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(-) Description

Title :  SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7
 
Authors :  K. Yamasaki, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Sep 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Transcription Factor, Sbp, Flower Development, Dna Binding Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, Y. Ishizuka, T. Terada, M. Shirouzu, T. Osanai, A. Tanaka, M. Seki, K. Shinozaki, S. Yokoyama
A Novel Zinc-Binding Motif Revealed By Solution Structures Of Dna-Binding Domains Of Arabidopsis Sbp-Family Transcription Factors.
J. Mol. Biol. V. 337 49 2004
PubMed-ID: 15001351  |  Reference-DOI: 10.1016/J.JMB.2004.01.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7
    Chains: A
    Engineered: YES
    Expression System Plasmid: PCR2.1
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN (SBP DOMAIN)
    Gene: SPL7
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL-FREE SYNTHESIS
    Synonym: SPL7

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:138 , CYS A:143 , CYS A:160 , CYS A:163BINDING SITE FOR RESIDUE ZN A 221
2AC2SOFTWARECYS A:179 , CYS A:182 , HIS A:186 , CYS A:198BINDING SITE FOR RESIDUE ZN A 222

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UL5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UL5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UL5)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_SBPPS51141 Zinc finger SBP-type profile.SPL7_ARATH135-212  1A:135-212

(-) Exons   (0, 0)

(no "Exon" information available for 1UL5)

(-) 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:86
 aligned with SPL7_ARATH | Q8S9G8 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:86
                                   144       154       164       174       184       194       204       214      
           SPL7_ARATH   135 VARCQVPDCEADISELKGYHKRHRVCLRCATASFVVLDGENKRYCQQCGKFHLLPDFDEGKRSCRRKLERHNNRRKRKPVDKGGVA 220
               SCOP domains d1ul5a_ A: Squamosa promoter binding protein-like 7, DNA-binding domain                SCOP domains
               CATH domains 1ul5A01 A:135-199                                                --------------------- CATH domains
               Pfam domains --SBP-1ul5A01 A:137-215                                                          ----- Pfam domains
         Sec.struct. author ....ee..ee.........hhhhh.hhhhhhhheeee..eeeee......eee.hhh............................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_SBP  PDB: A:135-212 UniProt: 135-212                                       -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1ul5 A 135 VARCQVPDCEADISELKGYHKRHRVCLRCATASFVVLDGENKRYCQQCGKFHLLPDFDEGKRSCRRKLERHNNRRKRKPVDKGGVA 220
                                   144       154       164       174       184       194       204       214
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  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)

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  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (SPL7_ARATH | Q8S9G8)
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.
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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