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Protein

cGMP-dependent 3',5'-cGMP phosphodiesterase A

Gene

pdeD

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Phosphodiesterase specific for cGMP, which is activated by cGMP but not by cAMP. Involved in the degradation of intracellular cGMP.1 Publication

Catalytic activityi

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

Cofactori

Mn2+1 Publication, Mg2+1 Publication, Zn2+1 PublicationNote: Divalent metal cation. Can use Mn2+ or, to a lower extent, Mg2+ or Zn2+. Half-maximal activation occurs between 10 and 100 uM of Mn2+ whereas maximal activation occurs with 10 mM of Zn2+ or Mg2+.1 Publication

Kineticsi

cAMP/cGMP selectivity of 0.003.

  1. KM=5.2 µM for cGMP2 Publications
  1. Vmax=390 pmol/min/mg enzyme2 Publications

pH dependencei

Optimum pH is 7.0.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi399Divalent metal cationSequence analysis1
Metal bindingi401Divalent metal cationSequence analysis1
Metal bindingi403Divalent metal cationSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi607 – 721cNMP 1Add BLAST115
Nucleotide bindingi734 – 851cNMP 2Add BLAST118

GO - Molecular functioni

  • 3',5'-cyclic-GMP phosphodiesterase activity Source: dictyBase
  • cGMP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • aggregation involved in sorocarp development Source: dictyBase
  • cGMP catabolic process Source: dictyBase
  • cGMP-mediated signaling Source: dictyBase
  • signal transduction Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

cGMP, cGMP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BRENDAi3.1.4.35. 1939.

Names & Taxonomyi

Protein namesi
Recommended name:
cGMP-dependent 3',5'-cGMP phosphodiesterase A (EC:3.1.4.35)
Alternative name(s):
Cyclic GMP-binding protein A
Phosphodiesterase 5
Short name:
DdPDE5
Phosphodiesterase D
Gene namesi
Name:pdeD
Synonyms:gbpA, pde5
ORF Names:DDB_G0274383
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
Proteomesi
  • UP000002195 Componentsi: Chromosome 2, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0274383. pdeD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003531051 – 867cGMP-dependent 3',5'-cGMP phosphodiesterase AAdd BLAST867

Proteomic databases

PaxDbiQ8MLZ3.

Expressioni

Developmental stagei

Expressed during growth and development, with the highest level of expression during aggregation.1 Publication

Structurei

3D structure databases

ProteinModelPortaliQ8MLZ3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni357 – 503Phosphodiesterase activityAdd BLAST147

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi124 – 127Poly-Ser4
Compositional biasi142 – 145Poly-Ser4
Compositional biasi151 – 154Poly-Gln4
Compositional biasi155 – 158Poly-Pro4
Compositional biasi178 – 185Poly-His8
Compositional biasi189 – 196Poly-Asn8
Compositional biasi200 – 203Poly-Asn4
Compositional biasi209 – 221Poly-GlnAdd BLAST13

Domaini

The beta lactamase-like domain catalyzes the hydrolysis of cGMP.

Sequence similaritiesi

Contains 2 cyclic nucleotide-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IEUW. Eukaryota.
ENOG4111CIN. LUCA.
InParanoidiQ8MLZ3.
OMAiGRENSTH.
PhylomeDBiQ8MLZ3.

