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P16113

- PYP_HALHA

UniProt

P16113 - PYP_HALHA

Protein

Photoactive yellow protein

Gene

pyp

Organism
Halorhodospira halophila (Ectothiorhodospira halophila)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.

    GO - Molecular functioni

    1. photoreceptor activity Source: UniProtKB-KW

    GO - Biological processi

    1. phototransduction Source: InterPro
    2. protein-chromophore linkage Source: UniProtKB-KW
    3. regulation of transcription, DNA-templated Source: InterPro

    Keywords - Molecular functioni

    Photoreceptor protein, Receptor

    Keywords - Biological processi

    Sensory transduction

    Keywords - Ligandi

    Chromophore

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Photoactive yellow protein
    Short name:
    PYP
    Gene namesi
    Name:pyp
    OrganismiHalorhodospira halophila (Ectothiorhodospira halophila)
    Taxonomic identifieri1053 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesEctothiorhodospiraceaeHalorhodospira

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 125125Photoactive yellow proteinPRO_0000144914Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei69 – 691S-(4-hydroxycinnamyl)cysteine1 Publication

    Post-translational modificationi

    The 4-hydroxycinnamic acid (p-coumaric acid) chromophore is covalently bound via a thioester linkage.

    Interactioni

    Subunit structurei

    Monomer.

    Structurei

    Secondary structure

    1
    125
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni8 – 103
    Helixi11 – 144
    Turni15 – 173
    Helixi20 – 234
    Beta strandi27 – 348
    Turni35 – 373
    Beta strandi38 – 425
    Helixi44 – 507
    Helixi54 – 574
    Helixi62 – 665
    Helixi68 – 703
    Turni73 – 753
    Helixi76 – 8510
    Beta strandi89 – 968
    Beta strandi98 – 1003
    Beta strandi103 – 1119
    Beta strandi113 – 12412

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1D7EX-ray1.39A4-125[»]
    1F98X-ray1.15A1-125[»]
    1F9IX-ray1.10A1-125[»]
    1GSVX-ray1.75A1-125[»]
    1GSWX-ray1.85A1-125[»]
    1GSXX-ray1.79A1-125[»]
    1KOUX-ray1.16A1-125[»]
    1NWZX-ray0.82A1-125[»]
    1ODVX-ray1.14A/B26-125[»]
    1OT6X-ray0.95A1-125[»]
    1OT9X-ray1.00A1-125[»]
    1OTAX-ray1.10A1-125[»]
    1OTBX-ray1.10A1-125[»]
    1OTDX-ray1.25A/B1-125[»]
    1OTEX-ray1.40A1-125[»]
    1OTIX-ray1.40A1-125[»]
    1S1YX-ray1.60A1-125[»]
    1S1ZX-ray1.60A1-125[»]
    1S4RX-ray1.90A1-125[»]
    1S4SX-ray1.90A1-125[»]
    1T18X-ray1.60A1-125[»]
    1T19X-ray1.60A1-125[»]
    1T1AX-ray1.60A1-125[»]
    1T1BX-ray1.60A1-125[»]
    1T1CX-ray1.60A1-125[»]
    1TS0X-ray1.60A1-125[»]
    1TS6X-ray1.60A1-125[»]
    1TS7X-ray1.60A1-125[»]
    1TS8X-ray1.60A1-125[»]
    1UGUX-ray1.20A1-125[»]
    1UWNX-ray1.20X1-125[»]
    1UWPX-ray1.20X1-125[»]
    1XFNNMR-A26-125[»]
    1XFQNMR-A26-125[»]
    2D01X-ray1.34A1-125[»]
    2D02X-ray1.42A1-125[»]
    2I9VX-ray2.20A1-125[»]
    2KX6Other-A1-125[»]
    2PHYX-ray1.40A1-125[»]
    2PYPX-ray1.90A1-125[»]
    2PYRX-ray1.90A1-125[»]
    2QJ5X-ray1.20A1-125[»]
    2QJ7X-ray1.05A1-125[»]
    2QWSX-ray2.50A1-125[»]
    2ZOHX-ray1.25A1-125[»]
    2ZOIneutron diffraction1.50A1-125[»]
    3PHYNMR-A1-125[»]
    3PYPX-ray0.85A1-125[»]
    3UMDX-ray1.80A1-125[»]
    3UMEX-ray1.80A1-125[»]
    3VE3X-ray1.60A1-125[»]
    3VE4X-ray1.60A1-125[»]
    4B9OX-ray1.60A1-125[»]
    4BBTX-ray1.60A1-125[»]
    4BBUX-ray1.60A1-125[»]
    4BBVX-ray1.60A1-125[»]
    4HY8X-ray1.60A1-125[»]
    4I38X-ray1.60A1-125[»]
    4I39X-ray1.60A1-125[»]
    4I3AX-ray1.60A1-125[»]
    4I3IX-ray1.60A1-125[»]
    4I3JX-ray1.60A1-125[»]
    ProteinModelPortaliP16113.
    SMRiP16113. Positions 1-125.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP16113.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini23 – 8664PASPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the photoactive yellow protein family.Curated
    Contains 1 PAS (PER-ARNT-SIM) domain.PROSITE-ProRule annotation

