Reviewed, UniProtKB/Swiss-Prot P35913 (PDE6B_HUMAN)

Names and origin

Protein names

Recommended name:
    Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
      Short name=GMP-PDE beta
    EC=3.1.4.35

Gene names

Name:	PDE6B
Synonyms:	PDEB

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	854 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	This protein participates in processes of transmission and amplification of the visual signal. Necessary for the formation of a functional phosphodiesterase holoenzyme.
Catalytic activity	Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
Subunit structure	Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain.
Subcellular location	Membrane; Lipid-anchor.
Involvement in disease	Defects in PDE6B are a cause of retinitis pigmentosa (RP) [MIM:268000]. RP leads to degeneration of retinal photoreceptor cells. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Defects in PDE6B are a cause of congenital stationary night blindness autosomal dominant type 2 (CSNBAD2) [MIM:163500]; also known as congenital stationary night blindness Rambusch type. Congenital stationary night blindness is a non-progressive retinal disorder characterized by impaired night vision. Ref.8
Sequence similarities	Belongs to the cyclic nucleotide phosphodiesterase family. Contains 2 GAF domains.

Ontologies

Keywords
Biological process	Sensory transduction Vision
Cellular component	Membrane
Coding sequence diversity	Alternative splicing Polymorphism
Disease	Congenital stationary night blindness Disease mutation Retinitis pigmentosa
Domain	Repeat
Ligand	cGMP
Molecular function	Hydrolase
PTM	Lipoprotein Prenylation
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	phototransduction, visible light Ref.11 Traceable author statement. Source: ProtInc signal transduction Inferred from electronic annotation. Source: InterPro
Cellular component	anchored to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3',5'-cyclic-GMP phosphodiesterase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P35913-1)

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.

Isoform 2 (identifier: P35913-2)

