PYP_HALHA
ID PYP_HALHA Reviewed; 125 AA.
AC P16113;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 3.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Photoactive yellow protein;
DE Short=PYP;
GN Name=pyp;
OS Halorhodospira halophila (Ectothiorhodospira halophila).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Chromatiales;
OC Ectothiorhodospiraceae; Halorhodospira.
OX NCBI_TaxID=1053;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHROMOPHORE.
RC STRAIN=BN9626;
RX PubMed=7981196; DOI=10.1021/bi00252a001;
RA Baca M., Borgstahl G.E., Boissinot M., Burke P.M., Williams D.R.,
RA Slater K.A., Getzoff E.D.;
RT "Complete chemical structure of photoactive yellow protein: novel
RT thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry.";
RL Biochemistry 33:14369-14377(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=BN9626;
RX PubMed=8670821; DOI=10.1002/j.1460-2075.1996.tb00685.x;
RA Kort R., Hoff W.D., van West M., Kroon A.R., Hoffer S.M., Vlieg K.H.,
RA Crielaard W., van Beeumen J.J., Hellingwerf K.J.;
RT "The xanthopsins: a new family of eubacterial blue-light photoreceptors.";
RL EMBO J. 15:3209-3218(1996).
RN [3]
RP PROTEIN SEQUENCE.
RX PubMed=8358295; DOI=10.1002/pro.5560020706;
RA van Beeumen J.J., Devreese B.V., van Bun S.M., Hoff W.D., Hellingwerf K.J.,
RA Meyer T.E., McRee D.E., Cusanovich M.A.;
RT "Primary structure of a photoactive yellow protein from the phototrophic
RT bacterium Ectothiorhodospira halophila, with evidence for the mass and the
RT binding site of the chromophore.";
RL Protein Sci. 2:1114-1125(1993).
RN [4]
RP CHROMOPHORE.
RX PubMed=8573584; DOI=10.1021/bi951755z;
RA Hoff W.D., Devreese B., Fokkens R., Nugteren-Roodzant I.M., Van Beeumen J.,
RA Nibbering N., Hellingwerf K.J.;
RT "Chemical reactivity and spectroscopy of the thiol ester-linked p-coumaric
RT acid chromophore in the photoactive yellow protein from Ectothiorhodospira
RT halophila.";
RL Biochemistry 35:1274-1281(1996).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RC STRAIN=BN9626;
RX PubMed=2771940; DOI=10.1073/pnas.86.17.6533;
RA McRee D.E., Tainer J.A., Meyer T.E., van Beeumen J., Cusanovich M.A.,
RA Getzoff E.D.;
RT "Crystallographic structure of a photoreceptor protein at 2.4-A
RT resolution.";
RL Proc. Natl. Acad. Sci. U.S.A. 86:6533-6537(1989).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RC STRAIN=BN9626;
RX PubMed=9045611; DOI=10.1126/science.275.5305.1471;
RA Genick U.K., Borgstahl G.E., Ng K., Ren Z., Pradervand C., Burke P.M.,
RA Srajer V., Teng T.Y., Schildkamp W., McRee D.E., Moffat K., Getzoff E.D.;
RT "Structure of a protein photocycle intermediate by millisecond time-
RT resolved crystallography.";
RL Science 275:1471-1475(1997).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (0.85 ANGSTROMS).
RC STRAIN=BN9626;
RX PubMed=9515969; DOI=10.1038/32462;
RA Genick U.K., Soltis M., Kuhn P., Canestrelli I.L., Getzoff E.D.;
RT "Structure at 0.85-A resolution of an early protein photocycle
RT intermediate.";
RL Nature 392:206-209(1998).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.39 ANGSTROMS).
RX PubMed=10739248; DOI=10.1110/ps.9.1.64;
RA van Aalten D.M., Crielaard W., Hellingwerf K.J., Joshua-Tor L.;
RT "Conformational substates in different crystal forms of the photoactive
RT yellow protein -- correlation with theoretical and experimental
RT flexibility.";
RL Protein Sci. 9:64-72(2000).
RN [9]
RP STRUCTURE BY NMR.
RX PubMed=9665170; DOI=10.1038/823;
RA Rubinstenn G., Vuister G.W., Mulder F.A., Dux P.E., Boelens R.,
RA Hellingwerf K.J., Kaptein R.;
RT "Structural and dynamic changes of photoactive yellow protein during its
RT photocycle in solution.";
RL Nat. Struct. Biol. 5:568-570(1998).
CC -!- FUNCTION: Photoactive blue light protein. Probably functions as a
CC photoreceptor for a negative phototaxis response.
