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Protein

cGMP-inhibited 3',5'-cyclic phosphodiesterase B

Gene

PDE3B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. May play a role in fat metabolism. Regulates cAMP binding of RAPGEF3. Through simultaneous binding to RAPGEF3 and PIK3R6 assembles a signaling complex in which the PI3K gamma complex is activated by RAPGEF3 and which is involved in angiogenesis.2 Publications

Catalytic activityi

Nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.

Cofactori

a divalent metal cation1 PublicationNote: 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.1 Publication

Enzyme regulationi

Inhibited by cGMP.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei737Proton donorBy similarity1
Metal bindingi741Divalent metal cation 11
Metal bindingi821Divalent metal cation 11
Metal bindingi822Divalent metal cation 11
Metal bindingi822Divalent metal cation 21
Metal bindingi937Divalent metal cation 11

GO - Molecular functioni

GO - Biological processi

  • angiogenesis Source: UniProtKB-KW
  • cAMP catabolic process Source: BHF-UCL
  • cellular response to insulin stimulus Source: BHF-UCL
  • negative regulation of angiogenesis Source: UniProtKB
  • negative regulation of cAMP-mediated signaling Source: BHF-UCL
  • negative regulation of cell adhesion Source: BHF-UCL
  • negative regulation of cell adhesion mediated by integrin Source: BHF-UCL
  • negative regulation of lipid catabolic process Source: BHF-UCL
  • signal transduction Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Angiogenesis

Keywords - Ligandi

cAMP, cGMP, Metal-binding

Enzyme and pathway databases

BioCyciZFISH:HS07803-MONOMER.
BRENDAi3.1.4.17. 2681.
ReactomeiR-HSA-165160. PDE3B signalling.
R-HSA-418457. cGMP effects.
R-HSA-418555. G alpha (s) signalling events.
SignaLinkiQ13370.
SIGNORiQ13370.

Names & Taxonomyi

Protein namesi
Recommended name:
cGMP-inhibited 3',5'-cyclic phosphodiesterase B (EC:3.1.4.17)
Alternative name(s):
CGIPDE1
Short name:
CGIP1
Cyclic GMP-inhibited phosphodiesterase B
Short name:
CGI-PDE B
Gene namesi
Name:PDE3B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:8779. PDE3B.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei88 – 108HelicalSequence analysisAdd BLAST21
Transmembranei117 – 137HelicalSequence analysisAdd BLAST21
Transmembranei152 – 172HelicalSequence analysisAdd BLAST21
Transmembranei192 – 212HelicalSequence analysisAdd BLAST21
Transmembranei220 – 240HelicalSequence analysisAdd BLAST21
Transmembranei247 – 267HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

  • cytosol Source: Reactome
  • endoplasmic reticulum Source: BHF-UCL
  • Golgi apparatus Source: BHF-UCL
  • guanyl-nucleotide exchange factor complex Source: BHF-UCL
  • integral component of membrane Source: UniProtKB-KW
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi2R → A: Abolishes interaction with RAPGEF3. 1 Publication1
Mutagenesisi3R → A: Abolishes interaction with RAPGEF3. 1 Publication1
Mutagenesisi6R → A: Abolishes interaction with RAPGEF3. 1 Publication1
Mutagenesisi8A → D: Impairs interaction with RAPGEF3. 1 Publication1
Mutagenesisi9K → A: Abolishes interaction with RAPGEF3. 1 Publication1
Mutagenesisi10A → D: Impairss interaction with RAPGEF3. 1 Publication1
Mutagenesisi12R → A: Abolishes interaction with RAPGEF3. 1 Publication1
Mutagenesisi439R → A: Impairss interaction with PIK3R6. 1 Publication1
Mutagenesisi440R → A: Impairss interaction with PIK3R6. 1 Publication1
Mutagenesisi445S → A: Impairss interaction with PIK3R6. 1 Publication1
Mutagenesisi449P → A: Impairss interaction with PIK3R6. 1 Publication1

Organism-specific databases

DisGeNETi5140.
OpenTargetsiENSG00000152270.
PharmGKBiPA33127.

