RP65B_DANRE
ID RP65B_DANRE Reviewed; 532 AA.
AC A9C3R9; A4FVJ4; A9JRQ7; Q4L0V3;
DT 05-SEP-2012, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=All-trans-retinyl ester 13-cis isomerohydrolase;
DE Short=13cIMH;
DE EC=3.1.1.90 {ECO:0000269|PubMed:21235714};
DE AltName: Full=Lutein isomerase;
DE AltName: Full=Meso-zeaxanthin isomerase;
DE EC=5.3.3.22 {ECO:0000250|UniProtKB:Q16518};
DE AltName: Full=Retinal pigment epithelium-specific 65 kDa protein homolog B;
DE Short=RPE56b;
GN Name=rpe65b; Synonyms=rpepb; ORFNames=si:ch211-198n5.5;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=17868371; DOI=10.1111/j.1460-9568.2007.05801.x;
RA Schonthaler H.B., Lampert J.M., Isken A., Rinner O., Mader A., Gesemann M.,
RA Oberhauser V., Golczak M., Biehlmaier O., Palczewski K., Neuhauss S.C.,
RA von Lintig J.;
RT "Evidence for RPE65-independent vision in the cone-dominated zebrafish
RT retina.";
RL Eur. J. Neurosci. 26:1940-1949(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=21235714; DOI=10.1111/j.1742-4658.2011.08019.x;
RA Takahashi Y., Moiseyev G., Chen Y., Farjo K., Nikolaeva O., Ma J.X.;
RT "An enzymatic mechanism for generating the precursor of endogenous 13-cis
RT retinoic acid in the brain.";
RL FEBS J. 278:973-987(2011).
CC -!- FUNCTION: Specifically generates 13-cis retinol, a stereoisomeric form
CC of retinoic acid. Capable of catalyzing the isomerization of lutein to
CC meso-zeaxanthin an eye-specific carotenoid (By similarity).
CC {ECO:0000250|UniProtKB:Q16518, ECO:0000269|PubMed:21235714}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an all-trans-retinyl ester + H2O = 13-cis-retinol + a fatty
CC acid + H(+); Xref=Rhea:RHEA:31779, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:28868, ChEBI:CHEBI:45479,
CC ChEBI:CHEBI:63410; EC=3.1.1.90;
CC Evidence={ECO:0000269|PubMed:21235714};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=lutein = (3R,3'S)-zeaxanthin; Xref=Rhea:RHEA:12729,
CC ChEBI:CHEBI:28838, ChEBI:CHEBI:138919; EC=5.3.3.22;
CC Evidence={ECO:0000250|UniProtKB:Q16518};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000305|PubMed:21235714};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000305|PubMed:21235714};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.6 uM for all-trans-retinyl ester {ECO:0000269|PubMed:21235714};
CC Note=kcat is 0.00044 sec(-1) with all-trans-retinyl ester as
CC substrate.;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:21235714}. Cell
CC membrane {ECO:0000269|PubMed:21235714}; Lipid-anchor
CC {ECO:0000269|PubMed:21235714}. Note=Attached to the membrane by a lipid
CC anchor when palmitoylated (membrane form), soluble when
CC unpalmitoylated. {ECO:0000250|UniProtKB:Q28175}.
CC -!- TISSUE SPECIFICITY: Predominantly expressed in brain. Expressed at a
CC low level in the eye. {ECO:0000269|PubMed:21235714}.
CC -!- DEVELOPMENTAL STAGE: Detectable in migrating neural crest cells during
CC somitogenesis. At early larval stages, expression is visible in the
CC ventricular zone, the upper and lower jaw and the developing pectoral
CC fins. At later larval stages, expression fades out.
CC {ECO:0000269|PubMed:17868371}.
CC -!- PTM: Palmitoylated. {ECO:0000250|UniProtKB:Q28175}.
CC -!- SIMILARITY: Belongs to the carotenoid oxygenase family. {ECO:0000305}.
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DR EMBL; AY646887; AAV65108.1; -; mRNA.
DR EMBL; CR759968; CAP19512.1; -; Genomic_DNA.
DR EMBL; BC133985; AAI33986.1; -; mRNA.
DR EMBL; BC155753; AAI55754.1; -; mRNA.
DR RefSeq; NP_001082902.2; NM_001089433.2.
DR AlphaFoldDB; A9C3R9; -.
DR SMR; A9C3R9; -.
DR STRING; 7955.ENSDARP00000071014; -.
DR PaxDb; A9C3R9; -.
DR PeptideAtlas; A9C3R9; -.
DR DNASU; 100002865; -.
DR Ensembl; ENSDART00000076542; ENSDARP00000071014; ENSDARG00000094752.
