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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO HARVEYI LUXQ PERIPLASMIC DOMAIN
 
Authors :  M. B. Neiditch, R. C. Kelly, F. M. Hughson
Date :  30 Jun 06  (Deposition) - 26 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Per/Arnt/Simple-Minded (Pas) Fold, Autoinducer-2 (Ai-2), Quorum Sensing, Histidine Sensor Kinase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. B. Neiditch, M. J. Federle, A. J. Pompeani, R. C. Kelly, D. L. Swem, P. D. Jeffrey, B. L. Bassler, F. M. Hughson
Ligand-Induced Asymmetry In Histidine Sensor Kinase Complex Regulates Quorum Sensing.
Cell(Cambridge, Mass. ) V. 126 1095 2006
PubMed-ID: 16990134  |  Reference-DOI: 10.1016/J.CELL.2006.07.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AUTOINDUCER 2 SENSOR KINASE/PHOSPHATASE LUXQ
    ChainsA
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentPERIPLASMIC DOMAIN (RESIDUES 53-271)
    GeneLUXQ
    Organism ScientificVIBRIO HARVEYI
    Organism Taxid669

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NI4Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:120 , ASP A:209 , ASP A:271 , HOH A:289 , HOH A:459 , HOH A:462BINDING SITE FOR RESIDUE NI A 272
2AC2SOFTWAREHIS A:131 , HOH A:343 , HOH A:362 , HOH A:370 , HOH A:436 , HOH A:456BINDING SITE FOR RESIDUE NI A 273
3AC3SOFTWAREHIS A:61 , ASP A:65 , HOH A:444 , HOH A:445BINDING SITE FOR RESIDUE NI A 274
4AC4SOFTWAREHIS A:110 , LYS A:201 , HOH A:414 , HOH A:435 , HOH A:438 , HOH A:466BINDING SITE FOR RESIDUE NI A 275

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HJE)

(-) 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:210
 aligned with LUXQ_VIBHA | P54302 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:220
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
           LUXQ_VIBHA    52 TKQQTSALIHNIFDSHFAAIQIHHDSNSKSEVIRDFYTDRDTDVLNFFFLSIDQSDPSHTPEFRFLTDHKGIIWDDGNAHFYGVNDLILDSLANRVSFSNNWYYINVMTSIGSRHMLVRRVPILDPSTGEVLGFSFNAVVLDNNFALMEKLKSESNVDNVVLVANSVPLANSLIGDEPYNVADVLQRKSSDKRLDKLLVIETPIVVNAVTTELCLLTVQD 271
               SCOP domains d2hjea_ A: Autoinducer 2 sensor kinase/phosphatase LuxQ                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeee.hhhhhhh.hhhhhhhhhhhh......eeeeeee..eeeeeeeeeeeee......eeeeeeeeee...hhhhhhhhhhhh...eeeeee..eeeee........hhhhhhh----------.eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hje A  52 SKQQTSALIHNIFDSHFAAIQIHHDSNSKSEVIRDFYTDRDTDVLNFFFLSIDQSDPSHTPEFRFLTDHKGIIWDDGNAHFYGVNDLILDSLANRVSFSNNWYYINVMTSIGSRHMLVRRVPILDPSTGEVLGFSFNAVVLDNNFALMEKLKSESNVDNVVLVANSVPLANSLIGDEPYNVADVLQ----------LLVIETPIVVNAVTTELCLLTVQD 271
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     |   -      |251       261       271
                                                                                                                                                                                                                   237        248                       

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LUXQ_VIBHA | P54302)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    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:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LUXQ_VIBHA | P543021zhh 2hj9

(-) Related Entries Specified in the PDB File

2hj9