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(-) Description

Title :  ZINC-BOUND C-TERMINAL DOMAIN OF NIKR
 
Authors :  C. M. Phillips, E. R. Schreiter, C. L. Drennan
Date :  06 Dec 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Keywords :  Nikr, Nickel Regulatory Protein, Transcription Factor, Beta Sandwich, Dna-Binding, Metal-Binding, Repressor, Transcription Regulation, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Phillips, E. R. Schreiter, Y. Guo, S. C. Wang, D. B. Zamble, C. L. Drennan
Structural Basis Of The Metal Specificity For Nickel Regulatory Protein Nikr.
Biochemistry V. 47 1938 2008
PubMed-ID: 18193897  |  Reference-DOI: 10.1021/BI702006H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICKEL-RESPONSIVE REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NIKR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , CYS A:95BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS A:87 , CYS A:95 , GLU A:97BINDING SITE FOR RESIDUE ZN A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BKF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BKF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BKF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BKF)

(-) Exons   (0, 0)

(no "Exon" information available for 3BKF)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:66
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:83
                                    58        68        78        88        98       108       118       128   
           NIKR_ECOLI    49 GTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d3bkfa1 A:49-                 131 Nickel responsive regulator NikR, C-terminal doma SCOP domains
               CATH domains 3bkfA00 A:49-                 131 ACT-like. Chain A, domain 2                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.-----------------...eeeeeeee.....eeeeeeeeeehhhhhhhhhhhhh...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 3bkf A  49 GTQGFAVLSYVYE-----------------HDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
                                    58  |      -         -|       88        98       108       118       128   
                                       61                79
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BKF)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (NIKR_ECOLI | P0A6Z6)
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:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0010045    response to nickel cation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nickel cation stimulus.
    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
        NIKR_ECOLI | P0A6Z6: 1q5v 1q5y 2hza 2hzv 3bkt 3bku 3od2

(-) Related Entries Specified in the PDB File

3bkt CU-BOUND C-TERMINAL DOMAIN OF NIKR
3bku APO C-TERMINAL DOMAIN OF NIKR