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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL WRKY DOMAINOF ATWRKY1, AN SA-INDUCED AND PARTIALLY NPR1-DEPENDENT TRANSCRIPTION FACTOR
 
Authors :  M. R. Duan, J. Nan, Y. Li, X. D. Su
Date :  07 Sep 05  (Deposition) - 31 Oct 06  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Strands, Zinc Finger, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Duan, J. Nan, Y. H. Liang, P. Mao, L. Lu, L. Li, C. Wei, L. Lai, Y. Li, X. D. Su
Dna Binding Mechanism Revealed By High Resolution Crystal Structure Of Arabidopsis Thaliana Wrky1 Protein.
Nucleic Acids Res. V. 35 1145 2007
PubMed-ID: 17264121  |  Reference-DOI: 10.1093/NAR/GKM001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WRKY TRANSCRIPTION FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21ADEST
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: WRKY1
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: WRKY DNA-BINDING PROTEIN 1, ZINC-DEPENDENT ACTIVATOR PROTEIN 1, TRANSCRIPTION FACTOR ZAP1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1SIN1Ligand/IonSUCCINIC ACID
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:332 , CYS A:337 , HIS A:361 , HIS A:363BINDING SITE FOR RESIDUE ZN A 369
2AC2SOFTWAREARG A:311 , SER A:333 , PRO A:367 , HOH A:619 , HOH A:624 , HOH A:668 , HOH A:674BINDING SITE FOR RESIDUE SIN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AYD)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WRKYPS50811 WRKY domain profile.WRKY1_ARATH105-169
301-366		  1-
A:301-366

(-) Exons   (0, 0)

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(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:76
 aligned with WRKY1_ARATH | Q9SI37 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:76
                                   302       312       322       332       342       352       362      
          WRKY1_ARATH   293 SRIVVHTQTLFDIVNDGYRWRKYGQKSVKGSPYPRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEGKHDHDMPPG 368
               SCOP domains d2ayda_ A: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...........eeeeeee........eeeeee.......eeeeee......eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------WRKY  PDB: A:301-366 UniProt: 301-366                             -- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2ayd A 293 SRIVVHTQTLFDIVNDGYRWRKYGQKSVKGSPYPRSYYRCSSPGCPVKKHVERSSHDTKLLITTYEGKHDHDMPPG 368
                                   302       312       322       332       342       352       362
   Legend:   → Mismatch (orange background)
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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/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AYD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AYD)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (WRKY1_ARATH | Q9SI37)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009863    salicylic acid mediated signaling pathway    A series of molecular signals mediated by salicylic acid.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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