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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METAL-SENSING TRANSCRIPTIONAL REPRESSOR CZRA FROM STAPHYLOCOCCUS AUREUS IN THE APO-FORM
 
Authors :  C. Eicken, M. A. Pennella, X. Chen, K. M. Koshlap, M. L. Vanzile, J. C. Sacchettini, D. P. Giedroc
Date :  25 Sep 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Zinc, Dna Binding, Transcriptional Regulation, Winged Hth Protein, Transcription Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Eicken, M. A. Pennella, X. Chen, K. M. Koshlap, M. L. Vanzile, J. C. Sacchettini, D. P. Giedroc
A Metal-Ligand-Mediated Intersubunit Allosteric Switch In Related Smtb/Arsr Zinc Sensor Proteins.
J. Mol. Biol. V. 333 683 2003
PubMed-ID: 14568530  |  Reference-DOI: 10.1016/J.JMB.2003.09.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPRESSOR PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: CZRA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R1U)

(-) Sites  (0, 0)

(no "Site" information available for 1R1U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R1U)

(-) Exons   (0, 0)

(no "Exon" information available for 1R1U)

(-) 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:94
 aligned with O85142_STAAU | O85142 from UniProtKB/TrEMBL  Length:106

    Alignment length:94
                                    18        28        38        48        58        68        78        88        98    
         O85142_STAAU     9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPK 102
               SCOP domains d1r1ua_ A: Metal-sensing transcriptional repressor CzrA                                        SCOP domains
               CATH domains 1r1uA00 A:9-102 'winged helix' repressor DNA binding domain                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1r1u A   9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPK 102
                                    18        28        38        48        58        68        78        88        98    


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with O85142_STAAU | O85142 from UniProtKB/TrEMBL  Length:106

    Alignment length:93
                                    18        28        38        48        58        68        78        88        98   
         O85142_STAAU     9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHP 101
               SCOP domains d1r1ub_ B: Metal-sensing transcriptional repressor CzrA                                       SCOP domains
               CATH domains 1r1uB00 B:9-101 'winged helix' repressor DNA binding domain                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1r1u B   9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHP 101
                                    18        28        38        48        58        68        78        88        98   


Chain C from PDB  Type:PROTEIN  Length:98
 aligned with O85142_STAAU | O85142 from UniProtKB/TrEMBL  Length:106

    Alignment length:98
                                    15        25        35        45        55        65        75        85        95        
         O85142_STAAU     6 SEINTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
               SCOP domains d1r1uc_ C: Metal-sensing transcriptional repressor CzrA                                            SCOP domains
               CATH domains 1r1uC00 C:6-103 'winged helix' repressor DNA binding domain                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1r1u C   6 SEINTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
                                    15        25        35        45        55        65        75        85        95        


Chain D from PDB  Type:PROTEIN  Length:95
 aligned with O85142_STAAU | O85142 from UniProtKB/TrEMBL  Length:106

    Alignment length:95
                                    18        28        38        48        58        68        78        88        98     
         O85142_STAAU     9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
               SCOP domains d1r1ud_ D: Metal-sensing transcriptional repressor CzrA                                         SCOP domains
               CATH domains 1r1uD00 D:9-103 'winged helix' repressor DNA binding domain                                     CATH domains
           Pfam domains (1) --------HTH_20-1r1uD01 D:17-76                                      --------------------------- Pfam domains (1)
           Pfam domains (2) --------HTH_20-1r1uD02 D:17-76                                      --------------------------- Pfam domains (2)
           Pfam domains (3) --------HTH_20-1r1uD03 D:17-76                                      --------------------------- Pfam domains (3)
           Pfam domains (4) --------HTH_20-1r1uD04 D:17-76                                      --------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1r1u D   9 NTDTLERVTEIFKALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHANHPKE 103
                                    18        28        38        48        58        68        78        88        98
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O85142_STAAU | O85142)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        O85142_STAAU | O85142: 1r1v 2kjb 2kjc 2m30

(-) Related Entries Specified in the PDB File

1r1t SMTB IN ITS APO-FORM (1.7 ANG)
1r1v ZN2-FORM OF CZRA
1r22 SMTB (C14S/C61S/C121S MUTANT) IN ITS ZN2-FORM
1r23 SMTB IN THE ZN1-FORM
1smt SMTB IN ITS APO-FORM (2.2 ANG)