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(-) Description

Title :  PROMISCUITY AND SPECIFICITY IN DNA BINDING TO SSB: INSIGHTS FROM THE STRUCTURE OF THE MYCOBACTERIUM SMEGMATIS SSB-SSDNA COMPLEX
 
Authors :  P. S. Kaushal, G. P. Manjunath, K. Sekar, K. Muniyappa, M. Vijayan
Date :  12 Aug 09  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Dna Binding Protein, Dna Damage, Dna Repair, Dna Replication, Dna- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Kaushal, G. P. Manjunath, K. Sekar, K. Muniyappa, M. Vijayan
Promiscuity And Specificity In Dna Binding To Ssb: Insights From The Structure Of The Mycobacterium Smegmatis Ssb-Ssdna Complex.
To Be Published 2009
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SINGLE-STRANDED DNA-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CHYMOTRYPTIC FRAGMENT, UNP RESIDUES 1-130
    Gene: SSB
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: MC(2)155
    Synonym: SSB, HELIX-DESTABILIZING PROTEIN
 
Molecule 2 - DNA (31-MER)
    Chains: C
    Engineered: YES
    Other Details: BIOMOLECULE HAS BEEN SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3A5U)

(-) Sites  (0, 0)

(no "Site" information available for 3A5U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A5U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A5U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A5U)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSBPS50935 Single-strand binding (SSB) domain profile.SSB_MYCS21-110
 		  2A:1-110
B:1-110
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSBPS50935 Single-strand binding (SSB) domain profile.SSB_MYCS21-110
 		  4A:1-110
B:1-110

(-) Exons   (0, 0)

(no "Exon" information available for 3A5U)

(-) 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:118
 aligned with SSB_MYCS2 | Q9AFI5 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
            SSB_MYCS2     1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNK 119
               SCOP domains d3a5ua_ A: automated matches                                                                                            SCOP domains
               CATH domains 3a5uA00 A:1-119 Nucleic acid-binding proteins                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....eeee.....eeeeeeeee.................eeeeeeeehhhhhhhhhhh....eeeeeeeeeee..-........eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SSB  PDB: A:1-110 UniProt: 1-110                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3a5u A   1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSF-TREGEKRTVVEVEVDEIGPSLRYATAKVNK 119
                                    10        20        30        40        50        60        70        80       |90       100       110         
                                                                                                                  88 |                             
                                                                                                                    90                             


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with SSB_MYCS2 | Q9AFI5 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
            SSB_MYCS2     1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNK 119
               SCOP domains d3a5ub_ B: automated matches                                                                                            SCOP domains
               CATH domains 3a5uB00 B:1-119 Nucleic acid-binding pr     oteins                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....eeee.....eeeeeeeee....-----........eeeeeeeehhhhhhhhhhh....eeeeeeeeeeeee....--.eeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SSB  PDB: B:1-110 UniProt: 1-110                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3a5u B   1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRM-----GEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETRE--KRTVVEVEVDEIGPSLRYATAKVNK 119
                                    10        20        30        |-    |   50        60        70        80        90 |  |  100       110         
                                                                 39    45                                             92 95                        


Chain C from PDB  Type:DNA  Length:31
                                                               
                 3a5u C   1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC  31
                                    10        20        30
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A5U)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SSB_MYCS2 | Q9AFI5)
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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SSB_MYCS2 | Q9AFI5: 1x3e 1x3f 1x3g

(-) Related Entries Specified in the PDB File

1x3e CONTAINS THE SAME PROTEIN UNCOMPLEXED
1x3f CONTAINS THE SAME PROTEIN UNCOMPLEXED
1x3g CONTAINS THE SAME PROTEIN UNCOMPLEXED