PDE6B_MOUSE
ID PDE6B_MOUSE Reviewed; 856 AA.
AC P23440; Q80UF0;
DT 01-NOV-1991, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 3.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta {ECO:0000305};
DE Short=GMP-PDE beta;
DE EC=3.1.4.35 {ECO:0000250|UniProtKB:P35913};
DE Flags: Precursor;
GN Name=Pde6b {ECO:0000312|MGI:MGI:97525}; Synonyms=Mpb, Pdeb, rd;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC STRAIN=C57BL/6J; TISSUE=Retina;
RX PubMed=1977087; DOI=10.1038/347677a0;
RA Bowes C., Li T., Danciger M., Baxter L.C., Applebury M.L., Farber D.B.;
RT "Retinal degeneration in the rd mouse is caused by a defect in the beta
RT subunit of rod cGMP-phosphodiesterase.";
RL Nature 347:677-680(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), ALTERNATIVE SPLICING (ISOFORM 2),
RP AND FUNCTION.
RC TISSUE=Retina;
RX PubMed=1847109; DOI=10.1016/0014-5793(91)80095-k;
RA Baehr W., Champagne M.S., Lee A.K., Pittler S.J.;
RT "Complete cDNA sequences of mouse rod photoreceptor cGMP phosphodiesterase
RT alpha- and beta-subunits, and identification of beta'-, a putative beta-
RT subunit isozyme produced by alternative splicing of the beta-subunit
RT gene.";
RL FEBS Lett. 278:107-114(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=C57BL/6J; TISSUE=Retina;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=30240620; DOI=10.1016/j.isci.2018.08.010;
RA Ota W., Nakane Y., Hattar S., Yoshimura T.;
RT "Impaired Circadian Photoentrainment in Opn5-Null Mice.";
RL IScience 6:299-305(2018).
CC -!- FUNCTION: Rod-specific cGMP phosphodiesterase that catalyzes the
CC hydrolysis of 3',5'-cyclic GMP (By similarity). Necessary for the
CC formation of a functional phosphodiesterase holoenzyme
CC (PubMed:1847109). Involved in retinal circadian rhythm photoentrainment
CC via modulation of UVA and orange light-induced phase-shift of the
CC retina clock (PubMed:30240620). May participate in processes of
CC transmission and amplification of the visual signal (By similarity).
CC {ECO:0000250|UniProtKB:P35913, ECO:0000269|PubMed:1847109,
CC ECO:0000269|PubMed:30240620}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3',5'-cyclic GMP + H2O = GMP + H(+); Xref=Rhea:RHEA:16957,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57746,
CC ChEBI:CHEBI:58115; EC=3.1.4.35;
CC Evidence={ECO:0000250|UniProtKB:P35913};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16958;
CC Evidence={ECO:0000250|UniProtKB:P35913};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250};
CC Note=Binds 2 divalent metal cations per subunit. Site 1 may
CC preferentially bind zinc ions, while site 2 has a preference for
CC magnesium and/or manganese ions. {ECO:0000250};
CC -!- SUBUNIT: Oligomer composed of two catalytic chains (alpha and beta), an
CC inhibitory chain (gamma) and the delta chain.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000250|UniProtKB:P35913}; Lipid-
CC anchor {ECO:0000250|UniProtKB:P35913}. Cell projection, cilium,
CC photoreceptor outer segment {ECO:0000250|UniProtKB:P35913}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=P23440-1; Sequence=Displayed;
CC Name=2; Synonyms=Beta';
CC IsoId=P23440-2; Sequence=VSP_004592;
CC -!- DISEASE: Note=Defects in Pde6b are the cause of retinal degeneration.
CC {ECO:0000269|PubMed:1977087}.
CC -!- DISRUPTION PHENOTYPE: Abolishes the retinal photoreceptor layer, outer
CC nuclear layer, and outer plexiform layer in the retinal ultrastructure
CC (PubMed:30240620). Loss of Opn1sw, Opn1mw and Rho expression in the
CC retina (PubMed:30240620). Reduced rate of circadian photoentrainment,
CC UVA and orange light-induced phase-shift response and Fos expression in
CC the suprachiasmatic nuclei (SCN) in the brain (PubMed:30240620). Pde6b
CC and Opn5 double knockout mice also show loss of retinal ultrastructures
CC and a more severe reduction in the rate of circadian photoentrainment,
CC light-induced phase-shift response and Fos expression in the SCN
CC (PubMed:30240620). {ECO:0000269|PubMed:30240620}.