DR GeneID; 100002865; -.
DR KEGG; dre:100002865; -.
DR CTD; 100002865; -.
DR ZFIN; ZDB-GENE-050410-16; rpe65b.
DR eggNOG; KOG1285; Eukaryota.
DR GeneTree; ENSGT00950000182913; -.
DR HOGENOM; CLU_016472_1_1_1; -.
DR InParanoid; A9C3R9; -.
DR OMA; FPNANCI; -.
DR OrthoDB; 895046at2759; -.
DR PhylomeDB; A9C3R9; -.
DR TreeFam; TF314019; -.
DR BioCyc; MetaCyc:MON-16789; -.
DR BRENDA; 3.1.1.64; 928.
DR PRO; PR:A9C3R9; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 8.
DR Bgee; ENSDARG00000094752; Expressed in zone of skin and 12 other tissues.
DR ExpressionAtlas; A9C3R9; baseline and differential.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; ISS:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IEA:InterPro.
DR GO; GO:0050251; F:retinol isomerase activity; IBA:GO_Central.
DR GO; GO:0001523; P:retinoid metabolic process; ISS:UniProtKB.
DR GO; GO:1901827; P:zeaxanthin biosynthetic process; IBA:GO_Central.
DR InterPro; IPR004294; Carotenoid_Oase.
DR PANTHER; PTHR10543; PTHR10543; 1.
DR Pfam; PF03055; RPE65; 1.
PE 1: Evidence at protein level;
KW Cell membrane; Cytoplasm; Hydrolase; Iron; Isomerase; Lipoprotein;
KW Membrane; Metal-binding; Palmitate; Reference proteome.
FT CHAIN 1..532
FT /note="All-trans-retinyl ester 13-cis isomerohydrolase"
FT /id="PRO_0000418731"
FT BINDING 180
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q28175"
FT BINDING 241
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q28175"
FT BINDING 313
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q28175"
FT BINDING 527
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q28175"
FT LIPID 112
FT /note="S-palmitoyl cysteine; in membrane form"
FT /evidence="ECO:0000250|UniProtKB:Q28175"
FT LIPID 329
FT /note="S-palmitoyl cysteine; in membrane form"
FT /evidence="ECO:0000250|UniProtKB:Q28175"
FT CONFLICT 19
FT /note="C -> R (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 33
FT /note="K -> E (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 52
FT /note="I -> V (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 58
FT /note="N -> Y (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 66..67
FT /note="LI -> PL (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 82
FT /note="K -> R (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 99
FT /note="V -> A (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 106
FT /note="A -> T (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 126
FT /note="T -> I (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 133
FT /note="S -> L (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 156
FT /note="N -> D (in Ref. 3; AAI33986)"
FT /evidence="ECO:0000305"
FT CONFLICT 163
FT /note="I -> V (in Ref. 3; AAI33986)"
FT /evidence="ECO:0000305"
FT CONFLICT 273
FT /note="S -> L (in Ref. 1; AAV65108)"
FT /evidence="ECO:0000305"
FT CONFLICT 388
FT /note="Y -> H (in Ref. 3; AAI55754)"
FT /evidence="ECO:0000305"
FT CONFLICT 424
FT /note="S -> G (in Ref. 3; AAI33986)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 532 AA; 60613 MW; E5725F6696CA7C51 CRC64;
MVSRLEHPAG GYKKVFESCE ELAEPIPAHV SGKIPAWLSG SLLRMGPGLF EIGDEPFNHL
FDGQALIHKF DLKDGRVTYH RKFIRTDAYV RAMTEKRVVI TELGTAAYPD PCKNIFSRFF
TYFQGTEVTD NCSVNIYPIG EDFYACTETN FITKVNPDTL ETIKKVDLCN YLSVNGLTAH
PHIEADGTVY NIGNCFGKNM SLAYNIVKIP PLQEEKSDPL AMSKVLVQFP SSERFKPSYV
HSFGMTENHF VFVETPVKIN LLKFLTSWSI RGSNYMDCFE SNDRMGTWFH LAAKNPGKYI
DHKFRTSAFN IFHHINCFED QGFIVVDLCT WKGHEFVYNY LYLANLRQNW EEVKKAALRA
PQPEVRRYVL PLDIHREEQG KNLVSLPYTT ATAVMCSDGT VWLEPEVLFS GPRQAFEFPQ
INYSKFNGKD YTFAYGLGLN HFVPDRICKL NVKSKETWIW QEPDAYPSEP LFVQSPDAED
EDDGVLLSIV VKPGVSQRPA FLLILKATDL TEIARAEVDV LIPLTLHGIY KP
