1SE8 - JenaLib

Title :   STRUCTURE OF SINGLE-STRANDED DNA-BINDING PROTEIN (SSB) FROM D. RADIODURANS

Authors :   D. A. Bernstein, J. M. Eggington, M. P. Killoran, A. M. Misic, M. M. Cox, J

Date :   16 Feb 04 (Deposition) - 15 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Single-Strand Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Bernstein, J. M. Eggington, M. P. Killoran, A. M. Misic, M. M. Cox, J. L. Keck
Crystal Structure Of The Deinococcus Radiodurans Single-Stranded Dna-Binding Protein Suggests A Mechanism Fo Coping With Dna Damage.
Proc. Natl. Acad. Sci. Usa V. 101 8575 2004
PubMed-ID: 15159541 | Reference-DOI: 10.1073/PNAS.0401331101

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:213
 aligned with SSB_DEIRA | Q9RY51 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
            SSB_DEIRA     3 RGMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAEWQAERNLKGGDAVVVEGTLEYRQWEAPEGGKRSAVNVKALRMEQLGTQPELIQDAGGGVRMSGAMNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAENMKELRKGDPVMIMGRLVNEGWTDKDGNKRNSTRVEATRVEALAR 233
               SCOP domains d1se8a_ A: ssDNA-binding protein                                                                                                                                                                                                        SCOP domains
               CATH domains 1se8A01 A:3-116 Nucleic acid-binding p       roteins                                                              1se8A02 A:117-233 Nucleic acid-binding proteins                                                                       CATH domains
           Pfam domains (1) --------------------------------------       ------------------------------------------     ----------------------------------SSB-1se8A01 A:129-231                                                                                  -- Pfam domains (1)
           Pfam domains (2) --------------------------------------       ------------------------------------------     ----------------------------------SSB-1se8A02 A:129-231                                                                                  -- Pfam domains (2)
         Sec.struct. author ..eeeeeeeeee....eeee.....eeeeeeeeeee..-------..eeeeeeeeeehhhhhhhhhh......eeeeeeeeeeeee.-----.eeeeeeeeeeeee......eee.....eeee..eeeeeeeeee....eeee.....eeeeeeeeeeeeee.....eeeeeeeeeeeeehhhhhhhh......eeeeeeeeeeee..------.eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SSB  PDB: A:5-110 UniProt: 5-110                                                                          ------------------SSB  PDB: A:129-232 UniProt: 129-232                                                                    - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1se8 A   3 RGmNHVYLIGALARDPELRYTGNGmAVFEATVAGEDRV-------RNLPWYHRVSILGKPAEWQAERNLKGGDAVVVEGTLEYRQWE-----KRSAVNVKALRmEQLGTQPELIQDAGGGVRmSGAmNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAENmKELRKGDPVmImGRLVNEGWT------RNSTRVEATRVEALAR 233
                              |     12        22    |   32       | -     |  52        62        72        82      |  -  |    102   |   112       122  |   |132       142       152       162       172       182       192       202        |-     | 222       232 
                              |                    27-MSE       40      48                                       89    95        106-MSE            125-MSE                                                          190-MSE   200-MSE    211    218               
                              5-MSE                                                                                                                     129-MSE                                                                  202-MSE

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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)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (SSB_DEIRA | Q9RY51)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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