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(-) Description

Title :  NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES.
 
Authors :  C. Dian, K. Schauer, U. Kapp, S. M. Mcsweeney, A. Labigne, L. Terradot
Date :  20 Dec 05  (Deposition) - 17 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Nickel Uptake, Transcription Regulator, Ribbon-Helix-Helix, Acidic-Adaptive Response, Transcriptional Regulation, Dna- Binding, Hypothetical Protein, Metal-Binding, Nickel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dian, K. Schauer, U. Kapp, S. M. Mcsweeney, A. Labigne, L. Terradot
Structural Basis Of The Nickel Response In Helicobacter Pylori: Crystal Structures Of Hpnikr In Apo And Nickel-Bound States.
J. Mol. Biol. V. 361 715 2006
PubMed-ID: 16872629  |  Reference-DOI: 10.1016/J.JMB.2006.06.058

(-) Compounds

Molecule 1 - PUTATIVE NICKEL-RESPONSIVE REGULATOR
    Chains: A, B
    Engineered: YES STA
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 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, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2FMT4Ligand/IonFORMIC ACID
3GOL3Ligand/IonGLYCEROL
4NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2FMT8Ligand/IonFORMIC ACID
3GOL6Ligand/IonGLYCEROL
4NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:74 , HIS A:101 , HOH A:2022 , HOH A:2062 , HIS B:88 , HOH B:2028BINDING SITE FOR RESIDUE NI A1152
02AC2SOFTWAREILE A:84 , HIS A:88 , HIS B:99 , HIS B:101 , CYS B:107BINDING SITE FOR RESIDUE NI B1151
03AC3SOFTWAREHIS B:74 , HIS B:75 , GLU B:104 , CIT B:1150BINDING SITE FOR RESIDUE NI B1152
04AC4SOFTWAREHIS A:88 , ALA A:89 , HOH A:2029 , HIS B:74 , HIS B:75 , GLU B:104 , GOL B:1148 , NI B:1152 , HOH B:2055BINDING SITE FOR RESIDUE CIT B1150
05AC5SOFTWAREILE A:84 , GLN A:87 , THR A:97 , HIS A:99 , GLU A:109 , HOH A:2060 , HIS B:99BINDING SITE FOR RESIDUE FMT A1147
06AC6SOFTWAREALA A:136BINDING SITE FOR RESIDUE FMT A1148
07AC7SOFTWAREGLN A:76 , ARG A:82 , ARG A:131 , FMT A:1150BINDING SITE FOR RESIDUE FMT A1149
08AC8SOFTWAREARG A:82 , LEU A:130 , ARG A:131 , FMT A:1149 , HOH A:2061BINDING SITE FOR RESIDUE FMT A1150
09AC9SOFTWARETYR A:72 , ASN A:80 , HIS A:99 , HOH A:2062 , HOH A:2063 , GOL B:1149 , HOH B:2028BINDING SITE FOR RESIDUE GOL A1151
10BC1SOFTWAREHIS B:75 , HIS B:105 , CIT B:1150BINDING SITE FOR RESIDUE GOL B1148
11BC2SOFTWAREGOL A:1151 , ASN B:80 , MET B:83 , GLN B:87 , THR B:97 , GLU B:109 , HOH B:2054BINDING SITE FOR RESIDUE GOL B1149

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CAD)

(-) 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:131
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:138
                                    18        28        38        48        58        68        78        88        98       108       118       128       138        
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEY 146
               SCOP domains d2cada1 A:9-60 automated matches                    d2cada2 A:61-146 automated matches                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhh..-------......eeeeeeeeee.....hhhhhhhhhhh...eeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhh...eeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cad A   9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLV-------NPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEY 146
                                    18        28        38        48 |      58        68        78        88        98       108       118       128       138        
                                                                    50      58                                                                                        


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:139
                                    18        28        38        48        58        68        78        88        98       108       118       128       138         
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYN 147
               SCOP domains d2cadb1 B:9-57 automated m atches                    d2cadb2 B:62-147 automated matches                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhh........-.hhhhhhhhhhhhhhhhhhh..----..eeeeeeeeee.....hhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeehhhhhhhhhhhh....eeeeeeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cad B   9 SIIRFSVSLQQNLLDELDNRIIKNGY-SRSELVRDMIREKLVEDNWAED----ESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYN 147
                                    18        28     | |38        48        |-   |    68        78        88        98       108       118       128       138         
                                                    34 |                   57   62                                                                                     
                                                      36
   Legend:   → Mismatch (orange background)
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    → 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 2CAD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NIKR_HELPY | O25896)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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_HELPY | O25896: 2ca9 2caj 2wvb 2wvc 2wvd 2wve 2wvf 3lgh 3pht 3qsi

(-) Related Entries Specified in the PDB File

2ca9 APO-NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION
2caj NI2-HPNIKR HPNIKR IN CLOSED TRANS- CONFORMATION AND NICKEL BOUND TO 4 INTERMEDIARY SITES