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(-) Description

Title :  SOLUTION STRUCTURE OF DNA BINDING DOMAIN A (DBD-A) OF S.CEREVISIAE REPLICATION PROTEIN A (RPA)
 
Authors :  C. J. Park, J. H. Lee, B. S. Choi
Date :  26 Jan 05  (Deposition) - 10 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (22x)
Keywords :  Canonical Ob Fold, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Park, J. H. Lee, B. S. Choi
Solution Structure Of The Dna-Binding Domain Of Rpa From Saccharomyces Cerevisiae And Its Interaction With Single-Stranded Dna And Sv40 T Antigen
Nucleic Acids Res. V. 33 4172 2005
PubMed-ID: 16043636  |  Reference-DOI: 10.1093/NAR/GKI736
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICATION FACTOR-A PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21 DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN A
    Gene: RFA1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: REPLICATION PROTEIN A, RF-A, SINGLE-STRANDED DNA- BINDING PROTEIN, DNA BINDING PROTEIN BUF2, REPLICATION PROTEIN A 69 KDA DNA- BINDING SUBUNIT

 Structural Features

(-) Chains, Units

  
NMR Structure (22x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1YNX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YAR007C1YAR007C.1I:158621-1567561866RFA1_YEAST1-6216211A:181-294114

(-) 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:114
 aligned with RFA1_YEAST | P22336 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:114
                                   190       200       210       220       230       240       250       260       270       280       290    
           RFA1_YEAST   181 TRPIFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDTSGEIRATAFNDFATKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN 294
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1ynxA01 A:181-289 Nucleic acid-binding proteins                                                              ----- CATH domains
               Pfam domains ----------------tRNA_anti-1ynxA01 A:197-286                                                               -------- Pfam domains
         Sec.struct. author .....hhhhh.......eeeeeeeeeeeeeeee....eeeeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeee..eeee...........eeeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:181-294 UniProt: 1-621 [INCOMPLETE]                                                               Transcript 1
                 1ynx A 181 TRPIFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDTSGEIRATAFNDFATKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN 294
                                   190       200       210       220       230       240       250       260       270       280       290
   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 1YNX)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: OB (224)

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (RFA1_YEAST | P22336)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    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: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:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    GO:0030491    heteroduplex formation    The formation of a stable duplex DNA that contains one strand from each of the two recombining DNA molecules.
    GO:0006312    mitotic recombination    The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0007131    reciprocal meiotic recombination    The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
    GO:0043934    sporulation    The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
    GO:0000722    telomere maintenance via recombination    Any recombinational process that contributes to the maintenance of proper telomeric length.
    GO:0007004    telomere maintenance via telomerase    The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.
    GO:0010833    telomere maintenance via telomere lengthening    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and lengthening the telomeric DNA.
cellular component
    GO:0005662    DNA replication factor A complex    A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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)

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        RFA1_YEAST | P22336: 5m1x

(-) Related Entries Specified in the PDB File

1fgu THE CRYSTAL STRUCTURE OF THE HUMAN HOMOLOG WITHOUT DNA
1jmc THE CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN HOMOLOG WITH DNA