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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE OF E82Q MUTANT, COMPLEXED WITH SO4 AND ZN
 
Authors :  S. Yoshiba, T. Ooga, N. Nakagawa, T. Shibata, Y. Inoue, S. Yokoyama, S. K R. Masui, Riken Structural Genomics/Proteomics Initiative (Rs
Date :  15 Jan 04  (Deposition) - 19 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
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: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:54 , ALA A:66 , GLY A:67 , LEU A:68 , HOH A:615 , HOH A:617 , HOH A:626 , HOH A:639BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWAREGLU A:44 , GLU A:70 , HOH A:619BINDING SITE FOR RESIDUE ZN A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V8W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V8W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V8W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V8W)

(-) Exons   (0, 0)

(no "Exon" information available for 1V8W)

(-) 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:154
 aligned with Q84CU3_THETH | Q84CU3 from UniProtKB/TrEMBL  Length:170

    Alignment length:158
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
         Q84CU3_THETH    11 RTYLYRGRILNLALEGRYEIVEHKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLIEPGEDPLEAARRELAEETGLSGDLTYLFSYFVSPGFTDEKTHVFLAENLKEVEAHPDEDEAIEVVWMRPEEALERHQRGEVEFSATGLVGVLYYHAFLR 168
               SCOP domains d1v8wa_ A: ADP-ribose pyrophosphatase                                                                                                                          SCOP domains
               CATH domains 1v8wA00 A:11-168 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                  CATH domains
               Pfam domains ----------------------NUDIX-1v8wA01 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
                 1v8w A  11 RTYLYRGRILNLALEGRYEIVEHKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLIEPGEDPLEAARRQLAEETGLSGDLTYLFSYFVSPGFTDEKTHVFLAENLKEVEAHP----AIEVVWMRPEEALERHQRGEVEFSATGLVGVLYYHAFLR 168
                                    20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160        
                                                                                                                                            125  130
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 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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  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 1v8l 1v8m 1v8n 1v8r 1v8s 1v8t 1v8u 1v8v 1v8y

(-) Related Entries Specified in the PDB File

1v8i THE SAME PROTEIN
1v8l THE SAME PROTEIN WITH ADP-RIBOSE
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
1v8y E86Q MUTANT, WITH ADP-RIBOSE AND ZN RELATED ID: TTK003001345.9 RELATED DB: TARGETDB