CC -!- SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase family.
CC {ECO:0000305}.
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DR EMBL; X55968; CAA39439.1; -; mRNA.
DR EMBL; X60133; CAA42719.1; -; mRNA.
DR EMBL; AK044364; BAC31885.1; -; mRNA.
DR EMBL; CH466529; EDL20122.1; -; Genomic_DNA.
DR CCDS; CCDS19510.1; -. [P23440-1]
DR PIR; S30762; S30762.
DR RefSeq; NP_032832.2; NM_008806.2. [P23440-1]
DR AlphaFoldDB; P23440; -.
DR SMR; P23440; -.
DR BioGRID; 202084; 20.
DR STRING; 10090.ENSMUSP00000031456; -.
DR iPTMnet; P23440; -.
DR PhosphoSitePlus; P23440; -.
DR MaxQB; P23440; -.
DR PaxDb; P23440; -.
DR PRIDE; P23440; -.
DR ProteomicsDB; 288016; -. [P23440-1]
DR ProteomicsDB; 288017; -. [P23440-2]
DR Antibodypedia; 8018; 115 antibodies from 26 providers.
DR DNASU; 18587; -.
DR Ensembl; ENSMUST00000031456; ENSMUSP00000031456; ENSMUSG00000029491. [P23440-1]
DR GeneID; 18587; -.
DR KEGG; mmu:18587; -.
DR UCSC; uc008ynz.1; mouse. [P23440-1]
DR CTD; 5158; -.
DR MGI; MGI:97525; Pde6b.
DR VEuPathDB; HostDB:ENSMUSG00000029491; -.
DR eggNOG; KOG3689; Eukaryota.
DR GeneTree; ENSGT00940000156471; -.
DR HOGENOM; CLU_006980_2_0_1; -.
DR InParanoid; P23440; -.
DR OMA; PGPTKFE; -.
DR OrthoDB; 904682at2759; -.
DR PhylomeDB; P23440; -.
DR TreeFam; TF316499; -.
DR Reactome; R-MMU-2485179; Activation of the phototransduction cascade.
DR Reactome; R-MMU-2514859; Inactivation, recovery and regulation of the phototransduction cascade.
DR Reactome; R-MMU-4086398; Ca2+ pathway.
DR BioGRID-ORCS; 18587; 3 hits in 71 CRISPR screens.
DR ChiTaRS; Pde6b; mouse.
DR PRO; PR:P23440; -.
DR Proteomes; UP000000589; Chromosome 5.
DR RNAct; P23440; protein.
DR Bgee; ENSMUSG00000029491; Expressed in retinal neural layer and 20 other tissues.
DR Genevisible; P23440; MM.
DR GO; GO:0001750; C:photoreceptor outer segment; IDA:MGI.
DR GO; GO:0042622; C:photoreceptor outer segment membrane; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; TAS:Reactome.
DR GO; GO:0047555; F:3',5'-cyclic-GMP phosphodiesterase activity; IEA:UniProtKB-EC.
DR GO; GO:0004114; F:3',5'-cyclic-nucleotide phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009583; P:detection of light stimulus; IMP:MGI.
DR GO; GO:0043153; P:entrainment of circadian clock by photoperiod; IMP:UniProtKB.
DR GO; GO:0060041; P:retina development in camera-type eye; IMP:MGI.
DR GO; GO:1990009; P:retinal cell apoptotic process; ISO:MGI.
DR GO; GO:0007165; P:signal transduction; IBA:GO_Central.
DR GO; GO:0007601; P:visual perception; IEA:UniProtKB-KW.
DR CDD; cd00077; HDc; 1.
DR Gene3D; 1.10.1300.10; -; 1.
DR Gene3D; 3.30.450.40; -; 2.
DR InterPro; IPR003018; GAF.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR023088; PDEase.
DR InterPro; IPR002073; PDEase_catalytic_dom.
