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(-) Description

Title :  NICKEL-BOUND C-TERMINAL REGULATORY DOMAIN OF 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 :  1.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nickel Binding, Regulatory Domain, Beta Sandwich, Metal Binding Protein (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
    Fragment: C-TERMINAL DOMAIN OF NIKR
    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  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2NI4Ligand/IonNICKEL (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:87 , HIS B:89 , CYS B:95 , VAL D:72 , HIS D:76BINDING SITE FOR RESIDUE NI D 434
2AC2SOFTWAREHIS A:87 , HIS A:89 , CYS A:95 , HIS C:76BINDING SITE FOR RESIDUE NI A 534
3AC3SOFTWAREHIS A:76 , HIS C:87 , HIS C:89 , CYS C:95BINDING SITE FOR RESIDUE NI C 634
4AC4SOFTWAREVAL B:72 , HIS B:76 , HIS D:87 , HIS D:89 , CYS D:95BINDING SITE FOR RESIDUE NI D 734
5AC5SOFTWAREHIS B:77 , ARG C:65 , SER C:69 , HIS D:92BINDING SITE FOR RESIDUE EDO C 301
6AC6SOFTWAREGLN A:127 , HIS B:123 , GLY B:124 , HOH B:155 , HOH B:173 , GLY C:124 , HIS C:125 , LEU C:126 , HOH C:646BINDING SITE FOR RESIDUE EDO C 302
7AC7SOFTWAREILE B:116 , VAL C:121 , ARG C:122 , HIS C:123 , GLY C:124 , EDO C:305 , HOH C:695BINDING SITE FOR RESIDUE EDO C 304
8AC8SOFTWAREALA B:117 , VAL C:121 , ARG C:122 , HIS C:123 , EDO C:304 , HOH C:655 , HOH C:698BINDING SITE FOR RESIDUE EDO C 305
9AC9SOFTWAREHIS A:125 , LEU A:126 , GLN A:127 , HIS B:125 , HIS C:125 , LEU C:126 , GLN C:127 , HOH C:636 , HIS D:125BINDING SITE FOR RESIDUE EDO C 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q5Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q5Y)

(-) 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:84
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:84
                                    59        69        79        89        99       109       119       129    
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED 133
               SCOP domains d1q5ya_ A: Nickel responsive regulator NikR, C-terminal domain                       SCOP domains
               CATH domains 1q5yA00 A:50-133 ACT-like. Chain A, domain 2                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1q5y A  50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKED 133
                                    59        69        79        89        99       109       119       129    


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

    Alignment length:83
                                    59        69        79        89        99       109       119       129   
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d1q5yb_ B: Nickel responsive regulator NikR, C-terminal domain                      SCOP domains
               CATH domains 1q5yB00 B:50-132 ACT-like. Chain A, domain 2                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1q5y B  50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    59        69        79        89        99       109       119       129   


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

    Alignment length:82
                                    60        70        80        90       100       110       120       130  
           NIKR_ECOLI    51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d1q5yc_ C: Nickel responsive regulator NikR, C-terminal domain                     SCOP domains
               CATH domains 1q5yC00 C:51-132 ACT-like. Chain A, domain 2                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeehhhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1q5y C  51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    60        70        80        90       100       110       120       130  


Chain D from PDB  Type:PROTEIN  Length:80
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:83
                                    59        69        79        89        99       109       119       129   
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d1q5yd_ D: Nic   kel responsive regulator NikR, C-terminal domain                   SCOP domains
               CATH domains 1q5yD00 D:50-1   32 ACT-like. Chain A, domain 2                                     CATH domains
           Pfam domains (1) ---NikR_C-1q5y   D01 D:53-131                                                     - Pfam domains (1)
           Pfam domains (2) ---NikR_C-1q5y   D02 D:53-131                                                     - Pfam domains (2)
           Pfam domains (3) ---NikR_C-1q5y   D03 D:53-131                                                     - Pfam domains (3)
           Pfam domains (4) ---NikR_C-1q5y   D04 D:53-131                                                     - Pfam domains (4)
         Sec.struct. author .eeeeeeeeeee..---hhhhhhhhhhh....eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 1q5y D  50 TQGFAVLSYVYEHE---LASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    59   |   |69        79        89        99       109       119       129   
                                        63  67
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        NIKR_ECOLI | P0A6Z6: 1q5v 2hza 2hzv 3bkf 3bkt 3bku 3od2

(-) Related Entries Specified in the PDB File

1q5v APO-NIKR