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(-) Description

Title :  CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3
 
Authors :  W. Ranatunga, E. E. Hill, J. L. Mooster, E. L. Holbrook, U. Schulze- Gahmen, W. Xu, M. J. Bessman, S. E. Brenner, S. R. Holbrook, Berkeley Structural Genomics Center (Bsgc)
Date :  15 Mar 04  (Deposition) - 11 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nudix Fold, Alpha-Beta-Alpha Sandwich, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ranatunga, E. E. Hill, J. L. Mooster, E. L. Holbrook, U. Schulze-Gahmen, W. Xu, M. J. Bessman, S. E. Brenner, S. R. Holbrook
Structural Studies Of The Nudix Hydrolase Dr1025 From Deinococcus Radiodurans And Its Ligand Complexes.
J. Mol. Biol. V. 339 103 2004
PubMed-ID: 15123424  |  Reference-DOI: 10.1016/J.JMB.2004.01.065
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21 TUNER CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DR1025
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 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, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SM3Ligand/IonSAMARIUM (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SM-1Ligand/IonSAMARIUM (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:65 , GLU A:68 , HOH A:730 , HOH A:772BINDING SITE FOR RESIDUE SM A 301
2AC2SOFTWAREASP A:147 , ARG A:150 , HOH A:743 , HOH A:774 , HOH A:788BINDING SITE FOR RESIDUE SM A 302
3AC3SOFTWAREGLU A:12 , GLY A:90 , HOH A:753BINDING SITE FOR RESIDUE SM A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1SOI)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:156
 aligned with Q9RVK2_DEIRA | Q9RVK2 from UniProtKB/TrEMBL  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
         Q9RVK2_DEIRA     2 EHDERTHVPVELRAAGVVLLNERGDILLVQEKGIPGHPEKAGLWHIPSGAVEDGENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMYQTKLFYADALREKGFPALPV 159
               SCOP domains d1soia_ A: Hypothetical protein DR  1025                                                                                                                       SCOP domains
               CATH domains 1soiA00 A:2-159 Nucleoside Triphos  phate Pyrophosphohydrolase                                                                                                 CATH domains
               Pfam domains ----------NUDIX-1soiA01 A:12-146                                                                                                                 ------------- Pfam domains
         Sec.struct. author ...........eeeeeeee......eeeeee...--.......ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeeeeeee.............eeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1soi A   2 EHDERTHVPVELRAAGVVLLNERGDILLVQEKGI--HPEKAGLWHIPSGAVEDGENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMYQTKLFYADALREKGFPALPV 159
                                    11        21        31   |  | 41        51        61        71        81        91       101       111       121       131       141       151        
                                                            35 38
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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  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9RVK2_DEIRA | Q9RVK2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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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        Q9RVK2_DEIRA | Q9RVK2: 1sjy 1su2 1sz3

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