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(-) Description

Title :  NICKEL BINDING DOMAIN OF NIKR FROM HELICOBACTER PYLORI DISCLOSING PARTIAL METAL OCCUPANCY
 
Authors :  J. M. Gonzalez, E. Pozharski
Date :  21 Feb 11  (Deposition) - 04 Apr 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.08
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J  (2x)
Keywords :  Nikr, Nickel, Helicobacter Pylori, Dna-Binding, Transcription Regulator, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. West, S. E. Evans, J. M. Gonzalez, L. G. Carter, H. Tsuruta, E. Pozharski, S. L. Michel
Ni(Ii) Coordination To Mixed Sites Modulates Dna Binding Of Hpnikr Via A Long-Range Effect.
Proc. Natl. Acad. Sci. Usa V. 109 5633 2012
PubMed-ID: 22451934  |  Reference-DOI: 10.1073/PNAS.1120283109

(-) Compounds

Molecule 1 - NIKR NICKEL-RESPONSIVE REGULATOR
    Chains: B, C, D, A, F, G, H, E, J, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NICKEL BINDING DOMAIN (UNP RESIDUES 61-148)
    Gene: HP_1338
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): ABCD      
Biological Unit 2 (1x):     EFGH  
Biological Unit 3 (2x):         IJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1NI9Ligand/IonNICKEL (II) ION
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS I:99 , HIS I:101 , CYS I:107 , ILE J:84 , HIS J:88BINDING SITE FOR RESIDUE NI I 1
02AC2SOFTWAREHIS G:99 , HIS G:101 , CYS G:107 , ILE H:84 , HIS H:88BINDING SITE FOR RESIDUE NI G 2
03AC3SOFTWAREHIS A:99 , HIS A:101 , CYS A:107 , ILE B:84 , HIS B:88BINDING SITE FOR RESIDUE NI A 3
04AC4SOFTWAREHIS C:99 , HIS C:101 , CYS C:107 , ILE D:84 , HIS D:88BINDING SITE FOR RESIDUE NI C 4
05AC5SOFTWAREHIS A:88 , HIS B:74 , HIS B:101BINDING SITE FOR RESIDUE NI B 5
06AC6SOFTWAREHIS E:88 , HIS F:74 , HIS F:101BINDING SITE FOR RESIDUE NI F 6
07AC7SOFTWAREHIS C:88 , HIS D:74 , HIS D:101BINDING SITE FOR RESIDUE NI D 7
08AC8SOFTWAREHIS E:99 , HIS E:101 , CYS E:107 , ILE F:84 , HIS F:88BINDING SITE FOR RESIDUE NI E 8
09AC9SOFTWARESO4 G:1 , HIS G:88 , HIS H:74 , HIS H:101BINDING SITE FOR RESIDUE NI H 9
10BC1SOFTWAREARG F:131 , GLN G:87 , HIS G:88 , THR G:92 , HIS G:93 , VAL G:94 , NI H:9 , HIS H:101BINDING SITE FOR RESIDUE SO4 G 1
11BC2SOFTWAREARG F:122BINDING SITE FOR RESIDUE SO4 F 2
12BC3SOFTWAREARG E:77BINDING SITE FOR RESIDUE SO4 E 3
13BC4SOFTWARELYS C:137 , LEU C:138 , THR C:139 , LYS C:140BINDING SITE FOR RESIDUE SO4 C 5

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QSI)

(-) 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:80
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:80
                                    71        81        91       101       111       121       131       141
           NIKR_HELPY    62 ESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
               SCOP domains d3qsia_ A: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 3qsi A  62 ESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
                                    71        81        91       101       111       121       131       141


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:81
                                    73        83        93       103       113       123       133       143 
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSF 144
               SCOP domains d3qsib_ B: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3qsi B  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSF 144
                                    73        83        93       103       113       123       133       143 


Chain C from PDB  Type:PROTEIN  Length:80
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:80
                                    72        82        92       102       112       122       132       142
           NIKR_HELPY    63 SKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3qsic_ C: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 3qsi C  63 SKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    72        82        92       102       112       122       132       142


Chain D from PDB  Type:PROTEIN  Length:79
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:79
                                    73        83        93       103       113       123       133         
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3qsid_ D: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3qsi D  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    73        83        93       103       113       123       133         


Chain E from PDB  Type:PROTEIN  Length:80
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:80
                                    72        82        92       102       112       122       132       142
           NIKR_HELPY    63 SKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3qsie_ E: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 3qsi E  63 SKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    72        82        92       102       112       122       132       142


Chain F from PDB  Type:PROTEIN  Length:78
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:78
                                    73        83        93       103       113       123       133        
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
               SCOP domains d3qsif_ F: automated matches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 3qsi F  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
                                    73        83        93       103       113       123       133        


Chain G from PDB  Type:PROTEIN  Length:79
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:79
                                    73        83        93       103       113       123       133         
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3qsig_ G: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3qsi G  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    73        83        93       103       113       123       133         


Chain H from PDB  Type:PROTEIN  Length:80
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:80
                                    73        83        93       103       113       123       133       143
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASS 143
               SCOP domains d3qsih_ H: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 3qsi H  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASS 143
                                    73        83        93       103       113       123       133       143


Chain I from PDB  Type:PROTEIN  Length:79
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:79
                                    73        83        93       103       113       123       133         
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3qsii_ I: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3qsi I  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    73        83        93       103       113       123       133         


Chain J from PDB  Type:PROTEIN  Length:79
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:79
                                    73        83        93       103       113       123       133         
           NIKR_HELPY    64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
               SCOP domains d3qsij_ J: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhh..eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3qsi J  64 KIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKAS 142
                                    73        83        93       103       113       123       133
   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, 10)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QSI)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (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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  3qsi
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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 2wvd 2wve 2wvf 3lgh 3pht

(-) Related Entries Specified in the PDB File

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