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(-) Description

Title :  CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEXED WITH GNP AND MG+2
 
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 :  02 Apr 04  (Deposition) - 11 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
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, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21 TUNER
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DR1025
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:65 , HOH A:765 , HOH A:846 , HOH A:853BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREGLU B:65 , HOH B:817 , HOH B:844 , HOH B:878BINDING SITE FOR RESIDUE MG B 202
3AC3SOFTWARELEU A:13 , ALA A:15 , HIS A:46 , SER A:49 , GLY A:50 , ALA A:51 , GLU A:69 , PHE A:87 , ASP A:89 , ILE A:93 , ARG A:95 , HOH A:810 , HOH A:845 , MET B:1 , GLU B:2 , ASP B:4 , ARG B:6BINDING SITE FOR RESIDUE GNP A 3030
4AC4SOFTWAREMET A:1 , GLU A:2 , ASP A:4 , HOH A:793 , HOH A:804 , HOH A:862 , LEU B:13 , ALA B:15 , SER B:49 , GLY B:50 , ALA B:51 , PHE B:87 , PRO B:88 , ASP B:89 , VAL B:91 , ILE B:93 , ARG B:95 , HOH B:817 , HOH B:867BINDING SITE FOR RESIDUE GNP A 2030

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SZ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SZ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 1SZ3)

(-) 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:155
 aligned with Q9RVK2_DEIRA | Q9RVK2 from UniProtKB/TrEMBL  Length:159

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q9RVK2_DEIRA     1 MEHDERTHVPVELRAAGVVLLNERGDILLVQEKGIPGHPEKAGLWHIPSGAVEDGENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMYQTKLFYADALREKGFPALP 158
               SCOP domains d1sz3a_ A: Hypothetical protein DR1   025                                                                                                                      SCOP domains
               CATH domains 1sz3A00 A:1-158 Nucleoside Triphosp   hate Pyrophosphohydrolase                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeeeeee......eeeee....---......ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeeeeeee...............eeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sz3 A   1 MEHDERTHVPVELRAAGVVLLNERGDILLVQEKGI---PEKAGLWHIPSGAVEDGENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMYQTKLFYADALREKGFPALP 158
                                    10        20        30    |   40        50        60        70        80        90       100       110       120       130       140       150        
                                                             35  39                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:155
 aligned with Q9RVK2_DEIRA | Q9RVK2 from UniProtKB/TrEMBL  Length:159

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q9RVK2_DEIRA     1 MEHDERTHVPVELRAAGVVLLNERGDILLVQEKGIPGHPEKAGLWHIPSGAVEDGENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMYQTKLFYADALREKGFPALP 158
               SCOP domains d1sz3b_ B: Hypothetical protein DR1   025                                                                                                                      SCOP domains
               CATH domains 1sz3B00 B:1-158 Nucleoside Triphosp   hate Pyrophosphohydrolase                                                                                                CATH domains
           Pfam domains (1) -----------NUDIX-1sz3B01 B:12-146                                                                                                                 ------------ Pfam domains (1)
           Pfam domains (2) -----------NUDIX-1sz3B02 B:12-146                                                                                                                 ------------ Pfam domains (2)
         Sec.struct. author ......ee....eeeeeeee......eeeeee...---......ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeeeeeee.............eeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sz3 B   1 MEHDERTHVPVELRAAGVVLLNERGDILLVQEKGI---PEKAGLWHIPSGAVEDGENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMYQTKLFYADALREKGFPALP 158
                                    10        20        30    |   40        50        60        70        80        90       100       110       120       130       140       150        
                                                             35  39
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  1sz3
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 Related Entries

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UniProtKB/TrEMBL
        Q9RVK2_DEIRA | Q9RVK2: 1sjy 1soi 1su2

(-) Related Entries Specified in the PDB File

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