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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHROMOPHORE-BINDING DOMAIN OF AN UNUSUAL BACTERIOPHYTOCHROME RPBPHP3 FROM R. PALUSTRIS
 
Authors :  X. Yang, E. A. Stojkovic, J. Kuk, K. Moffat
Date :  25 Jan 07  (Deposition) - 10 Jul 07  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacteriophytochrome, Photoconversion, Photoreceptor, Biliverdin, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Yang, E. A. Stojkovic, J. Kuk, K. Moffat
Crystal Structure Of The Chromophore Binding Domain Of An Unusual Bacteriophytochrome, Rpbphp3, Reveals Residues That Modulate Photoconversion.
Proc. Natl. Acad. Sci. Usa V. 104 12571 2007
PubMed-ID: 17640891  |  Reference-DOI: 10.1073/PNAS.0701737104

(-) Compounds

Molecule 1 - SENSOR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSETB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PHYB2
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 258594
    Strain: CGA009

 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
1LBV2Ligand/Ion3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:28 , LYS A:183 , SER A:215 , ASP A:216 , ILE A:217 , PRO A:218 , SER A:221 , TYR A:225 , ARG A:263 , VAL A:265 , SER A:266 , THR A:268 , HIS A:269 , TYR A:272 , ALA A:281 , SER A:283 , SER A:297 , HIS A:299 , HOH A:410 , HOH A:437 , HOH A:439 , HOH A:551BINDING SITE FOR RESIDUE LBV A 400
2AC2SOFTWARECYS B:28 , LYS B:183 , TYR B:185 , VAL B:195 , SER B:215 , ASP B:216 , ILE B:217 , PRO B:218 , SER B:221 , TYR B:225 , ARG B:263 , VAL B:265 , SER B:266 , HIS B:269 , TYR B:272 , ALA B:281 , SER B:283 , SER B:297 , HIS B:299 , HOH B:432 , HOH B:453BINDING SITE FOR RESIDUE LBV B 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:103 -Pro A:104
2Val A:244 -Pro A:245
3Asn B:103 -Pro B:104
4Val B:244 -Pro B:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OOL)

(-) Exons   (0, 0)

(no "Exon" information available for 2OOL)

(-) 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:304
 aligned with Q6N5G2_RHOPA | Q6N5G2 from UniProtKB/TrEMBL  Length:775

    Alignment length:308
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325        
         Q6N5G2_RHOPA    26 TECDREPIHIPGAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRDESRYTNEFFRSVRVAIRRLQTAADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRDSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSVLRSVSPTHLEYMVNMGMHAAMSISIVRDNRLWGMISCHNLTPRFVSYEVRQACELIAQVLTWQIGVLEEAEI 333
               SCOP domains d2oola2 A:26-139 Sensor protein PhyB2                                                                             d2oola1 A:140-333 Sensor protein PhyB2                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh......ee....eeeee......eeeee.hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhh.----....eeeeeee..eeeeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhhh..eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ool A  26 TECDREPIHIPGAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHG----AINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRDESRYTNEFFRSVRVAIRRLQTAADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRDSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSVLRSVSPTHLEYMVNMGMHAAMSISIVRDNRLWGMISCHNLTPRFVSYEVRQACELIAQVLTWQIGVLEEAEI 333
                                    35        45        55        65        75        85        95|    | 105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325        
                                                                                                 96  101                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with Q6N5G2_RHOPA | Q6N5G2 from UniProtKB/TrEMBL  Length:775

    Alignment length:306
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326      
         Q6N5G2_RHOPA    27 ECDREPIHIPGAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRDESRYTNEFFRSVRVAIRRLQTAADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRDSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSVLRSVSPTHLEYMVNMGMHAAMSISIVRDNRLWGMISCHNLTPRFVSYEVRQACELIAQVLTWQIGVLEEAE 332
               SCOP domains d2oolb2 B:27-138 Sensor protein PhyB2                                                                               d2oolb1 B:143-332 Sensor protein PhyB2                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -PAS_2-2oolB03 B:28-136                                                                                       --    ------------------GAF-2oolB01 B:161-327                                                                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) -PAS_2-2oolB04 B:28-136                                                                                       --    ------------------GAF-2oolB02 B:161-327                                                                                                                                                  ----- Pfam domains (2)
         Sec.struct. author hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh..----....eeeeeee..eeeeeeeeeeee..eeeeeee....----hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........ee.....hhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhhh..eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ool B  27 ECDREPIHIPGAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHG----AINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRDE----NEFFRSVRVAIRRLQTAADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRDSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSVLRSVSPTHLEYMVNMGMHAAMSISIVRDNRLWGMISCHNLTPRFVSYEVRQACELIAQVLTWQIGVLEEAE 332
                                    36        46        56        66        76        86        96    |  106       116       126       136 |    |146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326      
                                                                                                96  101                                  138  143
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GAF (44)
(-)
Family: GAF (30)
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6N5G2_RHOPA | Q6N5G2)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
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: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: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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        Q6N5G2_RHOPA | Q6N5G2: 4r70

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