Chemistry databases

ChEMBLiCHEMBL290.
DrugBankiDB00201. Caffeine.
GuidetoPHARMACOLOGYi1299.

Polymorphism and mutation databases

BioMutaiPDE3B.
DMDMi143811435.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001988021 – 1112cGMP-inhibited 3',5'-cyclic phosphodiesterase BAdd BLAST1112

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei13PhosphoserineBy similarity1
Modified residuei295Phosphoserine; by PKB/AKT1 or PKB/AKT2By similarity1
Modified residuei296PhosphoserineBy similarity1
Modified residuei442PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ13370.
MaxQBiQ13370.
PaxDbiQ13370.
PeptideAtlasiQ13370.
PRIDEiQ13370.

PTM databases

iPTMnetiQ13370.
PhosphoSitePlusiQ13370.

Expressioni

Tissue specificityi

Abundant in adipose tissues.

Gene expression databases

BgeeiENSG00000152270.
CleanExiHS_PDE3B.
GenevisibleiQ13370. HS.

Organism-specific databases

HPAiCAB009497.
HPA024342.

Interactioni

Subunit structurei

Interacts with PIK3CG (By similarity). Interacts with RAPGEF3 and PIK3R6.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PIK3CGP487363EBI-6172856,EBI-1030384
PIK3R6Q5UE933EBI-6172856,EBI-6172907
RAPGEF3O953988EBI-6172856,EBI-6172806

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111166. 27 interactors.
IntActiQ13370. 3 interactors.
STRINGi9606.ENSP00000282096.

Chemistry databases

BindingDBiQ13370.

Structurei

Secondary structure

11112
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi662 – 674Combined sources13
Helixi681 – 688Combined sources8
Helixi689 – 694Combined sources6
Helixi695 – 706Combined sources12
Helixi709 – 712Combined sources4
Helixi717 – 728Combined sources12
Beta strandi735 – 738Combined sources4
Helixi739 – 752Combined sources14
Helixi802 – 804Combined sources3
Helixi808 – 820Combined sources13
Turni821 – 824Combined sources4
Helixi830 – 835Combined sources6
Helixi839 – 843Combined sources5
Turni844 – 846Combined sources3
Helixi849 – 863Combined sources15
Helixi866 – 868Combined sources3
Turni870 – 873Combined sources4
Helixi876 – 891Combined sources16
Helixi895 – 897Combined sources3
Helixi898 – 909Combined sources12
Beta strandi911 – 913Combined sources3
Helixi922 – 937Combined sources16
Helixi940 – 942Combined sources3
Helixi945 – 968Combined sources24
Helixi984 – 994Combined sources11
Helixi996 – 1005Combined sources10
Beta strandi1012 – 1015Combined sources4
Beta strandi1055 – 1058Combined sources4
Helixi1060 – 1072Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SO2X-ray2.40A/B/C/D654-1073[»]
1SOJX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L654-1073[»]
ProteinModelPortaliQ13370.
SMRiQ13370.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13370.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 25Interaction with RAPGEF31 PublicationAdd BLAST25
Regioni436 – 460Interaction with PIK3R61 PublicationAdd BLAST25
Regioni713 – 1072CatalyticBy similarityAdd BLAST360

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1077 – 1080Poly-Glu4

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IEGG. Eukaryota.
ENOG410XT2V. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000060144.
HOVERGENiHBG053541.
KOiK13296.
OMAiCAFFFLT.
OrthoDBiEOG091G0BTI.
PhylomeDBiQ13370.
TreeFamiTF329631.

Family and domain databases

Gene3Di1.10.1300.10. 2 hits.
InterProiIPR003607. HD/PDEase_dom.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PfamiPF00233. PDEase_I. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
[Graphical view]
PROSITEiPS00126. PDEASE_I. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13370-1) [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