The sequence of this isoform differs from the canonical sequence as follows:
     835-835: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 851	851	Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta		PRO_0000023348
	Propeptide	852 – 854	3	Removed in mature form By similarity		PRO_0000023349
Regions
	Domain	71 – 220	150	GAF 1
	Domain	252 – 429	178	GAF 2
Amino acid modifications
	Lipidation	851	1	S-geranylgeranyl cysteine By similarity
Natural variations
	Alternative sequence	835	1	Missing in isoform 2.		VSP_036884
	Natural variant	74	1	R → C in RP; autosomal recessive.		VAR_009283
	Natural variant	166	1	E → K		VAR_009284
	Natural variant	212	1	Y → H		VAR_009285
	Natural variant	219	1	Y → H in RP; autosomal recessive.		VAR_009286
	Natural variant	228	1	L → H in RP; autosomal recessive and autosomal dominant. Ref.13		VAR_009287
	Natural variant	228	1	L → I		VAR_009288
	Natural variant	258	1	H → N in CSNBAD2. Ref.8		VAR_009289
	Natural variant	320	1	V → I: dbSNP rs10902758. Ref.2 Ref.3 Ref.5 Ref.7 Ref.10		VAR_054868
	Natural variant	527	1	L → P in RP; autosomal recessive.		VAR_009290
	Natural variant	535	1	I → N in RP; autosomal recessive. Ref.16		VAR_009291
	Natural variant	552	1	R → Q in RP; autosomal recessive. Ref.15		VAR_009292
	Natural variant	557	1	H → Y in RP; autosomal dominant. Ref.11		VAR_006050
	Natural variant	576	1	G → D in RP; autosomal recessive. Ref.12		VAR_006051
	Natural variant	654	1	E → D: dbSNP rs17849286. Ref.5 Ref.7		VAR_054869
	Natural variant	699	1	L → R in RP; autosomal recessive. Ref.14		VAR_006052
	Natural variant	854	1	L → R in RP; autosomal recessive.		VAR_009293
Experimental info
	Sequence conflict	33 – 35	3	AAA → GRG in CAA44569. Ref.1
	Sequence conflict	33 – 35	3	AAA → GRG in CAA46932. Ref.2
	Sequence conflict	33 – 35	3	AAA → GRG in AAB22690. Ref.3
	Sequence conflict	315	1	K → Q in CAA44569. Ref.1
	Sequence conflict	320	1	V → L in CAA44569. Ref.1
	Sequence conflict	360	1	A → R in CAA44569. Ref.1
	Sequence conflict	698	1	Y → I in CAA44569. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified April 14, 2009. Version 2. Checksum: BB11A519BE88C9DF	FASTA	854	98,336
	10 20 30 40 50 60 MSLSEEQARS FLDQNPDFAR QYFGKKLSPE NVAAACEDGC PPDCDSLRDL CQVEESTALL 70 80 90 100 110 120 ELVQDMQESI NMERVVFKVL RRLCTLLQAD RCSLFMYRQR NGVAELATRL FSVQPDSVLE 130 140 150 160 170 180 DCLVPPDSEI VFPLDIGVVG HVAQTKKMVN VEDVAECPHF SSFADELTDY KTKNMLATPI 190 200 210 220 230 240 MNGKDVVAVI MAVNKLNGPF FTSEDEDVFL KYLNFATLYL KIYHLSYLHN CETRRGQVLL 250 260 270 280 290 300 WSANKVFEEL TDIERQFHKA FYTVRAYLNC ERYSVGLLDM TKEKEFFDVW SVLMGESQPY 310 320 330 340 350 360 SGPRTPDGRE IVFYKVIDYV LHGKEEIKVI PTPSADHWAL ASGLPSYVAE SGFICNIMNA 370 380 390 400 410 420 SADEMFKFQE GALDDSGWLI KNVLSMPIVN KKEEIVGVAT FYNRKDGKPF DEQDEVLMES 430 440 450 460 470 480 LTQFLGWSVM NTDTYDKMNK LENRKDIAQD MVLYHVKCDR DEIQLILPTR ARLGKEPADC 490 500 510 520 530 540 DEDELGEILK EELPGPTTFD IYEFHFSDLE CTELDLVKCG IQMYYELGVV RKFQIPQEVL 550 560 570 580 590 600 VRFLFSISKG YRRITYHNWR HGFNVAQTMF TLLMTGKLKS YYTDLEAFAM VTAGLCHDID 610 620 630 640 650 660 HRGTNNLYQM KSQNPLAKLH GSSILERHHL EFGKFLLSEE TLNIYQNLNR RQHEHVIHLM 670 680 690 700 710 720 DIAIIATDLA LYFKKRAMFQ KIVDESKNYQ DKKSWVEYLS LETTRKEIVM AMMMTACDLS 730 740 750 760 770 780 AITKPWEVQS KVALLVAAEF WEQGDLERTV LDQQPIPMMD RNKAAELPKL QVGFIDFVCT 790 800 810 820 830 840 FVYKEFSRFH EEILPMFDRL QNNRKEWKAL ADEYEAKVKA LEEKEEEERV AAKKVGTEIC 850 NGGPAPKSST CCIL
	Isoform 2. Checksum: 1EE848D6E7BAB8BE	FASTA	853	98,237
	10 20 30 40 50 60 MSLSEEQARS FLDQNPDFAR QYFGKKLSPE NVAAACEDGC PPDCDSLRDL CQVEESTALL 70 80 90 100 110 120 ELVQDMQESI NMERVVFKVL RRLCTLLQAD RCSLFMYRQR NGVAELATRL FSVQPDSVLE 130 140 150 160 170 180 DCLVPPDSEI VFPLDIGVVG HVAQTKKMVN VEDVAECPHF SSFADELTDY KTKNMLATPI 190 200 210 220 230 240 MNGKDVVAVI MAVNKLNGPF FTSEDEDVFL KYLNFATLYL KIYHLSYLHN CETRRGQVLL 250 260 270 280 290 300 WSANKVFEEL TDIERQFHKA FYTVRAYLNC ERYSVGLLDM TKEKEFFDVW SVLMGESQPY 310 320 330 340 350 360 SGPRTPDGRE IVFYKVIDYV LHGKEEIKVI PTPSADHWAL ASGLPSYVAE SGFICNIMNA 370 380 390 400 410 420 SADEMFKFQE GALDDSGWLI KNVLSMPIVN KKEEIVGVAT FYNRKDGKPF DEQDEVLMES 430 440 450 460 470 480 LTQFLGWSVM NTDTYDKMNK LENRKDIAQD MVLYHVKCDR DEIQLILPTR ARLGKEPADC 490 500 510 520 530 540 DEDELGEILK EELPGPTTFD IYEFHFSDLE CTELDLVKCG IQMYYELGVV RKFQIPQEVL 550 560 570 580 590 600 VRFLFSISKG YRRITYHNWR HGFNVAQTMF TLLMTGKLKS YYTDLEAFAM VTAGLCHDID 610 620 630 640 650 660 HRGTNNLYQM KSQNPLAKLH GSSILERHHL EFGKFLLSEE TLNIYQNLNR RQHEHVIHLM 670 680 690 700 710 720 DIAIIATDLA LYFKKRAMFQ KIVDESKNYQ DKKSWVEYLS LETTRKEIVM AMMMTACDLS 730 740 750 760 770 780 AITKPWEVQS KVALLVAAEF WEQGDLERTV