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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 :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:36 , ARG A:42BINDING SITE FOR RESIDUE SO4 A1142
02AC2SOFTWARESER B:36 , SER B:38 , ARG B:42BINDING SITE FOR RESIDUE SO4 B1144
03AC3SOFTWAREARG B:37 , HOH B:2014 , HOH B:2015 , HOH B:2016 , HOH B:2017 , ARG C:12BINDING SITE FOR RESIDUE SO4 B1145
04AC4SOFTWARESER C:36 , SER C:38 , ARG C:42 , GLU C:78BINDING SITE FOR RESIDUE SO4 C1146
05AC5SOFTWARESER D:36 , ARG D:42 , HOH D:2019BINDING SITE FOR RESIDUE SO4 D1146
06AC6SOFTWAREARG A:12 , SER D:36 , ARG D:37 , HOH D:2004 , HOH D:2005BINDING SITE FOR RESIDUE SO4 D1147
07AC7SOFTWARETYR A:72 , HIS A:74 , ASN A:80 , HIS A:99 , HIS A:101 , HOH A:2009BINDING SITE FOR RESIDUE GOL A1143
08AC8SOFTWARETHR A:97 , HIS A:99 , TYR D:72 , HIS D:99BINDING SITE FOR RESIDUE GOL D1148
09AC9SOFTWAREARG B:42 , ARG B:46BINDING SITE FOR RESIDUE GOL B1146
10BC1SOFTWAREGLN C:18 , ASN C:20 , LEU C:21 , ARG D:46BINDING SITE FOR RESIDUE GOL C1147
11BC2SOFTWAREHIS A:74 , HIS A:75 , HIS A:101 , GLN D:87 , HIS D:93 , VAL D:94BINDING SITE FOR RESIDUE GOL D1149
12BC3SOFTWAREGLN A:87 , HIS A:88 , VAL A:94 , HIS D:75 , HIS D:101 , GLU D:104BINDING SITE FOR RESIDUE GOL D1150

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WVD)

(-) 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:133
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:136
                                    15        25        35        45        55        65        75        85        95       105       115       125       135      
           NIKR_HELPY     6 KDDSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
               SCOP domains d2wvda1 A:6-60 automated matches                       d2wvda2 A:61-141 automated matches                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...---.....eeeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvd A   6 KDDSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWA---PNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLSTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
                                    15        25        35        45        55   |    65        75        85        95       105       115       125       135      
                                                                            55  59                                                                                  


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:135
                                    18        28        38        48        58        68        78        88        98       108       118       128       138     
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASS 143
               SCOP domains d2wvdb1 B:9-60 automated matches                    d2wvdb2 B:61-143 automated matches                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhh...eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhh...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvd B   9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLSTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASS 143
                                    18        28        38        48        58        68        78        88        98       108       118       128       138     


Chain C from PDB  Type:PROTEIN  Length:133
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:138
                                    17        27        37        47        57        67        77        87        97       107       117       127       137        
           NIKR_HELPY     8 DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFE 145
               SCOP domains d2wvdc1 C:8-60 automated matches                     d2wvdc2 C:61-145 automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..-----....eeeeeeeee.....hhhhhhhhhhhh...eeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhh...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wvd C   8 DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNW-----NDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLSTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFE 145
                                    17        27        37        47      |  -  |     67        77        87        97       107       117       127       137        
                                                                         54    60                                                                                     


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

    Alignment length:138
                                    17        27        37        47        57        67        77        87        97       107       117       127       137        
           NIKR_HELPY     8 DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFE 145
               SCOP domains d2wvdd1 D:8-60 automated matches                     d2wvdd2 D:61-145 automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhh...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wvd D   8 DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLSTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFE 145
                                    17        27        37        47        57        67        77        87        97       107       117       127       137
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  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 2wvc 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
2wvc 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