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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  APO-NIKR
 
Authors :  E. R. Schreiter, M. D. Sintchak, Y. Guo, P. T. Chivers, R. T. Sauer, C. L. Drennan
Date :  11 Aug 03  (Deposition) - 30 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Homotetramer, Ribbon-Helix-Helix Domain, Beta Sandwich, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Schreiter, M. D. Sintchak, Y. Guo, P. T. Chivers, R. T. Sauer, C. L. Drennan
Crystal Structure Of The Nickel-Responsive Transcription Factor Nikr
Nat. Struct. Biol. V. 10 794 2003
PubMed-ID: 12970756  |  Reference-DOI: 10.1038/NSB985
(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
    Expression System Plasmid: PET-22B
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NIKR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: NIKR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Q5V)

(-) Sites  (0, 0)

(no "Site" information available for 1Q5V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q5V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q5V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q5V)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q5V)

(-) 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:115
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d1q5va1 A:1-48                                  d1q5va2 A:49-                132 Nickel responsive regulator NikR, C-terminal domain SCOP domains
               CATH domains 1q5vA01 A:1-46 Met repressor-like              1q5vA02 A:48-1                32 ACT-like. Chain A, domain 2                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.-...eeeeeeeeee.----------------....eeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q5v A   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQ-HGTQGFAVLSYVYE----------------HHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    10        20        30        40     | |50        60|        -       |80        90       100       110       120       130  
                                                                        46 |           61               78                                                      
                                                                          48                                                                                    


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED 133
               SCOP domains d1q5vb1 B:1-48                                  d1q5vb2 B:49-                 133 Nickel responsive regulator NikR, C-terminal domain SCOP domains
               CATH domains 1q5vB01 B:1-47 Met repressor-like              1q5vB02 B:48-1                 33 ACT-like. Chain A, domain 2                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.........eeeeeeeeee.-----------------...eeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q5v B   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYE-----------------HDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED 133
                                    10        20        30        40        50        60|        -        80        90       100       110       120       130   
                                                                                       61                79                                                      


Chain C from PDB  Type:PROTEIN  Length:115
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d1q5vc1 C:1-48                                  d1q5vc2 C:49-                 132 Nickel responsive regulator NikR, C-terminal domai SCOP domains
               CATH domains 1q5vC01 C:1-47 Met repressor-like              1q5vC02 C:48-1                 32 ACT-like. Chain A, domain 2                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......eeeeeeeeee.-----------------...eeeeeeee.....eeeeeeeeeehhhhhhhhhhhh.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q5v C   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYE-----------------HDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    10        20        30        40        50        60|        -        80        90       100       110       120       130  
                                                                                       61                79                                                     


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
           NIKR_ECOLI     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d1q5vd1 D:1-48                                  d1q5vd2 D:49-132 Nickel responsive regulator NikR, C-terminal domain                 SCOP domains
               CATH domains 1q5vD01 D:1-47 Met repr essor-like             1q5vD02 D:48-132 ACT-like. Chain A, domain 2                                          CATH domains
           Pfam domains (1) --RHH_1-1q5vD05 D:3-42                    ----------NikR_C-1q5vD01 D:53-131                                                        - Pfam domains (1)
           Pfam domains (2) --RHH_1-1q5vD06 D:3-42                    ----------NikR_C-1q5vD02 D:53-131                                                        - Pfam domains (2)
           Pfam domains (3) --RHH_1-1q5vD07 D:3-42                    ----------NikR_C-1q5vD03 D:53-131                                                        - Pfam domains (3)
           Pfam domains (4) --RHH_1-1q5vD08 D:3-42                    ----------NikR_C-1q5vD04 D:53-131                                                        - Pfam domains (4)
         Sec.struct. author .eeeeeeehhhhhhhhhhhh...-..hhhhhhhhhhhhhhh.........eeeeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhh-..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q5v D   1 MQRVTITLDDDLLETLDSLSQRR-YNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQ-GVRHGHLQCLPKE 132
                                    10        20  | |   30        40        50        60        70        80        90       100       110       120       130  
                                                 23 |                                                                                          118 |            
                                                   25                                                                                            120
   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, 8)

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

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: ACT (34)
(-)
Clan: Met_repress (26)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological 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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  1q5v
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  NIKR_ECOLI | P0A6Z6
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 Related Entries

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

UniProtKB/Swiss-Prot
        NIKR_ECOLI | P0A6Z6: 1q5y 2hza 2hzv 3bkf 3bkt 3bku 3od2

(-) Related Entries Specified in the PDB File

1q5y NICKEL-BOUND C-TERMINAL REGULATORY DOMAIN OF NIKR