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(-) Description

Title :  CRYSTAL STRUCTURE OF HEME DOMAIN OF DIRECT OXYGEN SENSOR FROM E. COLI
 
Authors :  H. J. Park, C. Suquet, J. D. Satterlee, C. H. Kang
Date :  22 Jan 04  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  L,U
Keywords :  Pas, Oxygen Sensor, Crystal Structure, Dos, Heme Protein, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Park, C. Suquet, J. D. Satterlee, C. H. Kang
Insights Into Signal Transduction Involving Pas Domain Oxygen-Sensing Heme Proteins From The X-Ray Crystal Structure Of Escherichia Coli Dos Heme Domain (Ec Dosh)
Biochemistry V. 43 2738 2004
PubMed-ID: 15005609  |  Reference-DOI: 10.1021/BI035980P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YDDU
    ChainsL, U
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneYDDU, B1489
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit LU

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL L:34 , ILE L:36 , ILE L:65 , LEU L:68 , ILE L:69 , PRO L:70 , LEU L:73 , HIS L:77 , TYR L:80 , ASN L:84 , MET L:95 , ARG L:97 , LEU L:99 , PHE L:113 , LEU L:115 , TYR L:126 , OXY L:1136 , HOH L:1156 , LEU U:99 , HEM U:2135BINDING SITE FOR RESIDUE HEM L 1135
2AC2SOFTWAREARG L:97 , PHE L:113 , HEM L:1135BINDING SITE FOR RESIDUE OXY L 1136
3AC3SOFTWAREHEM L:1135 , VAL U:34 , ILE U:36 , ILE U:65 , LEU U:68 , ILE U:69 , PRO U:70 , LEU U:73 , HIS U:77 , TYR U:80 , ASN U:84 , GLY U:94 , MET U:95 , PHE U:113 , LEU U:115 , TYR U:126 , ALA U:128 , HOH U:2140 , HOH U:2163 , HOH U:2173 , HOH U:2209 , HOH U:2216BINDING SITE FOR RESIDUE HEM U 2135

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S66)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S66)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S66)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.DOSP_ECOLI17-64
 
134-178
  2L:25-72
U:25-72
-

(-) Exons   (0, 0)

(no "Exon" information available for 1S66)

(-) 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 L from PDB  Type:PROTEIN  Length:119
 aligned with DOSP_ECOLI | P76129 from UniProtKB/Swiss-Prot  Length:799

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
           DOSP_ECOLI     8 NAADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRDAS 126
               SCOP domains d1s66l_ L: Direct oxygen sensor protein, DOS                                                                            SCOP domains
               CATH domains 1s66L00 L:16-134  [code=3.30.450.20, no name defined]                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh...eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhh.......hhhhhhhhhhhhh.......ee..eee.....eee..eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PAS  PDB: L:25-72 UniProt: 17-64                -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1s66 L  16 NAADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRDAS 134
                                    25        35        45        55        65        75        85        95       105       115       125         

Chain U from PDB  Type:PROTEIN  Length:115
 aligned with DOSP_ECOLI | P76129 from UniProtKB/Swiss-Prot  Length:799

    Alignment length:115
                                    21        31        41        51        61        71        81        91       101       111       121     
           DOSP_ECOLI    12 GIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRDAS 126
               SCOP domains d1s66u_ U: Direct oxygen sensor protein, DOS                                                                        SCOP domains
               CATH domains 1s66U00 U:20-134  [code=3.30.450.20, no name defined]                                                               CATH domains
           Pfam domains (1) ----------PAS_9-1s66U01 U:30-134                                                                                    Pfam domains (1)
           Pfam domains (2) ----------PAS_9-1s66U02 U:30-134                                                                                    Pfam domains (2)
         Sec.struct. author .hhhhhhhh...eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhh..........eeee.....eeeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PAS  PDB: U:25-72 UniProt: 17-64                -------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1s66 U  20 GIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRDAS 134
                                    29        39        49        59        69        79        89        99       109       119       129     

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L,U   (DOSP_ECOLI | P76129)
molecular function
    GO:0071111    cyclic-guanylate-specific phosphodiesterase activity    Catalysis of the reaction: cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine + H(+).
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019826    oxygen sensor activity    Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2).
    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).
biological process
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0070482    response to oxygen levels    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 stimulus reflecting the presence, absence, or concentration of oxygen.
    GO:0050896    response to stimulus    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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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
        DOSP_ECOLI | P761291s67 1v9y 1v9z 1vb6 4hu3 4hu4

(-) Related Entries Specified in the PDB File

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