CC -!- SUBUNIT: Monomer.
CC -!- INTERACTION:
CC P16113; P16113: pyp; NbExp=4; IntAct=EBI-15592191, EBI-15592191;
CC -!- PTM: The 4-hydroxycinnamic acid (p-coumaric acid) chromophore is
CC covalently bound via a thioester linkage.
CC -!- SIMILARITY: Belongs to the photoactive yellow protein family.
CC {ECO:0000305}.
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DR EMBL; U17017; AAA61735.1; -; Genomic_DNA.
DR EMBL; X98887; CAA67391.1; -; Genomic_DNA.
DR PIR; B55993; JC5446.
DR PDB; 1D7E; X-ray; 1.39 A; A=4-125.
DR PDB; 1F98; X-ray; 1.15 A; A=1-125.
DR PDB; 1F9I; X-ray; 1.10 A; A=1-125.
DR PDB; 1GSV; X-ray; 1.75 A; A=1-125.
DR PDB; 1GSW; X-ray; 1.85 A; A=1-125.
DR PDB; 1GSX; X-ray; 1.79 A; A=1-125.
DR PDB; 1KOU; X-ray; 1.16 A; A=1-125.
DR PDB; 1NWZ; X-ray; 0.82 A; A=1-125.
DR PDB; 1ODV; X-ray; 1.14 A; A/B=26-125.
DR PDB; 1OT6; X-ray; 0.95 A; A=1-125.
DR PDB; 1OT9; X-ray; 1.00 A; A=1-125.
DR PDB; 1OTA; X-ray; 1.10 A; A=1-125.
DR PDB; 1OTB; X-ray; 1.10 A; A=1-125.
DR PDB; 1OTD; X-ray; 1.25 A; A/B=1-125.
DR PDB; 1OTE; X-ray; 1.40 A; A=1-125.
DR PDB; 1OTI; X-ray; 1.40 A; A=1-125.
DR PDB; 1S1Y; X-ray; 1.60 A; A=1-125.
DR PDB; 1S1Z; X-ray; 1.60 A; A=1-125.
DR PDB; 1S4R; X-ray; 1.90 A; A=1-125.
DR PDB; 1S4S; X-ray; 1.90 A; A=1-125.
DR PDB; 1T18; X-ray; 1.60 A; A=1-125.
DR PDB; 1T19; X-ray; 1.60 A; A=1-125.
DR PDB; 1T1A; X-ray; 1.60 A; A=1-125.
DR PDB; 1T1B; X-ray; 1.60 A; A=1-125.
DR PDB; 1T1C; X-ray; 1.60 A; A=1-125.
DR PDB; 1TS0; X-ray; 1.60 A; A=1-125.
DR PDB; 1TS6; X-ray; 1.60 A; A=1-125.
DR PDB; 1TS7; X-ray; 1.60 A; A=1-125.
DR PDB; 1TS8; X-ray; 1.60 A; A=1-125.
DR PDB; 1UGU; X-ray; 1.20 A; A=1-125.
DR PDB; 1UWN; X-ray; 1.20 A; X=1-125.
DR PDB; 1UWP; X-ray; 1.20 A; X=1-125.
DR PDB; 1XFN; NMR; -; A=26-125.
DR PDB; 1XFQ; NMR; -; A=26-125.
DR PDB; 2D01; X-ray; 1.34 A; A=1-125.
DR PDB; 2D02; X-ray; 1.42 A; A=1-125.
DR PDB; 2I9V; X-ray; 2.20 A; A=1-125.
DR PDB; 2KX6; Other; -; A=1-125.
DR PDB; 2PHY; X-ray; 1.40 A; A=1-125.
DR PDB; 2PYP; X-ray; 1.90 A; A=1-125.
DR PDB; 2PYR; X-ray; 1.90 A; A=1-125.
DR PDB; 2QJ5; X-ray; 1.20 A; A=1-125.
DR PDB; 2QJ7; X-ray; 1.05 A; A=1-125.
DR PDB; 2QWS; X-ray; 2.50 A; A=1-125.
DR PDB; 2ZOH; X-ray; 1.25 A; A=1-125.
DR PDB; 2ZOI; Neutron; 1.50 A; A=1-125.
DR PDB; 3PHY; NMR; -; A=1-125.
DR PDB; 3PYP; X-ray; 0.85 A; A=1-125.
DR PDB; 3UMD; X-ray; 1.80 A; A=1-125.
DR PDB; 3UME; X-ray; 1.80 A; A=1-125.
DR PDB; 3VE3; X-ray; 1.60 A; A=1-125.
DR PDB; 3VE4; X-ray; 1.60 A; A=1-125.
