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(-) Description

Title :  OXYGEN-BINDING COMPLEX OF FIXL HEME DOMAIN
 
Authors :  W. Gong, B. Hao, M. K. Chan
Date :  23 Dec 99  (Deposition) - 23 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Fixl, Heme, Pas Domain, Signal Transduction, Histidine Kinase, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Gong, B. Hao, M. K. Chan
New Mechanistic Insights From Structural Studies Of The Oxygen-Sensing Domain Of Bradyrhizobium Japonicum Fixl.
Biochemistry V. 39 3955 2000
PubMed-ID: 10747783  |  Reference-DOI: 10.1021/BI992346W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIXL PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRJ7349
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHEME DOMAIN
    Organism ScientificBRADYRHIZOBIUM JAPONICUM
    Organism Taxid375

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:215 , ARG A:220 , LEU A:236 , ILE A:238 , HEM A:719BINDING SITE FOR RESIDUE OXY A 500
2AC2SOFTWAREILE A:157 , LEU A:191 , MET A:192 , ASP A:196 , HIS A:200 , TYR A:203 , ARG A:206 , HIS A:214 , ILE A:215 , ILE A:216 , ARG A:220 , MET A:234 , LEU A:236 , ILE A:238 , PHE A:249 , GLY A:251 , OXY A:500 , HOH A:796BINDING SITE FOR RESIDUE HEM A 719

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DP6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:194 -Pro A:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DP6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PACPS50113 PAC domain profile.FIXL_BRADU88-140
209-268
  1-
A:209-268

(-) Exons   (0, 0)

(no "Exon" information available for 1DP6)

(-) 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:116
 aligned with FIXL_BRADU | P23222 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:116
                                   163       173       183       193       203       213       223       233       243       253       263      
           FIXL_BRADU   154 DAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTEHQQTQARLQEL 269
               SCOP domains d1dp6a_ A: Histidine kinase FixL heme domain                                                                         SCOP domains
               CATH domains 1dp6A00 A:154-269  [code=3.30.450.20, no name defined]                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.......eeeeeee.....eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------PAC  PDB: A:209-268 UniProt: 209-268                        - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1dp6 A 154 DAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTEHQQTQARLQEL 269
                                   163       173       183       193       203       213       223       233       243       253       263      

   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DP6)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FIXL_BRADU | P23222)
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FIXL_BRADU | P232221dp8 1dp9 1drm 1lsv 1lsw 1lsx 1lt0 1xj2 1xj3 1xj4 1xj6 1y28 2cmn 2owh 2owj 2vv6 2vv7 2vv8 4gcz

(-) Related Entries Specified in the PDB File

1bv6 LIGAND-FREE FIXL HEME DOMAIN