DR InterPro; IPR036971; PDEase_catalytic_dom_sf.
DR InterPro; IPR023174; PDEase_CS.
DR Pfam; PF01590; GAF; 2.
DR Pfam; PF00233; PDEase_I; 1.
DR PRINTS; PR00387; PDIESTERASE1.
DR SMART; SM00065; GAF; 2.
DR SMART; SM00471; HDc; 1.
DR PROSITE; PS00126; PDEASE_I_1; 1.
DR PROSITE; PS51845; PDEASE_I_2; 1.
PE 2: Evidence at transcript level;
KW Acetylation; Alternative splicing; Cell projection; cGMP; Hydrolase;
KW Lipoprotein; Membrane; Metal-binding; Prenylation; Reference proteome;
KW Repeat; Sensory transduction; Vision.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P23439"
FT CHAIN 2..853
FT /note="Rod cGMP-specific 3',5'-cyclic phosphodiesterase
FT subunit beta"
FT /id="PRO_0000023350"
FT PROPEP 854..856
FT /note="Removed in mature form"
FT /evidence="ECO:0000250"
FT /id="PRO_0000023351"
FT DOMAIN 71..220
FT /note="GAF 1"
FT DOMAIN 252..429
FT /note="GAF 2"
FT DOMAIN 481..814
FT /note="PDEase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01192"
FT ACT_SITE 557
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 561
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 597
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 598
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 598
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 718
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:P23439"
FT LIPID 853
FT /note="S-geranylgeranyl cysteine"
FT /evidence="ECO:0000250"
FT VAR_SEQ 801..856
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_004592"
FT CONFLICT 5
FT /note="E -> G (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
FT CONFLICT 19
FT /note="A -> S (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
FT CONFLICT 49..50
FT /note="EL -> DV (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
FT CONFLICT 158
FT /note="P -> T (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
FT CONFLICT 176
FT /note="L -> C (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
FT CONFLICT 232
FT /note="E -> R (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
FT CONFLICT 236
FT /note="G -> S (in Ref. 1; CAA39439)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 856 AA; 98535 MW; 209F3A936DD16D46 CRC64;
MSLSEEQVRS FLDGNPTFAH QYFGKKLSPE NVAGACEDGW LADCGSLREL CQVEESAALF
ELVQDMQESV NMERVVFKIL RRLCTILHAD RCSLFMYRQR NGIAELATRL FSVQPDSLLE
DCLVPPDSEI VFPLDIGIVG HVAQTKKMIN VQDVAECPHF SSFADELTDY VTKNILSTPI
MNGKDVVAVI MAVNKLDGPC FTSEDEDVFT KYLNFATLNL KIYHLSYLHN CETRRGQVLL
WSANKVFEEL TDIERQFHKA FYTVRAYLNC ERYSVGLLDM TKEKEFFDVW PVLMGEAQPY
SGPRTPDGRE IVFYKVIDYI LHGKEDIKVI PTPPADHWAL ASGLPTYVAE SGFICNIMNA
SADEMFNFQE GPLDDSGWVI KNVLSMPIVN KKEEIVGVAT FYNRKDGKPF DDQDEVLMES
LTQFLGWSVL NTDTYDKMNK LENRKDIAQD MVLYHVRCDK DEIQEILPTR DRLGKEPADC
EEDELGKILK EELPGPTKFD IYEFHFSDLE CTELELVKCG IQMYYELGVV RKFQIPQEVL
VRFLFSVSKA YRRITYHNWR HGFNVAQTMF TLLMTGKLKS YYTDLEAFAM VTAGLCHDID
HRGTNNLYQM KSQNPLAKLH GSSILERHHL EFGKFLLAEE SLNIYQNLNR RQHEHVIHLM
DIAIIATDLA LYFKKRTMFQ KIVDESKNYE DKKSWVEYLS LETTRKEIVM AMMMTACDLS
AITKPWEVQS KVALLVAAEF WEQGDLERTV LDQQPIPMMD RNKAAELPKL QVGFIDFVCT
FVYKEFSRFH EEILPMFDRL QNNRKEWKAL ADEYEAKVKA LEEEKKKEED RVAAKKVGTE
VCNGGPAPKS STCCIL
