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(-) Description

Title :  CRYSTAL STRUCTURE OF ROVA FROM YERSINIA IN COMPLEX WITH A ROVA PROMOTER FRAGMENT
 
Authors :  N. Quade, C. Mendonca, K. Herbst, A. K. Heroven, D. W. Heinz, P. Dersch
Date :  10 Feb 12  (Deposition) - 12 Sep 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription, Transcription Factor, Global Regulator, Virulence Regulation, Thermosensing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Quade, C. Mendonca, K. Herbst, A. K. Heroven, C. Ritter, D. W. Heinz, P. Dersch
Structural Basis For Intrinsic Thermosensing By The Master Virulence Regulator Rova Of Yersinia.
J. Biol. Chem. V. 287 35796 2012
PubMed-ID: 22936808  |  Reference-DOI: 10.1074/JBC.M112.379156

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR SLYA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633
    Strain: YPIII
    Synonym: REGULATOR OF VIRULENCE PROTEIN A, TRANSCRIPTIONAL REGULATOR FOR CRYPTIC HEMOLYSIN, ROVA
 
Molecule 2 - ROVA PROMOTER FRAGMENT, 5'-D(*AP*AP*TP*TP*AP*TP*AP*TP *TP*AP*TP*TP*TP*GP*AP*AP*TP*TP*AP*AP*T)-3'
    Chains: C
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633
    Strain: YPIII
    Synthetic: YES
 
Molecule 3 - ROVA PROMOTER FRAGMENT, 5'-D(*TP*AP*TP*TP*AP*AP*TP*TP *CP*AP*AP*AP*TP*AP*AP*TP*AP*TP*AP*AP*T)-3'
    Chains: D
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633
    Strain: YPIII
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4AIJ)

(-) Sites  (0, 0)

(no "Site" information available for 4AIJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AIJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AIJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AIJ)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MARR_2PS50995 MarR-type HTH domain profile.SLYA_YERPY2-135  1B:2-135
2HTH_MARR_1PS01117 MarR-type HTH domain signature.SLYA_YERPY62-96
 		  2A:62-96
B:62-96

(-) Exons   (0, 0)

(no "Exon" information available for 4AIJ)

(-) 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    
   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:139
 aligned with SLYA_YERPY | B1JJ73 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132         
           SLYA_YERPY     3 STLGSDLARLVRVWRALIDHRLKPLELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTCANDRRAKRIKLTEQSSPIIEQVDGVICSTRKEILGGISSDEIAVLSGLIDKLEKNIIQLQ 141
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_MARR_2  PDB: - UniProt: 2-135                                                                                                    ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------HTH_MARR_1  PDB: A:62-96           --------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aij A   3 STLGSDLARLVRVWRALIDHRLKPLELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIEQVDGVISSTRKEILGGISSDEIAVLSGLIDKLEKNIIQLQ 141
                                    12        22        32        42        52        62        72        82        92       102       112       122       132         


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with SLYA_YERPY | B1JJ73 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
           SLYA_YERPY     2 ESTLGSDLARLVRVWRALIDHRLKPLELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTCANDRRAKRIKLTEQSSPIIEQVDGVICSTRKEILGGISSDEIAVLSGLIDKLEKNIIQLQTK 143
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_MARR_2  PDB: B:2-135 UniProt: 2-135                                                                                               -------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------HTH_MARR_1  PDB: B:62-96           ----------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aij B   2 ESTLGSDLARLVRVWRALIDHRLKPLELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIEQVDGVISSTRKEILGGISSDEIAVLSGLIDKLEKNIIQLQTK 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  


Chain C from PDB  Type:DNA  Length:21
                                                     
                 4aij C   1 AATTATATTATTTGAATTAAT  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 4aij D   1 TATTAATTCAAATAATATAAT  21
                                    10        20
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4AIJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AIJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AIJ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SLYA_YERPY | B1JJ73)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.

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  4aij
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SLYA_YERPY | B1JJ73: 4aih 4aik

(-) Related Entries Specified in the PDB File

4aih CRYSTAL STRUCTURE OF ROVA FROM YERSINIA IN ITS FREE FORM
4aik CRYSTAL STRUCTURE OF ROVA FROM YERSINIA IN COMPLEX WITH AN INVASIN PROMOTER FRAGMENT