LDQQPIPMMD RNKAAELPKL QVGFIDFVCT 790 800 810 820 830 840 FVYKEFSRFH EEILPMFDRL QNNRKEWKAL ADEYEAKVKA LEEKEEEERV AAKKGTEICN 850 GGPAPKSSTC CIL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genomic organization and complete sequence of the human gene encoding the beta-subunit of the cGMP phosphodiesterase and its localisation to 4p16.3." Weber B., Riess O., Hutchinson G., Collins C., Lin B., Kowbel D., Andrew S., Schappert K.T., Hayden M.R. Nucleic Acids Res. 19:6263-6268(1991) [PubMed: 1720239] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Structural studies of cDNA and the gene for the beta-subunit of cGMP phosphodiesterase from human retina." Khramtsov N.V., Feshchenko E.A., Suslova V.A., Terpugov B.E., Rakitina T.V., Atabekova N.V., Shmukler B.E., Lipkin V.M. Bioorg. Khim. 18:1551-1554(1992) [PubMed: 1338685] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT ILE-320. Tissue: Retinal rod cell.
[3]	"The human beta-subunit of rod photoreceptor cGMP phosphodiesterase: complete retinal cDNA sequence and evidence for expression in brain." Collins C., Hutchinson G., Kowbel D., Riess O., Weber B., Hayden M.R. Genomics 13:698-704(1992) [PubMed: 1322354] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT ILE-320. Tissue: Retina.
[4]	"The human rod photoreceptor cGMP phosphodiesterase beta-subunit. Structural studies of its cDNA and gene." Khramtsov N.V., Feshchenko E.A., Suslova V.A., Shmukler B.E., Terpugov B.E., Rakitina T.V., Atabekova N.V., Lipkin V.M. FEBS Lett. 327:275-278(1993) [PubMed: 8394243] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). Tissue: Retina.
[5]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANTS ILE-320 AND ASP-654.
[6]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed: 15815621] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANTS ILE-320 AND ASP-654. Tissue: Eye.
[8]	"Heterozygous missense mutation in the rod cGMP phosphodiesterase beta-subunit gene in autosomal dominant stationary night blindness." Gal A., Orth U., Baehr W., Schwinger E., Rosenberg T. Nat. Genet. 7:64-68(1994) [PubMed: 8075643] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 197-297, VARIANT CSNBAD2 ASN-258.
[9]	Erratum Gal A., Orth U., Baehr W., Schwinger E., Rosenberg T. Nat. Genet. 7:551-551(1994) [PubMed: 7951329] [Abstract]
[10]	"Organization of the gene for the beta-subunit of human photoreceptor cyclic GMP phosphodiesterase." Suslova V.A., Suslov O.N., Kim E.E., Lipkin V.M. Bioorg. Khim. 22:256-263(1996) [PubMed: 8768262] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 238-854, VARIANT ILE-320. Tissue: Retinal rod cell.
[11]	"Recessive mutations in the gene encoding the beta-subunit of rod phosphodiesterase in patients with retinitis pigmentosa." McLaughlin M.E., Sandberg M.A., Berson E.L., Dryja T.P. Nat. Genet. 4:130-134(1993) [PubMed: 8394174] [Abstract] Cited for: VARIANT RP TYR-557.
[12]	"Mutations in the PDE6B gene in autosomal recessive retinitis pigmentosa." Danciger M., Blaney J., Gao Y.Q., Zhao D.Y., Heckenlively J.R., Jacobson S.G., Farber D.B. Genomics 30:1-7(1995) [PubMed: 8595886] [Abstract] Cited for: VARIANT RP ASP-576.
[13]	"Screening of the PDE6B gene in patients with autosomal dominant retinitis pigmentosa." Gao Y.Q., Danciger M., Zhao D.Y., Blaney J., Piriev N.I., Shih J., Jacobson S.G., Heckenlively J.H., Farber D.B. Exp. Eye Res. 62:149-154(1996) [PubMed: 8698075] [Abstract] Cited for: VARIANT RP HIS-228, VARIANTS LYS-166 AND HIS-212.
[14]	"A novel mutation in exon 17 of the beta-subunit of rod phosphodiesterase in two RP sisters of a consanguineous family." Valverde D., Solans T., Grinberg D., Balcells S., Vilageliu L., Bayes M., Chivelet P., Besmond C., Goossens M., Gonzalez-Duarte R., Baiget M. Hum. Genet. 97:35-38(1996) [PubMed: 8557257] [Abstract] Cited for: VARIANT RP ARG-699.
[15]	"Identification of a novel R552Q mutation in exon 13 of the beta-subunit of rod phosphodiesterase gene in a Spanish family with autosomal recessive retinitis pigmentosa." Valverde D., Baiget M., Seminago R., del Rio E., Garcia-Sandoval B., del Rio T., Bayes M., Balcells S., Martinez A., Grinberg D., Ayuso C. Hum. Mutat. 8:393-394(1996) [PubMed: 8956055] [Abstract] Cited for: VARIANT RP GLN-552.
[16]	"A novel homozygous Ile535Asn mutation in the rod cGMP phosphodiesterase beta-subunit gene in two brothers of a Japanese family with autosomal recessive retinitis pigmentosa." Saga M., Mashima Y., Akeo K., Kudoh J., Oguchi Y., Shimizu N. Curr. Eye Res. 17:332-335(1998) [PubMed: 9543643] [Abstract] Cited for: VARIANT RP ASN-535.
+	Additional computationally mapped references.

Web resources

Mutations of the PDE6A/B/G genes

Retina International's Scientific Newsletter

GeneReviews

Cross-references

Sequence databases
EMBLGenBankDDBJ	X62692 , X62693, X62694, X62695 Genomic DNA. Translation: CAA44569.1. X66142 mRNA. Translation: CAA46932.1. S41458 mRNA. Translation: AAB22690.1. BT009794 mRNA. Translation: AAP88796.1. AC107464 Genomic DNA. No translation available. BC000249 mRNA. Translation: AAH00249.1. X90587 , X90588, X90589, X90590 Genomic DNA. Translation: CAA62215.1.
IPI	IPI00784027. IPI00922666.
PIR	A42828.
RefSeq	NP_000274.2. NP_001138763.1. NP_001138764.1.
UniGene	Hs.59872 Hs.623810 Hs.654544
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	P35913.
PTM databases
PhosphoSite	P35913.
Proteomic databases
PRIDE	P35913.
Genome annotation databases
Ensembl	ENST00000255622; ENSP00000255622; ENSG00000133256; Homo sapiens. [Genome view] ENST00000429163; ENSP00000406334; ENSG00000133256; Homo sapiens. [Genome view]
GeneID	5158.
KEGG	hsa:5158.
UCSC	uc003gao.2. human. uc003gap.1. human.
Organism-specific databases
CTD	5158.
GeneCards	GC04P000609.
H-InvDB	HIX0003999. HIX0031458. HIX0031649.
HGNC	HGNC:8786. PDE6B.
MIM	163500. phenotype. 180072. gene. 268000. phenotype.
Orphanet	215. Night blindness, stationary, congenital. 791. Retinitis pigmentosa.
PharmGKB	PA33134.
GenAtlas	Search...
Phylogenomic databases
HOVERGEN	P35913.
OMA	FQIPQEV.
Enzyme and pathway databases
BRENDA	3.1.4.35. 247.
Pathway_Interaction_DB	rhodopsin_pathway. Visual signal transduction: Rods.
Gene expression databases
ArrayExpress	P35913.
Bgee	P35913.
CleanEx	HS_PDE6B.
Genevestigator	P35913.
GermOnline	ENSG00000133256. Homo sapiens.
Family and domain databases
InterPro	IPR003018. GAF. IPR003607. Met-dep_phosphohydro_HD. IPR002073. PDEase. [Graphical view]
Pfam	PF01590. GAF. 2 hits. PF00233. PDEase_I. 1 hit. [Graphical view]
PRINTS	PR00387. PDIESTERASE1.
SMART	SM00065. GAF. 2 hits. SM00471. HDc. 1 hit. [Graphical view]
PROSITE	PS00126. PDEASE_I. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	19954.
SOURCE	Search...

Entry information

Entry name

PDE6B_HUMAN

Accession

Primary (citable) accession number: P35913
Secondary accession number(s): Q53XN5, Q9BWH5, Q9UD49

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	April 14, 2009
Last modified:	November 3, 2009
This is version 105 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.