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(-) Description

Title :  CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS
 
Authors :  S. Su, Y. -G. Gao, H. Robinson, Y. -C. Liaw, S. P. Edmondson, J. W. Shriver, A. H. -J. Wang
Date :  04 May 00  (Deposition) - 04 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Binding Protein, Protein-Dna Interaction, Protein Stability, Hyperthermophile, Achaeabacteria, X-Ray Crystallography, Electrostatics, Molecular Modeling, T-G Mismatch, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Su, Y. G. Gao, H. Robinson, Y. C. Liaw, S. P. Edmondson, J. W. Shriver, A. H. Wang
Crystal Structures Of The Chromosomal Proteins Sso7D/Sac7D Bound To Dna Containing T-G Mismatched Base-Pairs.
J. Mol. Biol. V. 303 395 2000
PubMed-ID: 11031116  |  Reference-DOI: 10.1006/JMBI.2000.4112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3'
    Chains: B, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA-BINDING PROTEIN 7A
    Atcc: DSM 1617
    Chains: A
    Collection: DSM 1617
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) 1617, #1616
    Synonym: SSO7D, 7 KDA DNA-BINDING PROTEIN D

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1C8C)

(-) Sites  (0, 0)

(no "Site" information available for 1C8C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C8C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:62 -Lys A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C8C)

(-) Exons   (0, 0)

(no "Exon" information available for 1C8C)

(-) 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:64
 aligned with DN7D_SULSO | P39476 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:64
                                    10        20        30        40        50        60    
           DN7D_SULSO     1 MATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK  64
               SCOP domains d1c8ca_ A: DNA-binding protein                                   SCOP domains
               CATH domains 1c8cA00 A:1-64  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeehhheeeeeee..eeeeeee.hhh.eeeeeee.....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1c8c A   1 MATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLAKQKK  64
                                    10        20        30        40        50        60    


Chain B from PDB  Type:DNA  Length:8
                                        
                 1c8c B 101 GTGATCGC 108


Chain C from PDB  Type:DNA  Length:8
                                        
                 1c8c C 109 GTGATCGC 116
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C8C)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DN7D_SULSO | P39476)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

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  Cis Peptide Bonds
    Gln A:62 - Lys A:63   [ RasMol ]  
 

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  1c8c
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  DN7D_SULSO | P39476
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 Related Entries

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

UniProtKB/Swiss-Prot
        DN7D_SULSO | P39476: 1bbx 1bnz 1jic 5b02 5b03 5b0i 5b0j 5b0k 5b0l 5b0m 5u1c

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1C8C)