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(-) Description

Title :  APO C-TERMINAL DOMAIN OF NIKR
 
Authors :  C. M. Phillips, E. R. Schreiter, C. L. Drennan
Date :  07 Dec 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
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, B, C, D
    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, YHHG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3BKU)

(-) Sites  (0, 0)

(no "Site" information available for 3BKU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BKU)

(-) 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:68
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:81
                                    60        70        80        90       100       110       120       130 
           NIKR_ECOLI    51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d3bkua_ A: Nick             el responsive regulator NikR, C-terminal domain       SCOP domains
               CATH domains 3bkuA00 A:51-13             1 ACT-like. Chain A, domain 2                         CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....-------------...eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3bku A  51 QGFAVLSYVYEHEKR-------------HDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
                                    60    |    -        80        90       100       110       120       130 
                                         65            79                                                    


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:84
                                    58        68        78        88        98       108       118       128    
           NIKR_ECOLI    49 GTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d3bkub_ B: Nic  kel responsive regulator NikR, C-terminal domain                     SCOP domains
               CATH domains 3bkuB00 B:49-1  32 ACT-like. Chain A, domain 2                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee.--hhhhhhhhhhh......eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 3bku B  49 GTQGFAVLSYVYEH--RDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    58   |  | 68        78        88        98       108       118       128    
                                        62 65                                                                   


Chain C from PDB  Type:PROTEIN  Length:83
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:83
                                    60        70        80        90       100       110       120       130   
           NIKR_ECOLI    51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED 133
               SCOP domains d3bkuc_ C: Nickel responsive regulator NikR, C-terminal domain                      SCOP domains
               CATH domains 3bkuC00 C:51-133 ACT-like. Chain A, domain 2                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeeeehhhhhhhhhhhhhh....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 3bku C  51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED 133
                                    60        70        80        90       100       110       120       130   


Chain D from PDB  Type:PROTEIN  Length:66
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:82
                                    59        69        79        89        99       109       119       129  
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d3bkud_ D: Nic                kel responsive regulator NikR, C-terminal domain     SCOP domains
               CATH domains 3bkuD00 D:50-1                31 ACT-like. Chain A, domain 2                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..----------------..eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3bku D  50 TQGFAVLSYVYEHE----------------DLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
                                    59   |     -         -|       89        99       109       119       129  
                                        63               80
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 3bkf 3bkt 3od2

(-) Related Entries Specified in the PDB File

3bkf ZINC-BOUND C-TERMINAL DOMAIN OF NIKR
3bkt COPPER-BOUND C-TERMINAL DOMAIN OF NIKR