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(-) Description

Authors :  J. R Wagner, J. S. Brunzelle, R. D. Vierstra, K. T. Forest
Date :  13 Dec 06  (Deposition) - 06 Mar 07  (Release) - 28 Sep 11  (Revision)
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phytochrome Chromophore, Figure-Of-Eight Knot, Phytochromobilin, Biliverdin, Pas, Gaf, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  J. R. Wagner, J. Zhang, J. S. Brunzelle, R. D. Vierstra, K. T. Forest
High Resolution Structure Of Deinococcus Bacteriophytochrom Yields New Insights Into Phytochrome Architecture And Evolution.
J. Biol. Chem. V. 282 12298 2007
PubMed-ID: 17322301  |  Reference-DOI: 10.1074/JBC.M611824200

(-) Compounds

    EC Number2.7.13.3
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A(+)
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism Taxid1299

 Structural Features

(-) Chains, Units

Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
1AC1SOFTWARECYS A:24 , MET A:174 , TYR A:176 , PHE A:198 , PHE A:203 , SER A:206 , ASP A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:254 , THR A:256 , SER A:257 , MET A:259 , HIS A:260 , TYR A:263 , MET A:267 , SER A:272 , SER A:274 , HIS A:290 , HOH A:330 , HOH A:331 , HOH A:335 , HOH A:340 , HOH A:451 , HOH A:491BINDING SITE FOR RESIDUE LBV A 328

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O9C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
1Asp A:235 -Pro A:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O9C)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
1PHYTOCHROME_2PS50046 Phytochrome chromophore attachment site domain profile.BPHY_DEIRA152-310  1A:152-310
Biological Unit 1 (1, 2)
1PHYTOCHROME_2PS50046 Phytochrome chromophore attachment site domain profile.BPHY_DEIRA152-310  2A:152-310

(-) Exons   (0, 0)

(no "Exon" information available for 2O9C)

(-) Sequences/Alignments

Asymmetric 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:319
 aligned with BPHY_DEIRA | Q9RZA4 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:319
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313         
               SCOP domains d2o9ca2 A:4-130 Bacteriophytochrome BphP                                                                                       ----d2o9ca1 A:135-322 Bacteriophytochrome BphP                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------PAS_2-2o9cA02 A:24-129                                                                                    ----------------------GAF-2o9cA01 A:152-316                                                                                                                                                ------ Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------PHYTOCHROME_2  PDB: A:152-310 UniProt: 152-310                                                                                                                 ------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313         

   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O9C)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
Clan: GAF (44)
Clan: PAS_Fold (84)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (BPHY_DEIRA | Q9RZA4)
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: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:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
    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:0009584    detection of visible light    The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
    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:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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)

        BPHY_DEIRA | Q9RZA41ztu 2o9b 3s7n 3s7o 3s7p 3s7q 4cqh 4ijg 4o01 4o0p 4o8g 4q0h 4q0i 4q0j 4y3i 4y5f 4z1w 4zrr 5ajg 5c5k 5k5b 5l8m 5lbr 5mg0 5mg1

(-) Related Entries Specified in the PDB File