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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZN(II) FORM OF E. COLI ZNTR, A ZINC-SENSING TRANSCRIPTIONAL REGULATOR (SPACE GROUP C222)
 
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) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A  (2x)
Biol. Unit 4:  B  (2x)
Keywords :  Merr Family Transcriptional Regulator, Zn(Ii)-Responsive Regulator Of Znta, Transcription (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

(-) 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: DIMERIZATION AND METAL-BINDING DOMAINS
    Gene: ZNTR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): AB
Biological Unit 3 (2x): A 
Biological Unit 4 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN5Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:79 , ALA 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:412 , HOH A:417 , HIS B:119BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREHIS A:119 , HOH A:412 , CYS B:79 , 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:434BINDING SITE FOR RESIDUE SO4 B 302
3AC3SOFTWARECYS A:79 , CYS A:114 , CYS A:124 , SO4 A:301 , ZN A:402BINDING SITE FOR RESIDUE ZN A 401
4AC4SOFTWARECYS A:79 , CYS A:115 , HIS A:119 , SO4 A:301 , ZN A:401BINDING SITE FOR RESIDUE ZN A 402
5AC5SOFTWARECYS B:79 , CYS B:114 , CYS B:124 , SO4 B:302 , ZN B:404BINDING SITE FOR RESIDUE ZN B 403
6AC6SOFTWARECYS B:79 , CYS B:115 , HIS B:119 , SO4 B:302 , ZN B:403BINDING SITE FOR RESIDUE ZN B 404
7AC7SOFTWAREHIS A:53BINDING SITE FOR RESIDUE ZN A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q0A)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q0A)

(-) 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:91
 aligned with ZNTR_ECOLI | P0ACS5 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:91
                                    53        63        73        83        93       103       113       123       133 
           ZNTR_ECOLI    44 DLQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQGA 134
               SCOP domains d1q0aa_ A: Transcriptional regulator ZntR                                                   SCOP domains
               CATH domains 1q0aA00 A:44-134  [code=1.10.1660.10, no name defined]                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1q0a A  44 DLQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQGA 134
                                    53        63        73        83        93       103       113       123       133 


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

    Alignment length:89
                                    53        63        73        83        93       103       113       123         
           ZNTR_ECOLI    44 DLQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQ 132
               SCOP domains d1q0ab_ B: Transcriptional regulator ZntR                                                 SCOP domains
               CATH domains 1q0aB00 B:44-132  [code=1.10.1660.10, no name defined]                                    CATH domains
           Pfam domains (1) -MerR-DNA-bind-1q0aB01 B:45-110                                    ---------------------- Pfam domains (1)
           Pfam domains (2) -MerR-DNA-bind-1q0aB02 B:45-110                                    ---------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1q0a B  44 DLQRLKFIRHARQLGFSLESIRELLSIRIDPEHHTCQESKGIVQERLQEVEARIAELQSMQRSLQRLNDACCGTAHSSVYCSILEALEQ 132
                                    53        63        73        83        93       103       113       123
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (7, 7)

Asymmetric 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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 Related Entries

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

UniProtKB/Swiss-Prot
        ZNTR_ECOLI | P0ACS5: 1q08 1q09

(-) Related Entries Specified in the PDB File

1q08 THE ZN(II) FORM OF E. COLI ZNTR (SPACE GROUP P212121)
1q09 THE ZN(II) FORM OF E. COLI ZNTR (SPACE GROUP I4122)