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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE SENSOR DOMAIN OF RMFIXL(FERROUS FORM)
 
Authors :  H. Miyatake, M. Mukai, S. -Y. Park, S. Adachi, K. Tamura, H. Nakamura, K. Nakamura, T. Tsuchiya, T. Iizuka, Y. Shiro
Date :  21 Apr 00  (Deposition) - 10 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxygen Sensor, Heme Protein, Histidine Kinase, Rhizobium Meliloti, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Miyatake, M. Mukai, S. -Y. Park, S. Adachi, K. Tamura, H. Nakamura, K. Nakamura, T. Tsuchiya, T. Iizuka, Y. Shiro
Sensory Mechanism Of Oxygen Sensor Fixl From Rhizobium Meliloti: Crystallographic, Mutagenesis And Resonance Raman Spectroscopic Studies
J. Mol. Biol. V. 301 415 2000
PubMed-ID: 10926518  |  Reference-DOI: 10.1006/JMBI.2000.3954
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIXL
    ChainsA
    EC Number2.7.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-14B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSENSOR DOMAIN
    Organism ScientificSINORHIZOBIUM MELILOTI
    Organism Taxid382

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:4 , HOH A:26 , VAL A:151 , LEU A:182 , LEU A:185 , MET A:186 , TYR A:190 , HIS A:194 , TYR A:197 , LEU A:198 , TYR A:201 , LYS A:207 , ARG A:208 , ILE A:209 , ILE A:210 , ARG A:214 , VAL A:216 , SER A:217 , MET A:228 , LEU A:230 , PHE A:243 , THR A:244 , GLY A:245BINDING SITE FOR RESIDUE HEM A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EW0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:188 -Pro A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EW0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.FIXL_RHIME135-205  1A:135-205
2PACPS50113 PAC domain profile.FIXL_RHIME203-262  1A:203-251

(-) Exons   (0, 0)

(no "Exon" information available for 1EW0)

(-) 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:130
 aligned with FIXL_RHIME | P10955 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:147
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       
           FIXL_RHIME   105 GSAVLLIVALGEVLEAARRAIDRTEDVVRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRSGGERFFTGFIRDLT 251
               SCOP domains d1ew0                 a_ A: Histidine kinase FixL heme domain                                                                                       SCOP domains
               CATH domains 1ew0A                 00 A:122-251  [code=3.30.450.20, no name defined]                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh-----------------hhhhhhhhhh.hhhhhhh....eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhh...hhhhhhhhhhhhhhhh........eeeeee.....eeeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------PAS  PDB: A:135-205 UniProt: 135-205                                   ---------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------PAC  PDB: A:203-251 UniProt: 203-262              PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ew0 A 122 GSHML-----------------ETEDVVRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRSGGERFFTGFIRDLT 251
                                |    -         -  |    134       144       154       164       174       184       194       204       214       224       234       244       
                              126               127                                                                                                                            

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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EW0)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FIXL_RHIME | P10955)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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:0009399    nitrogen fixation    The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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
        FIXL_RHIME | P109551d06

(-) Related Entries Specified in the PDB File

1d06 1D06 CONTAINS THE SAME PROTEIN IN FERRIC STATE