    Family and domain databases

    InterProiIPR000014. PAS.
    IPR013767. PAS_fold.
    IPR012130. PYP.
    [Graphical view]
    PfamiPF00989. PAS. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000087. PYP. 1 hit.
    SMARTiSM00091. PAS. 1 hit.
    [Graphical view]
    SUPFAMiSSF55785. SSF55785. 1 hit.
    TIGRFAMsiTIGR02373. photo_yellow. 1 hit.
    PROSITEiPS50112. PAS. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P16113-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEHVAFGSED IENTLAKMDD GQLDGLAFGA IQLDGDGNIL QYNAAEGDIT    50
    GRDPKQVIGK NFFKDVAPCT DSPEFYGKFK EGVASGNLNT MFEYTFDYQM 100
    TPTKVKVHMK KALSGDSYWV FVKRV 125
    Length:125
    Mass (Da):13,874
    Last modified:November 1, 1995 - v3
    Checksum:i291B08416510F0A3
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti56 – 561Q → E AA sequence (PubMed:8358295)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U17017 Genomic DNA. Translation: AAA61735.1.
    X98887 Genomic DNA. Translation: CAA67391.1.
    PIRiB55993. JC5446.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U17017 Genomic DNA. Translation: AAA61735.1 .
    X98887 Genomic DNA. Translation: CAA67391.1 .
    PIRi B55993. JC5446.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1D7E X-ray 1.39 A 4-125 [» ]
    1F98 X-ray 1.15 A 1-125 [» ]
    1F9I X-ray 1.10 A 1-125 [» ]
    1GSV X-ray 1.75 A 1-125 [» ]
    1GSW X-ray 1.85 A 1-125 [» ]
    1GSX X-ray 1.79 A 1-125 [» ]
    1KOU X-ray 1.16 A 1-125 [» ]
    1NWZ X-ray 0.82 A 1-125 [» ]
    1ODV X-ray 1.14 A/B 26-125 [» ]
    1OT6 X-ray 0.95 A 1-125 [» ]
    1OT9 X-ray 1.00 A 1-125 [» ]
    1OTA X-ray 1.10 A 1-125 [» ]
    1OTB X-ray 1.10 A 1-125 [» ]
    1OTD X-ray 1.25 A/B 1-125 [» ]
    1OTE X-ray 1.40 A 1-125 [» ]
    1OTI X-ray 1.40 A 1-125 [» ]
    1S1Y X-ray 1.60 A 1-125 [» ]
    1S1Z X-ray 1.60 A 1-125 [» ]
    1S4R X-ray 1.90 A 1-125 [» ]
    1S4S X-ray 1.90 A 1-125 [» ]
    1T18 X-ray 1.60 A 1-125 [» ]
    1T19 X-ray 1.60 A 1-125 [» ]
    1T1A X-ray 1.60 A 1-125 [» ]
    1T1B X-ray 1.60 A 1-125 [» ]
    1T1C X-ray 1.60 A 1-125 [» ]
    1TS0 X-ray 1.60 A 1-125 [» ]
    1TS6 X-ray 1.60 A 1-125 [» ]
    1TS7 X-ray 1.60 A 1-125 [» ]
    1TS8 X-ray 1.60 A 1-125 [» ]
    1UGU X-ray 1.20 A 1-125 [» ]
    1UWN X-ray 1.20 X 1-125 [» ]
    1UWP X-ray 1.20 X 1-125 [» ]
    1XFN NMR - A 26-125 [» ]
    1XFQ NMR - A 26-125 [» ]
    2D01 X-ray 1.34 A 1-125 [» ]
    2D02 X-ray 1.42 A 1-125 [» ]
    2I9V X-ray 2.20 A 1-125 [» ]
    2KX6 Other - A 1-125 [» ]
    2PHY X-ray 1.40 A 1-125 [» ]
    2PYP X-ray 1.90 A 1-125 [» ]
    2PYR X-ray 1.90 A 1-125 [» ]
    2QJ5 X-ray 1.20 A 1-125 [» ]
    2QJ7 X-ray 1.05 A 1-125 [» ]
    2QWS X-ray 2.50 A 1-125 [» ]
    2ZOH X-ray 1.25 A 1-125 [» ]
    2ZOI neutron diffraction 1.50 A 1-125 [» ]
    3PHY NMR - A 1-125 [» ]
    3PYP X-ray 0.85 A 1-125 [» ]
    3UMD X-ray 1.80 A 1-125 [» ]
    3UME X-ray 1.80 A 1-125 [» ]
    3VE3 X-ray 1.60 A 1-125 [» ]
    3VE4 X-ray 1.60 A 1-125 [» ]
    4B9O X-ray 1.60 A 1-125 [» ]
    4BBT X-ray 1.60 A 1-125 [» ]
    4BBU X-ray 1.60 A 1-125 [» ]
    4BBV X-ray 1.60 A 1-125 [» ]
    4HY8 X-ray 1.60 A 1-125 [» ]
    4I38 X-ray 1.60 A 1-125 [» ]
    4I39 X-ray 1.60 A 1-125 [» ]
    4I3A X-ray 1.60 A 1-125 [» ]
    4I3I X-ray 1.60 A 1-125 [» ]
    4I3J X-ray 1.60 A 1-125 [» ]
    ProteinModelPortali P16113.
    SMRi P16113. Positions 1-125.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P16113.

