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(-) Description

Title :  WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P65 FORM
 
Authors :  N. Shimizu, H. Kamikubo, Y. Yamazaki, Y. Imamoto, M. Kataoka
Date :  21 Jul 05  (Deposition) - 04 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Pas, Lov, Gaf-Domains, Photoreceptor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shimizu, H. Kamikubo, Y. Yamazaki, Y. Imamoto, M. Kataoka
The Crystal Structure Of The R52Q Mutant Demonstrates A Role For R52 In Chromophore Pk(A) Regulation In Photoactive Yellow Protein
Biochemistry V. 45 3542 2006
PubMed-ID: 16533035  |  Reference-DOI: 10.1021/BI051430A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOACTIVE YELLOW PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PYP
    Organism Scientific: HALORHODOSPIRA HALOPHILA
    Organism Taxid: 1053
    Synonym: PHOTORECEPTOR, 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 , ARG A:52 , VAL A:66 , ALA A:67 , PRO A:68 , CYS A:69 , PHE A:96 , TYR A:98BINDING SITE FOR RESIDUE HC4 A 169

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D01)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D01)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D01)

(-) 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 2D01)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:124
 aligned with PYP_HALHA | P16113 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
            PYP_HALHA     2 EHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 125
               SCOP domains d2d01a_ A: Photoactive yellow protein, PYP                                                                                   SCOP domains
               CATH domains 2d01A00 A:2-125  [code=3.30.450.20, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- 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
                 2d01 A   2 EHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 125
                                    11        21        31        41        51        61        71        81        91       101       111       121
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 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  (0, 0)

(no "Pfam Domain" information available for 2D01)

(-) 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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 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 2d02 2i9v 2kx6 2phy 2pyp 2pyr 2qj5 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

2d02 PYP(R52Q), P65 FORM
2phy ANOTHER CRYSTAL FORM OF PYP