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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEME PAS SENSOR DOMAIN OF EC DOS (FERRIC FORM)
 
Authors :  H. Kurokawa, D. S. Lee, M. Watanabe, I. Sagami, B. Mikami, C. S. Raman, T.
Date :  04 Feb 04  (Deposition) - 25 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heme, Pas, Sensor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kurokawa, D. S. Lee, M. Watanabe, I. Sagami, B. Mikami, C. S. Raman, T. Shimizu
A Redox-Controlled Molecular Switch Revealed By The Crystal Structure Of A Bacterial Heme Pas Sensor.
J. Biol. Chem. V. 279 20186 2004
PubMed-ID: 14982921  |  Reference-DOI: 10.1074/JBC.M314199200

(-) Compounds

Molecule 1 - HEME PAS SENSOR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HEME PAS DOMAIN
    Gene: DOS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:34 , ILE A:65 , LEU A:68 , ILE A:69 , PRO A:70 , HIS A:77 , TYR A:80 , ASN A:84 , LEU A:99 , GLN A:100 , PHE A:113 , LEU A:115 , TYR A:126 , HOH A:1141 , HOH A:1142 , HOH A:1174 , HOH A:1190 , HOH A:1274 , LEU B:99 , HEM B:1140BINDING SITE FOR RESIDUE HEM A 1140
2AC2SOFTWAREHEM A:1140 , VAL B:34 , ILE B:65 , LEU B:68 , ILE B:69 , PRO B:70 , LEU B:73 , HIS B:77 , TYR B:80 , LEU B:99 , GLN B:100 , LEU B:101 , PHE B:113 , LEU B:115 , TYR B:126 , ALA B:128 , HOH B:1141 , HOH B:1187 , HOH B:1206 , HOH B:1220 , HOH B:1241BINDING SITE FOR RESIDUE HEM B 1140

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V9Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V9Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V9Y)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1V9Y)

(-) 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:103
 aligned with DOSP_ECOLI | P76129 from UniProtKB/Swiss-Prot  Length:799

    Alignment length:113
                                    21        31        41        51        61        71        81        91       101       111       121   
           DOSP_ECOLI    12 GIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRD 124
               SCOP domains d1v9ya_ A: Direct oxygen sensor protein, DOS                                                                      SCOP domains
               CATH domains 1v9yA00 A:20-132  [code=3.30.450.20, no name defined]                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeeee.....eeeehhhhhhhhh.hhhhh...hhhhhhhhhhh.hhhhhhhhhhh----------.eeeee.....eeeeeeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PAS  PDB: A:25-72 UniProt: 17-64                ------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1v9y A  20 GIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNRE----------RELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRD 132
                                    29        39        49        59        69        79      |  -       |99       109       119       129   
                                                                                             86         97                                   


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with DOSP_ECOLI | P76129 from UniProtKB/Swiss-Prot  Length:799

    Alignment length:113
                                    21        31        41        51        61        71        81        91       101       111       121   
           DOSP_ECOLI    12 GIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRD 124
               SCOP domains d1v9yb_ B: Direct oxygen sensor protein, DOS                                                                      SCOP domains
               CATH domains 1v9yB00 B:20-132  [code=3.30.450.20, no name defined]                                                             CATH domains
           Pfam domains (1) ----------PAS_9-1v9yB01 B:30-132                                                                                  Pfam domains (1)
           Pfam domains (2) ----------PAS_9-1v9yB02 B:30-132                                                                                  Pfam domains (2)
         Sec.struct. author .hhhhhhhh...eeeee.....eeeehhhhhhhhh.hhhhh...hhhhhhhhhhh.hhhhhhhhhhh----------.eeeee.....eeeeeeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PAS  PDB: B:25-72 UniProt: 17-64                ------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1v9y B  20 GIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNRE----------RELQLEKKDGSKIWTRFALSKVSAEGKVYYLALVRD 132
                                    29        39        49        59        69        79      |  -       |99       109       119       129   
                                                                                             86         97
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) 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 A,B   (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 | P76129: 1s66 1s67 1v9z 1vb6 4hu3 4hu4

(-) Related Entries Specified in the PDB File

1v9z THE SAME PROTEIN, FERROUS FORM