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(-) Description

Title :  SOLUTION STRUCTURE OF THE HMG DOMAIN OF HUMAN DNA MISMATCH REPAIR PROTEIN
 
Authors :  C. Kurosaki, F. Hayashi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 May 05  (Deposition) - 20 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dna Mismatch Repair Protein Pms1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Kurosaki, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The Hmg Domain Of Human Dna Mismatch Repair Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PMS1 PROTEIN HOMOLOG 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP050111-24
    Expression System Vector TypePLASMID
    FragmentHMG_BOX DOMAIN
    GenePMS1, PMSL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymDNA MISMATCH REPAIR PROTEIN PMS1

 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 2CS1)

(-) Sites  (0, 0)

(no "Site" information available for 2CS1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CS1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CS1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014878N632SPMS1_HUMANPolymorphism2066456AN69S

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.PMS1_HUMAN571-639  1A:8-76

(-) Exons   (0, 0)

(no "Exon" information available for 2CS1)

(-) 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:92
 aligned with PMS1_HUMAN | P54277 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:190
                                   479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659
           PMS1_HUMAN   470 GNKDHIDESGENEEEAGLENSSEISADEWSRGNILKNSVGENIEPVKILVPEKSLPCKVSNNNYPIPEQMNLNEDSCNKKSNVIDNKSGKVTAYDLLSNRVIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMSLKDGRKKIKPTSA 659
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------...----------------------------------------------------------------------------..------------.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh............----.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------S--------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------HMG_BOX_2  PDB: A:8-76 UniProt: 571-639                              -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cs1 A   1 GS------SGS----------------------------------------------------------------------------SG------------IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMSLKDSG----PSSG  92
                             |      |4|        -         -         -         -         -         -         -       ||-         - |      16        26        36        46        56        66        76        86 |    | 92
                             2      3 5                                                                            6|            8                                                                              88   89   
                                                                                                                    7                                                                                                     

   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  (0, 0)

(no "SCOP Domain" information available for 2CS1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CS1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CS1)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (PMS1_HUMAN | P54277)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
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: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: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.
cellular component
    GO:0032389    MutLalpha complex    A heterodimer involved in the recognition of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MLH1 and PMS2.
    GO:0005712    chiasma    A connection formed between chromatids, visible during meiosis, thought to be the point of the interchange involved in crossing-over.
    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.
    GO:0000795    synaptonemal complex    A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.

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