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(-) Description

Title :  NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
 
Authors :  T. H. Tahirov
Date :  31 Jan 05  (Deposition) - 08 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transcription, Repressor, Pyrococcus Horikoshii, Nikr, Dna- Binding, Metal-Binding, Nickel, Transcription Regulation, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. T. Chivers, T. H. Tahirov
Structure Of Pyrococcus Horikoshii Nikr: Nickel Sensing And Implications For The Regulation Of Dna Recognition
J. Mol. Biol. V. 348 597 2005
PubMed-ID: 15826657  |  Reference-DOI: 10.1016/J.JMB.2005.03.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICKEL RESPONSIVE REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NI4Ligand/IonNICKEL (II) ION
4PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NI-1Ligand/IonNICKEL (II) ION
4PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , HIS A:91 , CYS A:97 , HIS B:78BINDING SITE FOR RESIDUE NI A1137
2AC2SOFTWAREHOH A:2004 , ARG B:30 , HOH B:2023BINDING SITE FOR RESIDUE CL B1139
3AC3SOFTWARELEU A:74 , HIS A:78 , HIS B:89 , HIS B:91 , CYS B:97BINDING SITE FOR RESIDUE NI B1140
4AC4SOFTWAREASP A:75 , HIS B:64 , ASP B:65BINDING SITE FOR RESIDUE NI B1141
5AC5SOFTWAREHIS A:64 , ASP A:65 , HOH A:2024 , HOH A:2025 , ASP B:75BINDING SITE FOR RESIDUE NI B1142
6AC6SOFTWAREPHE A:6 , SER A:7 , HOH A:2053 , LYS B:127 , LEU B:128 , MET B:130BINDING SITE FOR RESIDUE EDO A1138
7AC7SOFTWAREHIS A:45 , LYS A:111 , ASP A:115 , LEU A:118 , HIS A:125 , GLY A:126 , HOH A:2043 , ILE B:25 , TYR B:27 , HOH B:2020BINDING SITE FOR RESIDUE PG4 A1139
8AC8SOFTWAREASP A:19 , ILE A:22 , GLU A:23 , TYR A:27 , GLU A:28 , ARG A:30BINDING SITE FOR RESIDUE PG4 A1140
9AC9SOFTWAREMET A:1 , HIS B:125 , GLY B:126BINDING SITE FOR RESIDUE EDO B1143

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BJ7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BJ7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 2BJ7)

(-) 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:137
 aligned with NIKR_PYRHO | O58316 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       
           NIKR_PYRHO     1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKEL 137
               SCOP domains d2bj7a1 A:1-50                                    d2bj7a2 A:51-137 Nickel responsive regulator NikR, C-terminal domain                    SCOP domains
               CATH domains ---------2bj7A01 A:10-50 Met repressor-like       --------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bj7 A   1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKEL 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with NIKR_PYRHO | O58316 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           NIKR_PYRHO     1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKELV 138
               SCOP domains d2bj7b1 B:1-50                                    d2bj7b2 B:51-138 Nickel responsive regulator NikR, C-terminal domain                     SCOP domains
               CATH domains ----------2bj7B01 B:11-50 Met repressor-like      ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bj7 B   1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKELV 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BJ7)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NIKR_PYRHO | O58316)
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: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_PYRHO | O58316: 2bj1 2bj3 2bj8 2bj9

(-) Related Entries Specified in the PDB File

2bj1 NIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
2bj3 NIKR-APO
2bj8 NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH AND LOW-AFFINITY SITES
2bj9 NIKR WITH BOUND NICKEL AND PHOSPHATE