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P23440

- PDE6B_MOUSE

UniProt

P23440 - PDE6B_MOUSE

Protein

Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

Gene

Pde6b

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 128 (01 Oct 2014)
      Sequence version 3 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    This protein participates in processes of transmission and amplification of the visual signal. Necessary for the formation of a functional phosphodiesterase holoenzyme.

    Catalytic activityi

    Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.

    Cofactori

    Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions, while site 2 has a preference for magnesium and/or manganese ions By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei557 – 5571Proton donorBy similarity
    Metal bindingi561 – 5611Divalent metal cation 1By similarity
    Metal bindingi597 – 5971Divalent metal cation 1By similarity
    Metal bindingi598 – 5981Divalent metal cation 1By similarity
    Metal bindingi598 – 5981Divalent metal cation 2By similarity
    Metal bindingi718 – 7181Divalent metal cation 1By similarity

    GO - Molecular functioni

    1. 3',5'-cyclic-GMP phosphodiesterase activity Source: UniProtKB-EC
    2. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. cytosolic calcium ion homeostasis Source: Ensembl
    2. detection of light stimulus Source: MGI
    3. GMP metabolic process Source: Ensembl
    4. retina development in camera-type eye Source: MGI
    5. signal transduction Source: InterPro
    6. visual perception Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Sensory transduction, Vision

    Keywords - Ligandi

    cGMP, Metal-binding

    Enzyme and pathway databases

    ReactomeiREACT_188252. Activation of the phototransduction cascade.
    REACT_188266. Inactivation, recovery and regulation of the phototransduction cascade.
    REACT_221970. Ca2+ pathway.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (EC:3.1.4.35)
    Short name:
    GMP-PDE beta
    Gene namesi
    Name:Pde6b
    Synonyms:Mpb, Pdeb, rd
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 5

    Organism-specific databases

    MGIiMGI:97525. Pde6b.

    Subcellular locationi

    GO - Cellular componenti

    1. plasma membrane Source: Reactome

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Defects in Pde6b are the cause of retinal degeneration.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 853852Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit betaPRO_0000023350Add
    BLAST
    Propeptidei854 – 8563Removed in mature formBy similarityPRO_0000023351

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserineBy similarity
    Lipidationi853 – 8531S-geranylgeranyl cysteineBy similarity

    Keywords - PTMi

    Acetylation, Lipoprotein, Prenylation

    Proteomic databases

    MaxQBiP23440.
    PaxDbiP23440.
    PRIDEiP23440.

    PTM databases

    PhosphoSiteiP23440.

    Expressioni

    Gene expression databases

    BgeeiP23440.
    GenevestigatoriP23440.

    Interactioni

    Subunit structurei

    Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain.

    Structurei

    3D structure databases

    ProteinModelPortaliP23440.
    SMRiP23440. Positions 45-815.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini71 – 220150GAF 1Add
    BLAST
    Domaini252 – 429178GAF 2Add
    BLAST

    Sequence similaritiesi

    Contains 2 GAF domains.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG242608.
    GeneTreeiENSGT00750000117253.
    HOGENOMiHOG000007069.
    HOVERGENiHBG053539.
    InParanoidiQ80UF0.
    KOiK13756.
    OMAiGVVKKFQ.
    OrthoDBiEOG7BGHK1.
    TreeFamiTF316499.

    Family and domain databases

    Gene3Di1.10.1300.10. 1 hit.
    3.30.450.40. 3 hits.
    InterProiIPR003018. GAF.
    IPR029016. GAF_dom_like.
    IPR003607. HD/PDEase_dom.
    IPR023088. PDEase.
    IPR002073. PDEase_catalytic_dom.
    IPR023174. PDEase_CS.
    [Graphical view]
    PfamiPF01590. GAF. 2 hits.
    PF00233. PDEase_I. 1 hit.
    [Graphical view]
    PRINTSiPR00387. PDIESTERASE1.
    SMARTiSM00065. GAF. 2 hits.
    SM00471. HDc. 1 hit.
    [Graphical view]
    SUPFAMiSSF55781. SSF55781. 3 hits.
    PROSITEiPS00126. PDEASE_I. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: P23440-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSLSEEQVRS FLDGNPTFAH QYFGKKLSPE NVAGACEDGW LADCGSLREL    50
    CQVEESAALF ELVQDMQESV NMERVVFKIL RRLCTILHAD RCSLFMYRQR 100
    NGIAELATRL FSVQPDSLLE DCLVPPDSEI VFPLDIGIVG HVAQTKKMIN 150
    VQDVAECPHF SSFADELTDY VTKNILSTPI MNGKDVVAVI MAVNKLDGPC 200
    FTSEDEDVFT KYLNFATLNL KIYHLSYLHN CETRRGQVLL WSANKVFEEL 250
    TDIERQFHKA FYTVRAYLNC ERYSVGLLDM TKEKEFFDVW PVLMGEAQPY 300
    SGPRTPDGRE IVFYKVIDYI LHGKEDIKVI PTPPADHWAL ASGLPTYVAE 350
    SGFICNIMNA SADEMFNFQE GPLDDSGWVI KNVLSMPIVN KKEEIVGVAT 400
    FYNRKDGKPF DDQDEVLMES LTQFLGWSVL NTDTYDKMNK LENRKDIAQD 450
    MVLYHVRCDK DEIQEILPTR DRLGKEPADC EEDELGKILK EELPGPTKFD 500
    IYEFHFSDLE CTELELVKCG IQMYYELGVV RKFQIPQEVL VRFLFSVSKA 550
    YRRITYHNWR HGFNVAQTMF TLLMTGKLKS YYTDLEAFAM VTAGLCHDID 600
    HRGTNNLYQM KSQNPLAKLH GSSILERHHL EFGKFLLAEE SLNIYQNLNR 650
    RQHEHVIHLM DIAIIATDLA LYFKKRTMFQ KIVDESKNYE DKKSWVEYLS 700
    LETTRKEIVM AMMMTACDLS AITKPWEVQS KVALLVAAEF WEQGDLERTV 750
    LDQQPIPMMD RNKAAELPKL QVGFIDFVCT FVYKEFSRFH EEILPMFDRL 800
    QNNRKEWKAL ADEYEAKVKA LEEEKKKEED RVAAKKVGTE VCNGGPAPKS 850
    STCCIL 856
    Length:856
    Mass (Da):98,535
    Last modified:July 27, 2011 - v3
    Checksum:i209F3A936DD16D46
    GO
    Isoform 2 (identifier: P23440-2) [UniParc]FASTAAdd to Basket

    Also known as: Beta'

    The sequence of this isoform differs from the canonical sequence as follows:
         801-856: Missing.

    Show »
    Length:800
    Mass (Da):92,331
    Checksum:i23F1AC68F7CC7AF7
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti5 – 51E → G in CAA39439. (PubMed:1977087)Curated
    Sequence conflicti19 – 191A → S in CAA39439. (PubMed:1977087)Curated
    Sequence conflicti49 – 502EL → DV in CAA39439. (PubMed:1977087)Curated
    Sequence conflicti158 – 1581P → T in CAA39439. (PubMed:1977087)Curated
    Sequence conflicti176 – 1761L → C in CAA39439. (PubMed:1977087)Curated
    Sequence conflicti232 – 2321E → R in CAA39439. (PubMed:1977087)Curated
    Sequence conflicti236 – 2361G → S in CAA39439. (PubMed:1977087)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei801 – 85656Missing in isoform 2. CuratedVSP_004592Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X55968 mRNA. Translation: CAA39439.1.
    X60133 mRNA. Translation: CAA42719.1.
    AK044364 mRNA. Translation: BAC31885.1.
    CH466529 Genomic DNA. Translation: EDL20122.1.
    CCDSiCCDS19510.1. [P23440-1]
    PIRiS30762.
    RefSeqiNP_032832.2. NM_008806.2. [P23440-1]
    UniGeneiMm.1372.

    Genome annotation databases

    EnsembliENSMUST00000031456; ENSMUSP00000031456; ENSMUSG00000029491. [P23440-1]
    GeneIDi18587.
    KEGGimmu:18587.
    UCSCiuc008ynz.1. mouse. [P23440-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X55968 mRNA. Translation: CAA39439.1 .
    X60133 mRNA. Translation: CAA42719.1 .
    AK044364 mRNA. Translation: BAC31885.1 .
    CH466529 Genomic DNA. Translation: EDL20122.1 .
    CCDSi CCDS19510.1. [P23440-1 ]
    PIRi S30762.
    RefSeqi NP_032832.2. NM_008806.2. [P23440-1 ]
    UniGenei Mm.1372.

    3D structure databases

    ProteinModelPortali P23440.
    SMRi P23440. Positions 45-815.
    ModBasei Search...
    MobiDBi Search...

    PTM databases

    PhosphoSitei P23440.

    Proteomic databases

    MaxQBi P23440.
    PaxDbi P23440.
    PRIDEi P23440.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000031456 ; ENSMUSP00000031456 ; ENSMUSG00000029491 . [P23440-1 ]
    GeneIDi 18587.
    KEGGi mmu:18587.
    UCSCi uc008ynz.1. mouse. [P23440-1 ]

    Organism-specific databases

    CTDi 5158.
    MGIi MGI:97525. Pde6b.

    Phylogenomic databases

    eggNOGi NOG242608.
    GeneTreei ENSGT00750000117253.
    HOGENOMi HOG000007069.
    HOVERGENi HBG053539.
    InParanoidi Q80UF0.
    KOi K13756.
    OMAi GVVKKFQ.
    OrthoDBi EOG7BGHK1.
    TreeFami TF316499.

    Enzyme and pathway databases

    Reactomei REACT_188252. Activation of the phototransduction cascade.
    REACT_188266. Inactivation, recovery and regulation of the phototransduction cascade.
    REACT_221970. Ca2+ pathway.

    Miscellaneous databases

    NextBioi 294464.
    PROi P23440.
    SOURCEi Search...

    Gene expression databases

    Bgeei P23440.
    Genevestigatori P23440.

    Family and domain databases

    Gene3Di 1.10.1300.10. 1 hit.
    3.30.450.40. 3 hits.
    InterProi IPR003018. GAF.
    IPR029016. GAF_dom_like.
    IPR003607. HD/PDEase_dom.
    IPR023088. PDEase.
    IPR002073. PDEase_catalytic_dom.
    IPR023174. PDEase_CS.
    [Graphical view ]
    Pfami PF01590. GAF. 2 hits.
    PF00233. PDEase_I. 1 hit.
    [Graphical view ]
    PRINTSi PR00387. PDIESTERASE1.
    SMARTi SM00065. GAF. 2 hits.
    SM00471. HDc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55781. SSF55781. 3 hits.
    PROSITEi PS00126. PDEASE_I. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Retinal degeneration in the rd mouse is caused by a defect in the beta subunit of rod cGMP-phosphodiesterase."
      Bowes C., Li T., Danciger M., Baxter L.C., Applebury M.L., Farber D.B.
      Nature 347:677-680(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Strain: C57BL/6.
      Tissue: Retina.
    2. "Complete cDNA sequences of mouse rod photoreceptor cGMP phosphodiesterase alpha- and beta-subunits, and identification of beta'-, a putative beta-subunit isozyme produced by alternative splicing of the beta-subunit gene."
      Baehr W., Champagne M.S., Lee A.K., Pittler S.J.
      FEBS Lett. 278:107-114(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), ALTERNATIVE SPLICING (ISOFORM 2).
      Tissue: Retina.
    3. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Strain: C57BL/6J.
      Tissue: Retina.
    4. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

    Entry informationi

    Entry nameiPDE6B_MOUSE
    AccessioniPrimary (citable) accession number: P23440
    Secondary accession number(s): Q80UF0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1991
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 128 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3