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(-) Description

Title :  E. COLI NIKR SOAKED WITH EXCESS NICKEL IONS
 
Authors :  C. M. Phillips, E. R. Schreiter, C. L. Drennan
Date :  10 Aug 10  (Deposition) - 08 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Ribbon-Helix-Helix, Ferredoxin-Like Fold, Transcription Factor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Phillips, E. R. Schreiter, C. M. Stultz, C. L. Drennan
Structural Basis Of Low-Affinity Nickel Binding To The Nickel-Responsive Transcription Factor Nikr From Escherichi Coli.
Biochemistry V. 49 7830 2010
PubMed-ID: 20704276  |  Reference-DOI: 10.1021/BI100923J

(-) Compounds

Molecule 1 - NICKEL-RESPONSIVE REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ECS4348
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
13CM1Ligand/Ion3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
2NI11Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13CM2Ligand/Ion3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:87 , HIS A:89 , CYS A:95 , VAL B:72 , HIS B:76BINDING SITE FOR RESIDUE NI A 134
02AC2SOFTWAREMET A:1 , HOH A:149 , HOH A:150 , HOH B:145 , HOH B:156BINDING SITE FOR RESIDUE NI A 135
03AC3SOFTWAREHIS A:125 , HOH A:147 , HOH A:148 , HIS B:125BINDING SITE FOR RESIDUE NI A 136
04AC4SOFTWAREHIS A:78 , HIS A:110 , ASP A:114 , HOH A:144BINDING SITE FOR RESIDUE NI A 137
05AC5SOFTWAREHIS A:79 , HOH A:156 , HOH A:161 , HOH A:162 , HOH A:171 , HIS B:92BINDING SITE FOR RESIDUE NI A 138
06AC6SOFTWAREHIS A:123 , HOH A:153 , HOH A:164 , PRO B:130 , HOH B:165BINDING SITE FOR RESIDUE NI A 139
07AC7SOFTWAREARG A:3 , LEU A:19 , SER A:20 , ARG A:23 , TYR A:25 , ILE A:35 , GLU B:43 , GLY B:124 , HIS B:125 , LEU B:126BINDING SITE FOR RESIDUE 3CM B 134
08AC8SOFTWAREHIS A:76 , HIS B:87 , HIS B:89 , CYS B:95BINDING SITE FOR RESIDUE NI B 135
09AC9SOFTWAREHIS B:78 , HIS B:110 , ASP B:114 , HOH B:146 , HOH B:148 , HOH B:158BINDING SITE FOR RESIDUE NI B 136
10BC1SOFTWAREHOH A:160 , HOH A:165 , HIS B:123 , HOH B:149 , HOH B:168 , HOH B:169BINDING SITE FOR RESIDUE NI B 137
11BC2SOFTWAREHIS A:92 , HIS B:79 , ASP B:80 , HOH B:160 , HOH B:161 , HOH B:162 , HOH B:164BINDING SITE FOR RESIDUE NI B 138
12BC3SOFTWAREHOH A:157 , HOH A:158 , MET B:1 , HOH B:142 , HOH B:170BINDING SITE FOR RESIDUE NI B 139

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OD2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OD2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OD2)

(-) Exons   (0, 0)

(no "Exon" information available for 3OD2)

(-) 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:132
 aligned with C3SP37_ECOLX | C3SP37 from UniProtKB/TrEMBL  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
         C3SP37_ECOLX     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d3od2a1 A:1-48                                  d3od2a2 A:49-132 Nickel responsive regulator NikR, C-terminal domain                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......eeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3od2 A   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain A from PDB  Type:PROTEIN  Length:132
 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 d3od2a1 A:1-48                                  d3od2a2 A:49-132 Nickel responsive regulator NikR, C-terminal domain                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......eeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3od2 A   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with C3SP37_ECOLX | C3SP37 from UniProtKB/TrEMBL  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
         C3SP37_ECOLX     1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d3od2b1 B:1-45                               ---d3od2b2 B:49-132 Nickel responsive regulator NikR, C-terminal domain                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --RHH_1-3od2B03 B:3-42                    ----------NikR_C-3od2B01 B:53-131                                                        - Pfam domains (1)
           Pfam domains (2) --RHH_1-3od2B04 B:3-42                    ----------NikR_C-3od2B02 B:53-131                                                        - Pfam domains (2)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...---..eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3od2 B   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEAT---GTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130  
                                                                       45  49                                                                                   


Chain B from PDB  Type:PROTEIN  Length:129
 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 d3od2b1 B:1-45                               ---d3od2b2 B:49-132 Nickel responsive regulator NikR, C-terminal domain                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --RHH_1-3od2B03 B:3-42                    ----------NikR_C-3od2B01 B:53-131                                                        - Pfam domains (1)
           Pfam domains (2) --RHH_1-3od2B04 B:3-42                    ----------NikR_C-3od2B02 B:53-131                                                        - Pfam domains (2)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...---..eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3od2 B   1 MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEAT---GTQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130  
                                                                       45  49
   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  (0, 0)

(no "CATH Domain" information available for 3OD2)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (8, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain A,B   (C3SP37_ECOLX | C3SP37)
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_ECOLI | P0A6Z6: 1q5v 1q5y 2hza 2hzv 3bkf 3bkt 3bku

(-) Related Entries Specified in the PDB File

1q5v APO E. COLI NIKR
2hza NICKEL-BOUND FULL-LENGTH ESCHERICHIA COLI NIKR
2hzv NIKR-OPERATOR DNA COMPLEX