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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYANOBACTERIAL METALLOTHIONEIN REPRESSOR SMTB IN THE ZN1-FORM (ONE ZN(II) PER DIMER)
 
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./Biol. Unit :  A,B
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 - TRANSCRIPTIONAL REPRESSOR SMTB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMTB
    Organism Scientific: SYNECHOCOCCUS ELONGATUS PCC 7942
    Organism Taxid: 1140
    Strain: PCC7942

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:104 , HIS A:106 , HIS B:117 , GLU B:120BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R23)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R23)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R23)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ARSR_2PS50987 ArsR-type HTH domain profile.SMTB_SYNE728-122
 		  2A:28-121
B:28-121
2HTH_ARSR_1PS00846 Bacterial regulatory proteins, arsR family signature.SMTB_SYNE761-79
 		  2A:61-79
B:61-79

(-) Exons   (0, 0)

(no "Exon" information available for 1R23)

(-) 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:104
 aligned with SMTB_SYNE7 | P30340 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:104
                                    27        37        47        57        67        77        87        97       107       117    
           SMTB_SYNE7    18 HAAIASELQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQEC 121
               SCOP domains d1r23a_ A: SmtB repressor                                                                                SCOP domains
               CATH domains 1r23A00 A:18-121 'winged helix' repressor DNA binding domain                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------HTH_ARSR_2  PDB: A:28-121 UniProt: 28-122                                                      PROSITE (1)
                PROSITE (2) -------------------------------------------HTH_ARSR_1         ------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1r23 A  18 HAAIASELQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQEC 121
                                    27        37        47        57        67        77        87        97       107       117    


Chain B from PDB  Type:PROTEIN  Length:97
 aligned with SMTB_SYNE7 | P30340 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:97
                                    34        44        54        64        74        84        94       104       114       
           SMTB_SYNE7    25 LQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQEC 121
               SCOP domains d1r23b_ B: SmtB repressor                                                                         SCOP domains
               CATH domains 1r23B00 B:25-121 'winged helix' repressor DNA binding domain                                      CATH domains
           Pfam domains (1) --------------------HTH_5-1r23B01 B:45-91                          ------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------HTH_5-1r23B02 B:45-91                          ------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HTH_ARSR_2  PDB: B:28-121 UniProt: 28-122                                                      PROSITE (1)
                PROSITE (2) ------------------------------------HTH_ARSR_1         ------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1r23 B  25 LQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQEC 121
                                    34        44        54        64        74        84        94       104       114
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SMTB_SYNE7 | P30340)
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  1r23
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 Related Entries

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

UniProtKB/Swiss-Prot
        SMTB_SYNE7 | P30340: 1r1t 1r22 1smt

(-) Related Entries Specified in the PDB File

1r1t THE SAME PROTEIN IN ITS APO-FORM (1.7 ANG)
1r1u APO-FORM OF CZRA
1r1v ZN2-FORM OF CZRA
1r22 THE SAME PROTEIN (C14S/C61S/C121S MUTANT) IN ITS ZN2-FORM
1smt THE SAME PROTEIN IN ITS APO-FORM (2.2 ANG)