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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZN(II) FORM OF E. COLI ZNTR, A ZINC-SENSING TRANSCRIPTIONAL REGULATOR, AT 1.9 A RESOLUTION (SPACE GROUP P212121)
 
Authors :  A. Changela, K. Chen, Y. Xue, J. Holschen, C. E. Outten, T. V. O'Halloran, A. Mondragon
Date :  15 Jul 03  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Merr Family Transcriptional Regulator, Zn(Ii)-Responsive Regulator Of Znta (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Changela, K. Chen, Y. Xue, J. Holschen, C. E. Outten, T. V. O'Halloran, A. Mondragon
Molecular Basis Of Metal-Ion Selectivity And Zeptomolar Sensitivity By Cuer
Science V. 301 1383 2003
PubMed-ID: 12958362  |  Reference-DOI: 10.1126/SCIENCE.1085950
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZN(II)-RESPONSIVE REGULATOR OF ZNTA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZNTR DIMERIZATION AND METAL-BINDING DOMAINS
    Gene: ZNTR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:113 , CYS A:114 , CYS A:115 , HIS A:119 , TYR A:123 , CYS A:124 , SER A:125 , ZN A:401 , ZN A:402 , HOH A:503 , HOH A:508 , CYS B:79 , HIS B:119BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWARECYS A:79 , HIS A:119 , HOH A:503 , ALA B:113 , CYS B:114 , CYS B:115 , HIS B:119 , TYR B:123 , CYS B:124 , SER B:125 , ZN B:403 , ZN B:404 , HOH B:408BINDING SITE FOR RESIDUE PO4 B 302
3AC3SOFTWARECYS A:114 , CYS A:124 , PO4 A:301 , ZN A:402 , CYS B:79BINDING SITE FOR RESIDUE ZN A 401
4AC4SOFTWARECYS A:115 , HIS A:119 , PO4 A:301 , ZN A:401 , CYS B:79BINDING SITE FOR RESIDUE ZN A 402
5AC5SOFTWARECYS A:79 , CYS B:114 , CYS B:124 , PO4 B:302 , ZN B:404BINDING SITE FOR RESIDUE ZN B 403
6AC6SOFTWARECYS A:79 , CYS B:115 , HIS B:119 , PO4 B:302 , ZN B:403BINDING SITE FOR RESIDUE ZN B 404
7AC7SOFTWAREHOH A:502 , HOH A:503 , HOH A:504 , HOH A:505 , HOH A:506 , HOH A:507BINDING SITE FOR RESIDUE MG A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q08)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q08)

(-) 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:94
 aligned with ZNTR_ECOLI | P0ACS5 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:94
                                    52        62        72        82        92       102       112       122       132    
           ZNTR_ECOLI    43 SDLQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQGASG 136
               SCOP domains d1q08a_ A: Transcriptional regulator ZntR                                                      SCOP domains
               CATH domains 1q08A00 A:43-136  [code=1.10.1660.10, no name defined]                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1q08 A  43 SDLQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQGASG 136
                                    52        62        72        82        92       102       112       122       132    


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with ZNTR_ECOLI | P0ACS5 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:89
                                    54        64        74        84        94       104       114       124         
           ZNTR_ECOLI    45 LQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQG 133
               SCOP domains d1q08b_ B: Transcriptional regulator ZntR                                                 SCOP domains
               CATH domains 1q08B00 B:45-133  [code=1.10.1660.10, no name defined]                                    CATH domains
           Pfam domains (1) MerR-DNA-bind-1q08B01 B:45-110                                    ----------------------- Pfam domains (1)
           Pfam domains (2) MerR-DNA-bind-1q08B02 B:45-110                                    ----------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1q08 B  45 LQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQG 133
                                    54        64        74        84        94       104       114       124
   Legend:   → Mismatch (orange background)
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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/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  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ZNTR_ECOLI | P0ACS5)
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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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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  1q08
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 Related Entries

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

UniProtKB/Swiss-Prot
        ZNTR_ECOLI | P0ACS5: 1q09 1q0a

(-) Related Entries Specified in the PDB File

1q09 THE ZN(II) FORM OF E. COLI ZNTR (SPACE GROUP I4122)
1q0a THE ZN(II) FORM OF E. COLI ZNTR (SPACE GROUP C222)