        10         20         30         40         50
MRRDERDAKA MRSLQPPDGA GSPPESLRNG YVKSCVSPLR QDPPRGFFFH
60 70 80 90 100
LCRFCNVELR PPPASPQQPR RCSPFCRARL SLGALAAFVL ALLLGAEPES
110 120 130 140 150
WAAGAAWLRT LLSVCSHSLS PLFSIACAFF FLTCFLTRTK RGPGPGRSCG
160 170 180 190 200
SWWLLALPAC CYLGDFLVWQ WWSWPWGDGD AGSAAPHTPP EAAAGRLLLV
210 220 230 240 250
LSCVGLLLTL AHPLRLRHCV LVLLLASFVW WVSFTSLGSL PSALRPLLSG
260 270 280 290 300
LVGGAGCLLA LGLDHFFQIR EAPLHPRLSS AAEEKVPVIR PRRRSSCVSL
310 320 330 340 350
GETAASYYGS CKIFRRPSLP CISREQMILW DWDLKQWYKP HYQNSGGGNG
360 370 380 390 400
VDLSVLNEAR NMVSDLLTDP SLPPQVISSL RSISSLMGAF SGSCRPKINP
410 420 430 440 450
LTPFPGFYPC SEIEDPAEKG DRKLNKGLNR NSLPTPQLRR SSGTSGLLPV
460 470 480 490 500
EQSSRWDRNN GKRPHQEFGI SSQGCYLNGP FNSNLLTIPK QRSSSVSLTH
510 520 530 540 550
HVGLRRAGVL SSLSPVNSSN HGPVSTGSLT NRSPIEFPDT ADFLNKPSVI
560 570 580 590 600
LQRSLGNAPN TPDFYQQLRN SDSNLCNSCG HQMLKYVSTS ESDGTDCCSG
610 620 630 640 650
KSGEEENIFS KESFKLMETQ QEEETEKKDS RKLFQEGDKW LTEEAQSEQQ
660 670 680 690 700
TNIEQEVSLD LILVEEYDSL IEKMSNWNFP IFELVEKMGE KSGRILSQVM
710 720 730 740 750
YTLFQDTGLL EIFKIPTQQF MNYFRALENG YRDIPYHNRI HATDVLHAVW
760 770 780 790 800
YLTTRPVPGL QQIHNGCGTG NETDSDGRIN HGRIAYISSK SCSNPDESYG
810 820 830 840 850
CLSSNIPALE LMALYVAAAM HDYDHPGRTN AFLVATNAPQ AVLYNDRSVL
860 870 880 890 900
ENHHAASAWN LYLSRPEYNF LLHLDHVEFK RFRFLVIEAI LATDLKKHFD
910 920 930 940 950
FLAEFNAKAN DVNSNGIEWS NENDRLLVCQ VCIKLADING PAKVRDLHLK
960 970 980 990 1000
WTEGIVNEFY EQGDEEANLG LPISPFMDRS SPQLAKLQES FITHIVGPLC
1010 1020 1030 1040 1050
NSYDAAGLLP GQWLEAEEDN DTESGDDEDG EELDTEDEEM ENNLNPKPPR
1060 1070 1080 1090 1100
RKSRRRIFCQ LMHHLTENHK IWKEIVEEEE KCKADGNKLQ VENSSLPQAD
1110
EIQVIEEADE EE
Length:1,112
Mass (Da):124,333
Last modified:April 3, 2007 - v2
Checksum:i55451C3DA142EF6A
GO
Isoform 2 (identifier: Q13370-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     376-426: Missing.

Note: No experimental confirmation available.
Show »
Length:1,061
Mass (Da):118,809
Checksum:i755DBD55004867DC
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti84A → D in AAC50724 (PubMed:8884271).Curated1
Sequence conflicti84A → D in BAA09306 (PubMed:8706823).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03146287A → V.1 PublicationCorresponds to variant rs1056584dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_054138376 – 426Missing in isoform 2. 1 PublicationAdd BLAST51

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38178 Genomic DNA. Translation: AAC50724.1.
D50640 Genomic DNA. Translation: BAA09306.1.
X95520 mRNA. Translation: CAA64774.1.
AY459346 mRNA. Translation: AAR24292.1.
AC018795 Genomic DNA. No translation available.
AC087207 Genomic DNA. No translation available.
AC090835 Genomic DNA. No translation available.
CH471064 Genomic DNA. Translation: EAW68474.1.
BC136565 mRNA. Translation: AAI36566.1.
BC136566 mRNA. Translation: AAI36567.1.
BC144248 mRNA. Translation: AAI44249.1.
CCDSiCCDS7817.1. [Q13370-1]
PIRiS70522.
RefSeqiNP_000913.2. NM_000922.3. [Q13370-1]
UniGeneiHs.445711.

