP-RIBOSE AND ZN RELATED ID: TTK003001345.2 RELATED DB: TARGETDB