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(-) Description

Title :  SOLUTION STRUCTURE OF BRCT DOMAIN OF DNA POLYMERASE MU
 
Authors :  T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Jul 06  (Deposition) - 25 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  3 Layers A/B/A, Parallel Beta-Sheet Of 4 Strands, Non- Homologous End Jonting, Somatic Hypermutation, V(D)J Recombination, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of Brct Domain Of Dna Polymerase Mu
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE MU
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression System PlasmidP041213-12
    Expression System Vector TypePLASMID
    FragmentBRCT DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPOL MU

 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 2DUN)

(-) Sites  (0, 0)

(no "Site" information available for 2DUN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DUN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DUN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022287E107DDPOLM_HUMANPolymorphism28382635AE91D

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.DPOLM_HUMAN22-118  1A:9-102

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002422481aENSE00001907873chr7:44122139-44121850290DPOLM_HUMAN1-63631A:1-47 (gaps)53
1.2ENST000002422482ENSE00001233342chr7:44120515-44120332184DPOLM_HUMAN63-124621A:47-10862
1.4aENST000002422484aENSE00001651403chr7:44119558-4411946099DPOLM_HUMAN125-157331A:109-133 (gaps)31
1.5cENST000002422485cENSE00001599909chr7:44119340-44119170171DPOLM_HUMAN158-214570--
1.6bENST000002422486bENSE00000832554chr7:44118410-4411833972DPOLM_HUMAN215-238240--
1.8bENST000002422488bENSE00001659532chr7:44116228-44116108121DPOLM_HUMAN239-279410--
1.9aENST000002422489aENSE00001761705chr7:44114129-44113997133DPOLM_HUMAN279-323450--
1.9eENST000002422489eENSE00001233387chr7:44113832-44113730103DPOLM_HUMAN323-357350--
1.9jENST000002422489jENSE00001800039chr7:44113624-44113382243DPOLM_HUMAN358-438810--
1.10ENST0000024224810ENSE00001596969chr7:44113307-4411322484DPOLM_HUMAN439-466280--
1.11eENST0000024224811eENSE00001086868chr7:44112976-441118461131DPOLM_HUMAN467-494280--

(-) 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:133
 aligned with DPOLM_HUMAN | Q9NP87 from UniProtKB/Swiss-Prot  Length:494

    Alignment length:145
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150     
          DPOLM_HUMAN    11 GSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACQRPTPLTHHNTG 155
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-......-----..eeeeeeeehhhhhhhhhhhhhhhhhhhhheee.........eeee...hhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhh...................................------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------BRCT  PDB: A:9-102 UniProt: 22-118                                                               ------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-47 (gaps) UniProt: 1-63          -------------------------------------------------------------Exon 1.4a  PDB: A:109-133 (gaps Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.2  PDB: A:47-108 UniProt: 63-124                       ------------------------------- Transcript 1 (2)
                 2dun A   1 GS-SGSSGS-----TRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACSGPS------SG 133
                             | |    |-    |   14        24        34        44        54        64        74        84        94       104       114       124      |  -   | 
                             2 3    8     9                                                                                                                       131    132 

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2DUN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DUN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DUN)

(-) Gene Ontology  (16, 22)

NMR Structure(hide GO term definitions)
Chain A   (DPOLM_HUMAN | Q9NP87)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034061    DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    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: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:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0016446    somatic hypermutation of immunoglobulin genes    Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
cellular component
    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)

UniProtKB/Swiss-Prot
        DPOLM_HUMAN | Q9NP872htf 4lzd 4lzg 4m04 4m0a 4ycx 4yd1 4yd2 5twp 5twq 5twr 5tws 5vz7 5vz8 5vz9 5vza 5vzb 5vzc 5vzd 5vze 5vzf 5vzg 5vzh 5vzi

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