Genome annotation databases

EnsembliENST00000282096; ENSP00000282096; ENSG00000152270. [Q13370-1]
ENST00000455098; ENSP00000388644; ENSG00000152270. [Q13370-2]
GeneIDi5140.
KEGGihsa:5140.
UCSCiuc001mln.4. human. [Q13370-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38178 Genomic DNA. Translation: AAC50724.1.
D50640 Genomic DNA. Translation: BAA09306.1.
X95520 mRNA. Translation: CAA64774.1.
AY459346 mRNA. Translation: AAR24292.1.
AC018795 Genomic DNA. No translation available.
AC087207 Genomic DNA. No translation available.
AC090835 Genomic DNA. No translation available.
CH471064 Genomic DNA. Translation: EAW68474.1.
BC136565 mRNA. Translation: AAI36566.1.
BC136566 mRNA. Translation: AAI36567.1.
BC144248 mRNA. Translation: AAI44249.1.
CCDSiCCDS7817.1. [Q13370-1]
PIRiS70522.
RefSeqiNP_000913.2. NM_000922.3. [Q13370-1]
UniGeneiHs.445711.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SO2X-ray2.40A/B/C/D654-1073[»]
1SOJX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L654-1073[»]
ProteinModelPortaliQ13370.
SMRiQ13370.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111166. 27 interactors.
IntActiQ13370. 3 interactors.
STRINGi9606.ENSP00000282096.

Chemistry databases

BindingDBiQ13370.
ChEMBLiCHEMBL290.
DrugBankiDB00201. Caffeine.
GuidetoPHARMACOLOGYi1299.

PTM databases

iPTMnetiQ13370.
PhosphoSitePlusiQ13370.

Polymorphism and mutation databases

BioMutaiPDE3B.
DMDMi143811435.

Proteomic databases

EPDiQ13370.
MaxQBiQ13370.
PaxDbiQ13370.
PeptideAtlasiQ13370.
PRIDEiQ13370.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000282096; ENSP00000282096; ENSG00000152270. [Q13370-1]
ENST00000455098; ENSP00000388644; ENSG00000152270. [Q13370-2]
GeneIDi5140.
KEGGihsa:5140.
UCSCiuc001mln.4. human. [Q13370-1]

Organism-specific databases

CTDi5140.
DisGeNETi5140.
GeneCardsiPDE3B.
HGNCiHGNC:8779. PDE3B.
HPAiCAB009497.
HPA024342.
MIMi602047. gene.
neXtProtiNX_Q13370.
OpenTargetsiENSG00000152270.
PharmGKBiPA33127.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IEGG. Eukaryota.
ENOG410XT2V. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000060144.
HOVERGENiHBG053541.
KOiK13296.
OMAiCAFFFLT.
OrthoDBiEOG091G0BTI.
PhylomeDBiQ13370.
TreeFamiTF329631.

Enzyme and pathway databases

BioCyciZFISH:HS07803-MONOMER.
BRENDAi3.1.4.17. 2681.
ReactomeiR-HSA-165160. PDE3B signalling.
R-HSA-418457. cGMP effects.
R-HSA-418555. G alpha (s) signalling events.
SignaLinkiQ13370.
SIGNORiQ13370.

Miscellaneous databases

ChiTaRSiPDE3B. human.
EvolutionaryTraceiQ13370.
GenomeRNAii5140.
PROiQ13370.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000152270.
CleanExiHS_PDE3B.
GenevisibleiQ13370. HS.

Family and domain databases

Gene3Di1.10.1300.10. 2 hits.
InterProiIPR003607. HD/PDEase_dom.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PfamiPF00233. PDEase_I. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
[Graphical view]
PROSITEiPS00126. PDEASE_I. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDE3B_HUMAN
AccessioniPrimary (citable) accession number: Q13370
Secondary accession number(s): B7ZM37
, O00639, Q14408, Q6SEI4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: April 3, 2007
Last modified: November 2, 2016
This is version 159 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.