    Family and domain databases

    InterProi IPR000014. PAS.
    IPR013767. PAS_fold.
    IPR012130. PYP.
    [Graphical view ]
    Pfami PF00989. PAS. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000087. PYP. 1 hit.
    SMARTi SM00091. PAS. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55785. SSF55785. 1 hit.
    TIGRFAMsi TIGR02373. photo_yellow. 1 hit.
    PROSITEi PS50112. PAS. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry."
      Baca M., Borgstahl G.E., Boissinot M., Burke P.M., Williams D.R., Slater K.A., Getzoff E.D.
      Biochemistry 33:14369-14377(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHROMOPHORE.
      Strain: BN9626.
    2. "The xanthopsins: a new family of eubacterial blue-light photoreceptors."
      Kort R., Hoff W.D., van West M., Kroon A.R., Hoffer S.M., Vlieg K.H., Crielaard W., van Beeumen J.J., Hellingwerf K.J.
      EMBO J. 15:3209-3218(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: BN9626.
    3. "Primary structure of a photoactive yellow protein from the phototrophic bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding site of the chromophore."
      van Beeumen J.J., Devreese B.V., van Bun S.M., Hoff W.D., Hellingwerf K.J., Meyer T.E., McRee D.E., Cusanovich M.A.
      Protein Sci. 2:1114-1125(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE.
    4. "Chemical reactivity and spectroscopy of the thiol ester-linked p-coumaric acid chromophore in the photoactive yellow protein from Ectothiorhodospira halophila."
      Hoff W.D., Devreese B., Fokkens R., Nugteren-Roodzant I.M., Van Beeumen J., Nibbering N., Hellingwerf K.J.
      Biochemistry 35:1274-1281(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHROMOPHORE.
    5. Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
      Strain: BN9626.
    6. "Structure of a protein photocycle intermediate by millisecond time-resolved crystallography."
      Genick U.K., Borgstahl G.E., Ng K., Ren Z., Pradervand C., Burke P.M., Srajer V., Teng T.Y., Schildkamp W., McRee D.E., Moffat K., Getzoff E.D.
      Science 275:1471-1475(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
      Strain: BN9626.
    7. "Structure at 0.85-A resolution of an early protein photocycle intermediate."
      Genick U.K., Soltis M., Kuhn P., Canestrelli I.L., Getzoff E.D.
      Nature 392:206-209(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (0.85 ANGSTROMS).
      Strain: BN9626.
    8. "Conformational substates in different crystal forms of the photoactive yellow protein -- correlation with theoretical and experimental flexibility."
      van Aalten D.M., Crielaard W., Hellingwerf K.J., Joshua-Tor L.
      Protein Sci. 9:64-72(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.39 ANGSTROMS).
    9. "Structural and dynamic changes of photoactive yellow protein during its photocycle in solution."
      Rubinstenn G., Vuister G.W., Mulder F.A., Dux P.E., Boelens R., Hellingwerf K.J., Kaptein R.
      Nat. Struct. Biol. 5:568-570(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.

    Entry informationi

    Entry nameiPYP_HALHA
    AccessioniPrimary (citable) accession number: P16113
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 97 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3