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(-) Description

Title :  CRYSTAL STRUCTURE OF YYCF DNA-BINDING DOMAIN FROM STAPHYLOCOCCUS AUREUS
 
Authors :  T. Okajima, A. Doi, R. Utsumi
Date :  26 Dec 08  (Deposition) - 20 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Two-Component System, Yycg, Response Regulator, Helix-Turn-Helix Motif, Dna-Binding Domain, Transcriptional Regulation, Activator, Dna-Binding, Phosphoprotein, Transcription, Transcription Regulation, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Doi, T. Okajima, Y. Gotoh, K. Tanizawa, R. Utsumi
Novel Antibiotics Target Protein Of Gram-Positive Pathogens X-Ray Crystal Structures And Search Of Potential Drug-Binding Sites
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN WALR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DNA-BINDING DOMAIN
    Gene: YYCF
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: 209P
    Synonym: RESPONSE REGULATOR YYCF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2ZXJ)

(-) Sites  (0, 0)

(no "Site" information available for 2ZXJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZXJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZXJ)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2ZXJ)

(-) Sequences/Alignments

Asymmetric 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    
   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:100
 aligned with WALR_STAAU | Q9RDT5 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:100
                                   142       152       162       172       182       192       202       212       222       232
           WALR_STAAU   133 NEITIKDIVIYPDAYSIKKRGEDIELTHREFELFHYLSKHMGQVMTREHLLQTVWGYDYFGDVRTVDVTIRRLREKIEDDPSHPEYIVTRRGVGYFLQQH 232
               SCOP domains d2zxja_ A: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeehhhheeee..eee..hhhhhhhhhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhhh........eeee...eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2zxj A 133 NEITIKDIVIYPDAYSIKKRGEDIELTHREFELFHYLSKHMGQVMTREHLLQTVWGYDYFGDVRTVDVTIRRLREKIEDDPSHPEYIVTRRGVGYFLQQH 232
                                   142       152       162       172       182       192       202       212       222       232


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with WALR_STAAU | Q9RDT5 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:100
                                   142       152       162       172       182       192       202       212       222       232
           WALR_STAAU   133 NEITIKDIVIYPDAYSIKKRGEDIELTHREFELFHYLSKHMGQVMTREHLLQTVWGYDYFGDVRTVDVTIRRLREKIEDDPSHPEYIVTRRGVGYFLQQH 232
               SCOP domains d2zxjb_ B: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------Trans_reg_C-2zxjB01 B:153-229                                                --- Pfam domains (1)
           Pfam domains (2) --------------------Trans_reg_C-2zxjB02 B:153-229                                                --- Pfam domains (2)
         Sec.struct. author ..eee..eeeehhhheeee..eee..hhhhhhhhhhhhh.....eehhhhhhhhh.......hhhhhhhhhhhhhhhh........eeee...eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2zxj B 133 NEITIKDIVIYPDAYSIKKRGEDIELTHREFELFHYLSKHMGQVMTREHLLQTVWGYDYFGDVRTVDVTIRRLREKIEDDPSHPEYIVTRRGVGYFLQQH 232
                                   142       152       162       172       182       192       202       212       222       232
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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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (WALR_STAAU | Q9RDT5)
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:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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