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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  S. Satoh, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Pro Initiative (Rsgi)
Date :  17 Jun 05  (Deposition) - 17 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Ssb, Single-Stranded Dna Binding Protein, Thermus Thermophilus Hb8, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Satoh, S. Yokoyama, S. Kuramitsu
Crystal Structure Of The Single-Stranded Dna Binding Protei From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SINGLE-STRAND BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: SSB, HELIX-DESTABILIZING PROTEIN, SINGLE-STRANDED DNA BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2NO33Ligand/IonNITRATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:60 , ARG A:61 , ARG A:144 , VAL A:152 , ARG A:154 , GLN A:176 , TRP A:178 , NO3 A:502 , HOH A:584BINDING SITE FOR RESIDUE NO3 A 501
2AC2SOFTWARELEU A:59 , GLY A:60 , ARG A:61 , GLN A:62 , ARG A:100 , ARG A:144 , THR A:146 , PRO A:147 , NO3 A:501BINDING SITE FOR RESIDUE NO3 A 502
3AC3SOFTWARELYS A:112 , GLU A:113 , ARG A:114 , HOH A:593BINDING SITE FOR RESIDUE NO3 A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CWA)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSBPS50935 Single-strand binding (SSB) domain profile.SSB_THET85-108
128-227		  2A:5-108
A:128-227

(-) Exons   (0, 0)

(no "Exon" information available for 2CWA)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:206
 aligned with SSB_THET8 | Q5SLP9 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
            SSB_THET8     3 RGLNRVFLIGALATRPDMRYTPAGLAILDLTLAGQDLLLSDNGGEREVSWYHRVRLLGRQAEMWGDLLDQGQLVFVEGRLEYRQWEREGERRSELQIRADFLDPLDDRGKERAEDSRGQPRLRAALNQVFLMGNLTRDPELRYTPQGTAVARLGLAVNERRQGAEERTHFVEVQAWRDLAEWAAELRKGDGLFVIGRLVNDSWTSSSGERRFQTRVEALRLERPTR 228
               SCOP domains d2cwaa_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeee.....eeeeeeeeeeee.-------.eeeeeeeeeeehhhhhh.........eeeeeeeeeee.--------.eeeeeeeeeeee......eee.....eeee..eeeeeeeeee....eeee.....eeeeeeeeeee.-----.eeeeeeeeeehhhhhhhh......eeeeeeeeeeeeee.....eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SSB  PDB: A:5-108 UniProt: 5-108                                                                        -------------------SSB  PDB: A:128-227 UniProt: 128-227                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwa A   3 RGLNRVFLIGALATRPDmRYTPAGLAILDLTLAGQDLL-------REVSWYHRVRLLGRQAEmWGDLLDQGQLVFVEGRLEYRQ--------SELQIRADFLDPLDDRGKERAEDSRGQPRLRAALNQVFLmGNLTRDPELRYTPQGTAVARLGLAVNER-----ERTHFVEVQAWRDLAEWAAELRKGDGLFVIGRLVNDSWTSSSGERRFQTRVEALRLERPTR 228
                                    12       |22        32       | -     |  52        62  |     72        82   |     -  |    102       112       122       132 |     142       152       162     | 172       182       192       202       212       222      
                                            20-MSE              40      48               65-MSE               86       95                                    134-MSE                     162   168
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SSB_THET8 | Q5SLP9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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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