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(-) Description

Title :  SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT
 
Authors :  M. A. Massiah, V. Saraswat, H. F. Azurmendi, A. S. Mildvan
Date :  25 Jun 03  (Deposition) - 26 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Mutator Protein, Nucleoside Triphosphate Pyrophosphohydrolase, Mutt Pyrophosphohydrolase-Metal- Product Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Massiah, V. Saraswat, H. F. Azurmendi, A. S. Mildvan
Solution Structure And Nh Exchange Studies Of The Mutt Pyrophosphohydrolase Complexed With Mg(2+) And 8-Oxo-Dgmp, A Tightly Bound Product.
Biochemistry V. 42 10140 2003
PubMed-ID: 12939141  |  Reference-DOI: 10.1021/BI030105P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUTATOR MUTT PROTEIN
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET MUTT, T7 PROMOTER
    Expression System Strain: HMS174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE, 8-OXO- DGTPASE, DGTP PYROPHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
18OG1Ligand/Ion8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:38 , LYS A:39 , GLU A:53 , GLU A:56 , GLU A:57 , HOH A:5011 , HOH A:5012BINDING SITE FOR RESIDUE MG A 130
2AC2SOFTWARELEU A:4 , ILE A:6 , GLU A:34 , ARG A:78 , ILE A:80 , LEU A:82 , PRO A:116 , ASN A:119BINDING SITE FOR RESIDUE 8OG A 131

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.MUTT_ECOLI1-129  1A:1-129
2NUDIX_BOXPS00893 Nudix box signature.MUTT_ECOLI38-59  1A:38-59

(-) Exons   (0, 0)

(no "Exon" information available for 1PUS)

(-) Sequences/Alignments

NMR Structure
   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:129
 aligned with MUTT_ECOLI | P08337 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           MUTT_ECOLI     1 MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
               SCOP domains d1pusa_ A: Nucleoside triphosphate pyrophosphorylase (MutT)                                                                       SCOP domains
               CATH domains 1pusA00 A:1-129 Nucleoside Triphosphate Pyrophosphohydrolase                                                                      CATH domains
               Pfam domains ---NUDIX-1pusA01 A:4-129                                                                                                          Pfam domains
         Sec.struct. author ..eeeeeeeeee.....eeee.........................hhhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeee..............eeeehhhhh.....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: A:1-129 UniProt: 1-129                                                                                                PROSITE (1)
                PROSITE (2) -------------------------------------NUDIX_BOX  PDB: A:38-5---------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pus A   1 MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (MUTT_ECOLI | P08337)
molecular function
    GO:0035539    8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity    Catalysis of the reaction: 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate + H2O = 8-oxo-7,8-dihydrodeoxyguanosine phosphate + diphosphate. 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate, or 8-oxo-dGTP, is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for DNA synthesis causing transversion mutations. 8-oxo-dGTPase hydrolyses 8-oxo-dGTP to its monophosphate form to prevent the misincorporation of 8-oxo-dGTP into cellular DNA.
    GO:0008413    8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity    Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate = 8-oxo-7,8-dihydroguanosine phosphate + diphosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription.
    GO:0044716    8-oxo-GDP phosphatase activity    Catalysis of the reaction 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate.
    GO:0044715    8-oxo-dGDP phosphatase activity    Catalysis of the reaction 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate.
    GO:0047693    ATP diphosphatase activity    Catalysis of the reaction: ATP + H2O = AMP + diphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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  1pus
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 Related Entries

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

UniProtKB/Swiss-Prot
        MUTT_ECOLI | P08337: 1mut 1ppx 1pun 1puq 1tum 3a6s 3a6t 3a6u 3a6v

(-) Related Entries Specified in the PDB File

1mut THE FREE SOLUTION STRUCTURE.
1ppx SOLUTION STRUCTURE OF THE SAME COMPLEX WITHOUT ASSUMED DISTANCES LIGAND/PROTEIN.
1pun SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT
1puq SOLUTION STRUCTURE OF THE MUTT PYROPHOSPHOHYDROLASE COMPLEXED WITH MG(2+) AND 8-OXO-DGMP, A TIGHTLY-BOUND PRODUCT
1tum COMPLEXED WITH AMPCPP-MG.