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P16113 (PYP_HALHA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Photoactive yellow protein
Short name=PYP
Gene names
Name:pyp
OrganismHalorhodospira halophila (Ectothiorhodospira halophila)
Taxonomic identifier1053 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Chromatiales › Ectothiorhodospiraceae › Halorhodospira

Protein attributes

Sequence length125 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Subunit structure

Monomer.

Post-translational modification

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

Sequence similarities

Belongs to the photoactive yellow protein family.

Contains 1 PAS (PER-ARNT-SIM) domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 125125Photoactive yellow protein
PRO_0000144914

Regions

Domain23 – 8664PAS

Amino acid modifications

Modified residue691S-(4-hydroxycinnamyl)cysteine Ref.1

Experimental info

Sequence conflict561Q → E AA sequence Ref.3

Secondary structure

1 .............................. 125
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P16113 [UniParc].

Last modified November 1, 1995. Version 3.
Checksum: 291B08416510F0A3

FASTA12513,874
        10         20         30         40         50         60 
MEHVAFGSED IENTLAKMDD GQLDGLAFGA IQLDGDGNIL QYNAAEGDIT GRDPKQVIGK 

        70         80         90        100        110        120 
NFFKDVAPCT DSPEFYGKFK EGVASGNLNT MFEYTFDYQM TPTKVKVHMK KALSGDSYWV 


FVKRV

« Hide

References

[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]"Crystallographic structure of a photoreceptor protein at 2.4-A resolution."
McRee D.E., Tainer J.A., Meyer T.E., van Beeumen J., Cusanovich M.A., Getzoff E.D.
Proc. Natl. Acad. Sci. U.S.A. 86:6533-6537(1989) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		U17017 Genomic DNA. Translation: AAA61735.1.
X98887 Genomic DNA. Translation: CAA67391.1.
PIRJC5446. B55993.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
4B9OX-ray1.60A1-125[»]
4BBTX-ray1.60A1-125[»]
4BBUX-ray1.60A1-125[»]
4BBVX-ray1.60A1-125[»]
ProteinModelPortalP16113.
SMRP16113. Positions 1-125.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR000014. PAS.
IPR013767. PAS_fold.
IPR012130. PYP.
[Graphical view]
PfamPF00989. PAS. 1 hit.
[Graphical view]
PIRSFPIRSF000087. PYP. 1 hit.
SMARTSM00091. PAS. 1 hit.
[Graphical view]
TIGRFAMsTIGR02373. photo_yellow. 1 hit.
PROSITEPS50112. PAS. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP16113.

Entry information

Entry namePYP_HALHA
AccessionPrimary (citable) accession number: P16113
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: November 1, 1995
Last modified: April 3, 2013
This is version 93 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents