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(-) Description

Title :  PYP ULTRA-HIGH RESOLUTION OF A BACTERIAL PHOTORECEPTOR
 
Authors :  P. D. Coureux, Z. P. Fan, V. Stojanoff, U. K. Genick
Date :  06 Jul 07  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Pas Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Coureux, Z. P. Fan, V. Stojanoff, U. K. Genick
Picometer-Scale Conformational Heterogeneity Separates Functional From Nonfunctional States Of A Photoreceptor Protein.
Structure V. 16 863 2008
PubMed-ID: 18547519  |  Reference-DOI: 10.1016/J.STR.2008.02.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOACTIVE YELLOW PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Gene: PYP
    Organism Scientific: HALORHODOSPIRA HALOPHILA
    Synonym: PYP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HC41Ligand/Ion4'-HYDROXYCINNAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:31 , TYR A:42 , GLU A:46 , THR A:50 , ALA A:67 , PRO A:68 , CYS A:69 , PHE A:96 , TYR A:98BINDING SITE FOR RESIDUE HC4 A 126

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QJ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QJ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QJ5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.PYP_HALHA23-86  1A:23-86

(-) Exons   (0, 0)

(no "Exon" information available for 2QJ5)

(-) 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:121
 aligned with PYP_HALHA | P16113 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:123
                                    12        22        32        42        52        62        72        82        92       102       112       122   
            PYP_HALHA     3 HVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 125
               SCOP domains d2qj5a_ A: Photoactive yellow protein, PYP                                                                                  SCOP domains
               CATH domains 2qj5A00 A:3-125  [code=3.30.450.20, no name defined]                                                                        CATH domains
               Pfam domains --------------PAS-2qj5A01 A:17-125                                                                                          Pfam domains
         Sec.struct. author .......hhhhhhhh.hhhhhhh...eeeee.....eeeehhhhhhhhh.hhhhhh........hhhhh...hhhhhhhhhhhh..eeeeeeee......eeeeeeeee..--..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------PAS  PDB: A:23-86 UniProt: 23-86                                --------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qj5 A   3 HVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKAL--DSYWVFVKRV 125
                                    12        22        32        42        52        62        72        82        92       102       112|  |   122   
                                                                                                                                        113  |         
                                                                                                                                           116
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYP_HALHA | P16113)
molecular function
    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:0007602    phototransduction    The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
    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.

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  2qj5
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  PYP_HALHA | P16113
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYP_HALHA | P16113: 1d7e 1f98 1f9i 1gsv 1gsw 1gsx 1kou 1nwz 1odv 1ot6 1ot9 1ota 1otb 1otd 1ote 1oti 1s1y 1s1z 1s4r 1s4s 1t18 1t19 1t1a 1t1b 1t1c 1ts0 1ts6 1ts7 1ts8 1ugu 1uwn 1uwp 1xfn 1xfq 2d01 2d02 2i9v 2kx6 2phy 2pyp 2pyr 2qj7 2qws 2zoh 2zoi 3phy 3pyp 3umd 3ume 3ve3 3ve4 4b9o 4bbt 4bbu 4bbv 4hy8 4i38 4i39 4i3a 4i3i 4i3j 4wl9 4wla 5hd3 5hd5 5hdc 5hdd 5hds

(-) Related Entries Specified in the PDB File

2qj7 PHOTOACTIVE YELLOW PROTEIN, LIGHT STATE