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(-) Description

Title :  SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 12 LACKING THE SECOND ZINC-BINDING SITE
 
Authors :  K. Yamasaki, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dna-Binding Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamasaki, T. Kigawa, M. Inoue, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, Y. Tomo, T. Terada, M. Shirouzu, A. Tanaka, M. Seki, K. Shinozaki, S. Yokoyama
Structure Of The Sbp Domain That Lacks The Second Zinc-Binding Site
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 12
    Chains: A
    Engineered: YES
    Expression System Plasmid: PCR2.1
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN (SHORT FRAGMENT)
    Gene: SPL12
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL-FREE SYNTHESIS
    Synonym: SPL12, TRANSCRIPTION FACTOR SPL12

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:127 , CYS A:132 , CYS A:149 , HIS A:152BINDING SITE FOR RESIDUE ZN A 182

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WJ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WJ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJ0)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_SBPPS51141 Zinc finger SBP-type profile.SPL12_ARATH124-201  1A:124-181

(-) Exons   (0, 0)

(no "Exon" information available for 1WJ0)

(-) Sequences/Alignments

NMR Structure
   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:58
 aligned with SPL12_ARATH | Q9S7P5 from UniProtKB/Swiss-Prot  Length:927

    Alignment length:58
                                   133       143       153       163       173        
          SPL12_ARATH   124 AICCQVDNCGADLSKVKDYHRRHKVCEIHSKATTALVGGIMQRFCQQCSRFHVLEEFD 181
               SCOP domains d1wj0a_ A:                                                 SCOP domains
               CATH domains 1wj0A00 A:124-181                                          CATH domains
               Pfam domains --SBP-1wj0A01 A:126-181                                    Pfam domains
         Sec.struct. author .ee........ee............hhhhhh...eee..eee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_SBP  PDB: A:124-181 UniProt: 124-201                    PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1wj0 A 124 AICCQVDNCGADLSKVKDYHRRHKVCEIHSKATTALVGGIMQRFCQQCSRFHVLEEFD 181
                                   133       143       153       163       173
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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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: SBP] (3)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (SPL12_ARATH | Q9S7P5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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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