DR PDB; 4B9O; X-ray; 1.60 A; A=1-125.
DR PDB; 4BBT; X-ray; 1.60 A; A=1-125.
DR PDB; 4BBU; X-ray; 1.60 A; A=1-125.
DR PDB; 4BBV; X-ray; 1.60 A; A=1-125.
DR PDB; 4HY8; X-ray; 1.60 A; A=1-125.
DR PDB; 4I38; X-ray; 1.60 A; A=1-125.
DR PDB; 4I39; X-ray; 1.60 A; A=1-125.
DR PDB; 4I3A; X-ray; 1.60 A; A=1-125.
DR PDB; 4I3I; X-ray; 1.60 A; A=1-125.
DR PDB; 4I3J; X-ray; 1.60 A; A=1-125.
DR PDB; 4WL9; X-ray; 1.60 A; A=1-125.
DR PDB; 4WLA; X-ray; 1.60 A; A=1-125.
DR PDB; 5GX9; Neutron; 1.49 A; A=1-125.
DR PDB; 5HD3; X-ray; 1.60 A; A=1-125.
DR PDB; 5HD5; X-ray; 1.60 A; A=1-125.
DR PDB; 5HDC; X-ray; 1.60 A; A=1-125.
DR PDB; 5HDD; X-ray; 1.60 A; A=1-125.
DR PDB; 5HDS; X-ray; 1.60 A; A=1-125.
DR PDB; 6MHI; X-ray; 1.35 A; A=1-125.
DR PDB; 6MHN; X-ray; 1.67 A; A=1-125.
DR PDB; 6MKT; X-ray; 1.60 A; A=1-125.
DR PDB; 6MMD; X-ray; 1.23 A; A/B=1-125.
DR PDB; 6P4I; X-ray; 1.60 A; A=1-125.
DR PDB; 6P5D; X-ray; 1.60 A; A=1-125.
DR PDB; 6P5E; X-ray; 1.60 A; A=1-125.
DR PDB; 6P5F; X-ray; 1.70 A; A=1-125.
DR PDB; 6P5G; X-ray; 1.60 A; A=1-125.
DR PDB; 6UMY; X-ray; 0.92 A; A=1-125.
DR PDB; 6UMZ; X-ray; 0.90 A; A=1-125.
DR PDB; 6UN0; X-ray; 0.85 A; A=1-125.
DR PDB; 6UN2; X-ray; 0.97 A; A=1-125.
DR PDB; 7AV6; X-ray; 1.50 A; A=1-125.
DR PDBsum; 1D7E; -.
DR PDBsum; 1F98; -.
DR PDBsum; 1F9I; -.
DR PDBsum; 1GSV; -.
DR PDBsum; 1GSW; -.
DR PDBsum; 1GSX; -.
DR PDBsum; 1KOU; -.
DR PDBsum; 1NWZ; -.
DR PDBsum; 1ODV; -.
DR PDBsum; 1OT6; -.
DR PDBsum; 1OT9; -.
DR PDBsum; 1OTA; -.
DR PDBsum; 1OTB; -.
DR PDBsum; 1OTD; -.
DR PDBsum; 1OTE; -.
DR PDBsum; 1OTI; -.
DR PDBsum; 1S1Y; -.
DR PDBsum; 1S1Z; -.
DR PDBsum; 1S4R; -.
DR PDBsum; 1S4S; -.
DR PDBsum; 1T18; -.
DR PDBsum; 1T19; -.
DR PDBsum; 1T1A; -.
DR PDBsum; 1T1B; -.
DR PDBsum; 1T1C; -.
DR PDBsum; 1TS0; -.
DR PDBsum; 1TS6; -.
DR PDBsum; 1TS7; -.
DR PDBsum; 1TS8; -.
DR PDBsum; 1UGU; -.
DR PDBsum; 1UWN; -.
DR PDBsum; 1UWP; -.
DR PDBsum; 1XFN; -.
DR PDBsum; 1XFQ; -.
DR PDBsum; 2D01; -.
DR PDBsum; 2D02; -.
DR PDBsum; 2I9V; -.
DR PDBsum; 2KX6; -.
DR PDBsum; 2PHY; -.
DR PDBsum; 2PYP; -.
DR PDBsum; 2PYR; -.
DR PDBsum; 2QJ5; -.
DR PDBsum; 2QJ7; -.
DR PDBsum; 2QWS; -.
DR PDBsum; 2ZOH; -.
DR PDBsum; 2ZOI; -.
DR PDBsum; 3PHY; -.
DR PDBsum; 3PYP; -.
DR PDBsum; 3UMD; -.
