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(-) Description

Title :  CRYSTAL STRUCTURE OF A STWHY2 K67A-DT32 COMPLEX
 
Authors :  L. Cappadocia, N. Brisson, J. Sygusch
Date :  26 Mar 11  (Deposition) - 28 Sep 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Biol. Unit 2:  A,B  (24x)
Keywords :  Stwhy2, Single-Stranded Dna Binding Protein, Plant, Potato, Whirly, Protein-Dna Complex, Mitochondria, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Cappadocia, J. S. Parent, E. Zampini, E. Lepage, J. Sygusch, N. Brisson
A Conserved Lysine Residue Of Plant Whirly Proteins Is Necessary For Higher Order Protein Assembly And Protection Against Dna Damage.
Nucleic Acids Res. V. 40 258 2012
PubMed-ID: 21911368  |  Reference-DOI: 10.1093/NAR/GKR740

(-) Compounds

Molecule 1 - WHY2 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 48-216
    Gene: STWHY2
    Mutation: YES
    Organism Common: POTATOES
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Strain: KENNEBEC
 
Molecule 2 - DNA 32-MER DT32
    Chains: B
    Engineered: YES
    Other Details: DNA SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB
Biological Unit 2 (24x): AB

Summary Information (see also Sequences/Alignments below)

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

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(-) Sequences/Alignments

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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with WHY2_SOLTU | D9J034 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:161
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
           WHY2_SOLTU    55 GRVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHIMGWDRFTNR 215
               SCOP domains d3ra0a_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eeeeeeee...eee.....eee....eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ra0 A  55 GRVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHIMGWDRFTNR 215
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 


Chain B from PDB  Type:DNA  Length:9
                                         
                 3ra0 B   1 TTTTTTTTT   9
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (WHY2_SOLTU | D9J034)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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: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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        WHY2_SOLTU | D9J034: 3n1h 3n1i 3n1j 3n1k 3n1l 3r9y 3r9z

(-) Related Entries Specified in the PDB File

1l3a PARALOGUE PROTEIN
3n1h SAME PROTEIN WITHOUT K67A MUTATION
3n1i SAME PROTEIN WITHOUT K67A MUTATION
3n1j SAME PROTEIN WITHOUT K67A MUTATION
3n1k SAME PROTEIN WITHOUT K67A MUTATION
3n1l SAME PROTEIN WITHOUT K67A MUTATION
3r9y STWHY2 K67A (FORM I)
3r9z STWHY2 K67A (FORM II)