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(-) Description

Authors :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 May 05  (Deposition) - 15 Nov 05  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nudix Domain, Dna Repair, Alpha-3 Isoform, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Nudix Domain From Human A/G-Specific Adenine Dna Glycosylase Alpha-3 Splice Isoform
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    EC Number3.2.2.-
    Expression System PlasmidP040906-16
    Expression System Vector TypePLASMID
    FragmentNUDIX DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1X51)

(-) Sites  (0, 0)

(no "Site" information available for 1X51)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X51)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X51)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

NMR Structure (19, 19)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_077665S319NMUTYH_HUMANPolymorphism  ---AS2N
03UniProtVAR_077667P377TMUTYH_HUMANDisease (FAP2)  ---AP29T
04UniProtVAR_077668L385PMUTYH_HUMANDisease (FAP2)  ---AL37P
05UniProtVAR_018875G393DMUTYH_HUMANDisease (FAP2)36053993AG45D
06UniProtVAR_077669P402LMUTYH_HUMANDisease (FAP2)529008617AP54L
07UniProtVAR_026049P402SMUTYH_HUMANDisease (GASC)121908382AP54S
08UniProtVAR_026050Q411RMUTYH_HUMANUnclassified (GASC)121908383AQ63R
09UniProtVAR_077670L417MMUTYH_HUMANUnclassified (FAP2)144079536AL69M
10UniProtVAR_077671R423CMUTYH_HUMANUnclassified (FAP2)150792276AR75C
11UniProtVAR_077672R434PMUTYH_HUMANUnclassified  ---AR86P
13UniProtVAR_077674A470DMUTYH_HUMANDisease (FAP2)200844166AA122D
15UniProtVAR_077676T474MMUTYH_HUMANUnclassified (FAP2)767747402AT126M
16UniProtVAR_077677A486TMUTYH_HUMANDisease (FAP2)587782263AA138T
17UniProtVAR_077678V490FMUTYH_HUMANUnclassified (FAP2)587782228AV142F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1NUDIXPS51462 Nudix hydrolase domain profile.MUTYH_HUMAN364-495  1A:16-147

(-) Exons   (6, 6)

NMR Structure (6, 6)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.9cENST000003720989cENSE00001141279chr1:45797758-4579769564MUTYH_HUMAN309-330221A:1-5 (gaps)6
1.9iENST000003720989iENSE00001767258chr1:45797521-45797333189MUTYH_HUMAN330-393641A:6-45 (gaps)61
1.14gENST0000037209814gENSE00001456937chr1:45795109-45794914196MUTYH_HUMAN504-546431A:150-155 (gaps)12

(-) 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:155
 aligned with MUTYH_HUMAN | Q9UIF7 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:205
                                   327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517     
               SCOP domains --------------------------------------d1x51a1 A:8-149 A/G-specific adenine DNA glycosylase                                                                                          ------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
             SAPs(SNPs) (1) -N--------------------------------------------------V------T-------P-------D--------L--------R-----M-----C----------P-----------------------------------D---M-----------T---F---------------------FL--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------S-------------------------------Q-----------------------------------T---------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------NUDIX  PDB: A:16-147 UniProt: 364-495                                                                                               --------------------------- PROSITE
           Transcript 1 (1) Exon 1.9c    --------------------------------------------------------------Exon 1.10  PDB: A:45-90 UniProt: 393-438      Exon 1.11a  PDB: A:91-141 UniProt: 439-489         Exon 1.12     Exon 1.14g          Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.9i  PDB: A:6-45 (gaps) UniProt: 330-393 [INCOMPLETE]     --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                             | | |   -     ||  -         -        |9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         -   |   | -    |
                             2 3 5         6|                     8                                                                                                                                          149           150 154    155

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X51)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X51)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (MUTYH_HUMAN | Q9UIF7)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0032405    MutLalpha complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutLalpha.
    GO:0032406    MutLbeta complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutLbeta.
    GO:0032407    MutSalpha complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutSalpha.
    GO:0032408    MutSbeta complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutSbeta.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    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.
    GO:0045007    depurination    The disruption of the bond between the sugar in the backbone and the A or G base, causing the base to be removed and leaving a depurinated sugar.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.


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 Related Entries

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

        MUTYH_HUMAN | Q9UIF73n5n

(-) Related Entries Specified in the PDB File

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