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(-) Description

Title :  STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
 
Authors :  C. Dian, C. Bahlawane, C. Muller, A. Round, C. Delay, C. Fauquant, K. Schauer, H. De Reuse, I. Michaud-Soret, L. Terradot
Date :  16 Oct 09  (Deposition) - 19 Jan 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Factor, Transcription Regulation, Rhh, Dna-Binding, Transcription, Metal-Binding, Metalloregulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bahlawane, C. Dian, C. Muller, A. Round, C. Fauquant, K. Schauer, H. De Reuse, L. Terradot, I. Michaud-Soret
Structural And Mechanistic Insights Into Helicobacter Pylori Nikr Activation.
Nucleic Acids Res. V. 38 3106 2010
PubMed-ID: 20089510  |  Reference-DOI: 10.1093/NAR/GKP1216

(-) Compounds

Molecule 1 - PUTATIVE NICKEL-RESPONSIVE REGULATOR
    Atcc: 43504
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: HPNIKR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
2GOL5Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:139 , GOL A:1145 , LEU B:138 , THR B:139 , HOH B:2052BINDING SITE FOR RESIDUE FMT B1149
02AC2SOFTWARELYS A:31 , ARG B:82 , ILE B:86 , HOH B:2027 , HOH B:2053BINDING SITE FOR RESIDUE FMT B1150
03AC3SOFTWAREARG B:77BINDING SITE FOR RESIDUE FMT B1151
04AC4SOFTWAREGLU A:78 , GLN A:81 , ARG A:82 , LEU A:130 , HOH A:2021 , HOH A:2051 , HOH A:2052 , ARG B:77BINDING SITE FOR RESIDUE GOL A1143
05AC5SOFTWAREARG A:82 , GLY A:129 , LEU A:130 , ARG A:131 , HOH A:2039 , HOH A:2053BINDING SITE FOR RESIDUE GOL A1144
06AC6SOFTWAREHOH A:2017 , MET B:83 , GLN B:87 , THR B:97 , GLU B:109BINDING SITE FOR RESIDUE GOL B1152
07AC7SOFTWAREGLY B:128 , VAL B:133 , PHE B:135 , ALA B:136BINDING SITE FOR RESIDUE GOL B1153
08AC8SOFTWARELEU A:138 , THR A:139 , LYS A:140 , LYS B:137 , FMT B:1149BINDING SITE FOR RESIDUE GOL A1145
09AC9SOFTWAREHIS A:88 , GLY B:74 , HIS B:99 , HIS B:101 , CYS B:107 , HOH B:2054 , HOH B:2055BINDING SITE FOR RESIDUE SO4 B1154
10BC1SOFTWARESER A:36 , SER A:38 , ARG A:42 , SER B:16BINDING SITE FOR RESIDUE SO4 A1146
11BC2SOFTWAREARG A:42 , ASP A:43 , ARG A:46 , HOH A:2054BINDING SITE FOR RESIDUE SO4 A1147
12BC3SOFTWARESER A:16 , SER B:38 , ARG B:42BINDING SITE FOR RESIDUE SO4 B1155

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WVC)

(-) 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:132
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:135
                                    17        27        37        47        57        67        77        87        97       107       117       127       137     
           NIKR_HELPY     8 DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d2wvca1 A:8-60 automated matches                     d2wvca2 A:61-142 automated matches                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..---........eeeeeeeeee....hhhhhhhhhhhhhh.eeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvc A   8 DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVED---EDNPNDESKIAVLVVIYDGGQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    17        27        37        47    |   57        67        77        87        97       107       117       127       137     
                                                                       52  56                                                                                      


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:140
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYNE 148
               SCOP domains d2wvcb1 B:9-60 autom  ated matches                  d2wvcb2 B:61-148 automated matches                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---RHH_1-2wvcB03 B:1  2-51                 -------------NikR_C-2wvcB01 B:65-143                                                        ----- Pfam domains (1)
           Pfam domains (2) ---RHH_1-2wvcB04 B:1  2-51                 -------------NikR_C-2wvcB02 B:65-143                                                        ----- Pfam domains (2)
         Sec.struct. author .eeeeeeeeehhhhhhhhhh--.....hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee.....hhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvc B   9 SIIRFSVSLQQNLLDELDNR--KNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDGGQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYNE 148
                                    18        28  |     38        48        58        68        78        88        98       108       118       128       138       148
                                              28 31
   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/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WVC)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological 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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  2wvc
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  NIKR_HELPY | O25896
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 Related Entries

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

UniProtKB/Swiss-Prot
        NIKR_HELPY | O25896: 2ca9 2cad 2caj 2wvb 2wvd 2wve 2wvf 3lgh 3pht 3qsi

(-) Related Entries Specified in the PDB File

2ca9 APO-NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION
2cad NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES
2caj NI2-HPNIKR HPNIKR IN CLOSED TRANS- CONFORMATION AND NICKEL BOUND TO 4 INTERMEDIARY SITES
2wvb STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wvd STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wve STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION
2wvf STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION