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P16113

- PYP_HALHA

UniProt

P16113 - PYP_HALHA

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Protein

Photoactive yellow protein

Gene

pyp

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

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
Complete GO annotation...

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 – 103Combined sources
Helixi11 – 144Combined sources
Turni15 – 173Combined sources
Helixi20 – 234Combined sources
Beta strandi27 – 348Combined sources
Turni35 – 373Combined sources
Beta strandi38 – 425Combined sources
Helixi44 – 507Combined sources
Helixi54 – 574Combined sources
Helixi62 – 665Combined sources
Helixi68 – 703Combined sources
Turni73 – 753Combined sources
Helixi76 – 8510Combined sources
Beta strandi89 – 968Combined sources
Beta strandi98 – 1003Combined sources
Beta strandi103 – 1119Combined sources
Beta strandi113 – 12412Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MEHVAFGSED IENTLAKMDD GQLDGLAFGA IQLDGDGNIL QYNAAEGDIT
60 70 80 90 100
GRDPKQVIGK NFFKDVAPCT DSPEFYGKFK EGVASGNLNT MFEYTFDYQM
110 120
TPTKVKVHMK KALSGDSYWV FVKRV
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:
EMBLi
GenBanki
DDBJi
Links Updated
U17017 Genomic DNA. Translation: AAA61735.1.
X98887 Genomic DNA. Translation: CAA67391.1.
PIRiB55993. JC5446.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U17017 Genomic DNA. Translation: AAA61735.1 .
X98887 Genomic DNA. Translation: CAA67391.1 .
PIRi B55993. JC5446.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 98 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