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(-) Description

Title :  CRYSTAL STRUCTURE OF STWHY2
 
Authors :  L. Cappadocia, N. Brisson, J. Sygusch
Date :  15 May 10  (Deposition) - 11 Aug 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (24x)
Keywords :  Stwhy2, Single-Stranded Dna Binding Protein, Plant, Potato, Whirly, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Cappadocia, A. Marechal, J. S. Parent, E. Lepage, J. Sygusch, N. Brisson
Crystal Structures Of Dna-Whirly Complexes And Their Role I Arabidopsis Organelle Genome Repair.
Plant Cell V. 22 1849 2010
PubMed-ID: 20551348  |  Reference-DOI: 10.1105/TPC.109.071399

(-) Compounds

Molecule 1 - STWHY2
    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: WHIRLY DOMAIN
    Gene: STWHY2
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Strain: KENNEBEC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A
Biological Unit 2 (24x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1PO48Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 48)
No.NameCountTypeFull Name
1PO448Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:75 , ARG A:91 , ARG A:92BINDING SITE FOR RESIDUE PO4 A 1
2AC2SOFTWAREPHE A:116 , ALA A:117 , HIS A:139 , LYS A:153 , HOH A:234BINDING SITE FOR RESIDUE PO4 A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N1H)

(-) Exons   (0, 0)

(no "Exon" information available for 3N1H)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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: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 d3n1ha_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eeeeeeee...eee.....eee....eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee.....eeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1h A  55 GRVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHIMGWDRFTNR 215
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
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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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3N1H)

(-) 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: 3n1i 3n1j 3n1k 3n1l 3r9y 3r9z 3ra0

(-) Related Entries Specified in the PDB File

3n1i CRYSTAL STRUCTURE OF STWHY2-ERE32 COMPLEX
3n1j CRYSTAL STRUCTURE OF STWHY2-DT32 COMPLEX
3n1k CRYSTAL STRUCTURE OF STWHY2-CERE32 COMPLEX
3n1l CRYSTAL STRUCTURE OF STWHY2-RCERE32 COMPLEX