DR PDBsum; 3UME; -.
DR PDBsum; 3VE3; -.
DR PDBsum; 3VE4; -.
DR PDBsum; 4B9O; -.
DR PDBsum; 4BBT; -.
DR PDBsum; 4BBU; -.
DR PDBsum; 4BBV; -.
DR PDBsum; 4HY8; -.
DR PDBsum; 4I38; -.
DR PDBsum; 4I39; -.
DR PDBsum; 4I3A; -.
DR PDBsum; 4I3I; -.
DR PDBsum; 4I3J; -.
DR PDBsum; 4WL9; -.
DR PDBsum; 4WLA; -.
DR PDBsum; 5GX9; -.
DR PDBsum; 5HD3; -.
DR PDBsum; 5HD5; -.
DR PDBsum; 5HDC; -.
DR PDBsum; 5HDD; -.
DR PDBsum; 5HDS; -.
DR PDBsum; 6MHI; -.
DR PDBsum; 6MHN; -.
DR PDBsum; 6MKT; -.
DR PDBsum; 6MMD; -.
DR PDBsum; 6P4I; -.
DR PDBsum; 6P5D; -.
DR PDBsum; 6P5E; -.
DR PDBsum; 6P5F; -.
DR PDBsum; 6P5G; -.
DR PDBsum; 6UMY; -.
DR PDBsum; 6UMZ; -.
DR PDBsum; 6UN0; -.
DR PDBsum; 6UN2; -.
DR PDBsum; 7AV6; -.
DR AlphaFoldDB; P16113; -.
DR BMRB; P16113; -.
DR SMR; P16113; -.
DR DIP; DIP-61234N; -.
DR DrugBank; DB01880; 3,4-Dihydroxycinnamic Acid.
DR DrugBank; DB04066; p-Coumaric acid.
DR EvolutionaryTrace; P16113; -.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0009881; F:photoreceptor activity; IEA:UniProtKB-KW.
DR GO; GO:0007602; P:phototransduction; IEA:InterPro.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR CDD; cd00130; PAS; 1.
DR InterPro; IPR000014; PAS.
DR InterPro; IPR035965; PAS-like_dom_sf.
DR InterPro; IPR013767; PAS_fold.
DR InterPro; IPR012130; PYP.
DR Pfam; PF00989; PAS; 1.
DR PIRSF; PIRSF000087; PYP; 1.
DR SMART; SM00091; PAS; 1.
DR SUPFAM; SSF55785; SSF55785; 1.
DR TIGRFAMs; TIGR02373; photo_yellow; 1.
DR PROSITE; PS50112; PAS; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromophore; Direct protein sequencing;
KW Photoreceptor protein; Receptor; Sensory transduction.
FT CHAIN 1..125
FT /note="Photoactive yellow protein"
FT /id="PRO_0000144914"
FT DOMAIN 23..86
FT /note="PAS"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT MOD_RES 69
FT /note="S-(4-hydroxycinnamyl)cysteine"
FT /evidence="ECO:0000269|PubMed:7981196"
FT CONFLICT 56
FT /note="Q -> E (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT TURN 8..10
FT /evidence="ECO:0007829|PDB:3PHY"
FT HELIX 11..14
FT /evidence="ECO:0007829|PDB:1NWZ"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:1NWZ"
FT HELIX 20..23
FT /evidence="ECO:0007829|PDB:1NWZ"
FT STRAND 27..34
FT /evidence="ECO:0007829|PDB:1NWZ"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:3PHY"
FT STRAND 38..42
FT /evidence="ECO:0007829|PDB:1NWZ"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:1NWZ"
FT HELIX 54..57
FT /evidence="ECO:0007829|PDB:1NWZ"
FT HELIX 62..66
FT /evidence="ECO:0007829|PDB:1NWZ"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:1NWZ"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:1NWZ"
FT HELIX 76..85
FT /evidence="ECO:0007829|PDB:1NWZ"
FT STRAND 89..96
FT /evidence="ECO:0007829|PDB:1NWZ"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:1OT6"
FT STRAND 103..111
FT /evidence="ECO:0007829|PDB:1NWZ"
FT STRAND 113..124
FT /evidence="ECO:0007829|PDB:1NWZ"
SQ SEQUENCE 125 AA; 13874 MW; 291B08416510F0A3 CRC64;
MEHVAFGSED IENTLAKMDD GQLDGLAFGA IQLDGDGNIL QYNAAEGDIT GRDPKQVIGK
NFFKDVAPCT DSPEFYGKFK EGVASGNLNT MFEYTFDYQM TPTKVKVHMK KALSGDSYWV
FVKRV