Family and domain databases

Gene3Di2.60.120.10. 2 hits.
3.60.15.10. 1 hit.
InterProiIPR018490. cNMP-bd-like.
IPR018488. cNMP-bd_CS.
IPR000595. cNMP-bd_dom.
IPR001279. Metallo-B-lactamas.
IPR014710. RmlC-like_jellyroll.
[Graphical view]
PfamiPF00027. cNMP_binding. 2 hits.
PF00753. Lactamase_B. 1 hit.
[Graphical view]
SMARTiSM00100. cNMP. 2 hits.
SM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF51206. SSF51206. 2 hits.
SSF56281. SSF56281. 1 hit.
PROSITEiPS00889. CNMP_BINDING_2. 1 hit.
PS50042. CNMP_BINDING_3. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8MLZ3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMFSKRKSIR FNPEGDYTEL PRGGYVVPSK LGGIQFGVPP ETIKDSMALK
60 70 80 90 100
IDVPTIYVFP EELWDRKTGI NAAEAEFPAY FNYFILKRKV SFVCTKEQEQ
110 120 130 140 150
RIRIVFQETL LGPPEFNTGI IINSSSSTTD TSKTSPIKKQ TSSSSPPLSP
160 170 180 190 200
QQQQPPPPLV KQPSQQQLEE LATMDTCHYH HHHHHQEVND NDNNNNTTTN
210 220 230 240 250
NNNIEILEQQ QQQQQQQQQQ QDEDSTDVDE EFQKEFSSTF PRSEIPNLEK
260 270 280 290 300
ECKYLRTFNS VDELFDFILF DDNGIAKLSD DVEIHFQEDQ SLFKVLQFEE
310 320 330 340 350
TGKGNKVQTL VATIPSKILF PDMINSISTI NDNKIFDPPT FGITIIGSSH
360 370 380 390 400
GFDPKKSTTG FVLWINKRGI MVDPPLNSSS FLQSQGVPTR MVDHIILTHC
410 420 430 440 450
HADHDSGTFQ KLLEEYQITV VTTPTILGSF LRKYGALSNL STDLLRRLFI
460 470 480 490 500
FRPVMIGEPM IISGAEFRFF YTIHTIPTIS FEVFYGGKSI FYSGDTCYDP
510 520 530 540 550
NRIKDMNKRG IMKTSRMKFF LRPWNHTVVL HEAGVPPIHT PVSVLRALPD
560 570 580 590 600
EVKNRLYLVH ISEHTLPAGS GLKIAKEGVA HTLSLDVMKS SHSEAVDILK
610 620 630 640 650
LVESVDIFRS IPLTQACEIL QTATKRKYSQ GSVIIARDTE PDAFYVVASG
660 670 680 690 700
VVCVNIGELK KNLIVGDYFG EMSLVMGGLR SANVQAVTDV EVLSFNKEDF
710 720 730 740 750
LSITRNSTES IQFITRLWEM RNEKSWETMS LNSVFSRCTN SQKTAIQSIL
760 770 780 790 800
VRELIKKDET LWCKGEEALF GCLVAEGSFV FKEDDSLESF SQGSFLGDIN
810 820 830 840 850
AMTTQPPSIH KTTVVAKEES VIYKVLSQDL IKFFSNNPGI QLAFLDTIFV
860
DALRDQVQQL VNSKLTY
Length:867
Mass (Da):97,992
Last modified:October 1, 2002 - v1
Checksum:iE203EED614E6F386
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF481921 Genomic DNA. Translation: AAM34039.1.
AY047363 Genomic DNA. Translation: AAL06059.1.
AAFI02000012 Genomic DNA. Translation: EAL70084.1.
RefSeqiXP_644314.1. XM_639222.1.

Genome annotation databases

EnsemblProtistsiEAL70084; EAL70084; DDB_G0274383.
GeneIDi8619742.
KEGGiddi:DDB_G0274383.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF481921 Genomic DNA. Translation: AAM34039.1.
AY047363 Genomic DNA. Translation: AAL06059.1.
AAFI02000012 Genomic DNA. Translation: EAL70084.1.
RefSeqiXP_644314.1. XM_639222.1.

3D structure databases

ProteinModelPortaliQ8MLZ3.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PaxDbiQ8MLZ3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiEAL70084; EAL70084; DDB_G0274383.
GeneIDi8619742.
KEGGiddi:DDB_G0274383.

Organism-specific databases

dictyBaseiDDB_G0274383. pdeD.

Phylogenomic databases

eggNOGiENOG410IEUW. Eukaryota.
ENOG4111CIN. LUCA.
InParanoidiQ8MLZ3.
OMAiGRENSTH.
PhylomeDBiQ8MLZ3.

Enzyme and pathway databases

BRENDAi3.1.4.35. 1939.

Miscellaneous databases

PROiQ8MLZ3.

Family and domain databases

Gene3Di2.60.120.10. 2 hits.
3.60.15.10. 1 hit.
InterProiIPR018490. cNMP-bd-like.
IPR018488. cNMP-bd_CS.
IPR000595. cNMP-bd_dom.
IPR001279. Metallo-B-lactamas.
IPR014710. RmlC-like_jellyroll.
[Graphical view]
PfamiPF00027. cNMP_binding. 2 hits.
PF00753. Lactamase_B. 1 hit.
[Graphical view]
SMARTiSM00100. cNMP. 2 hits.
SM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF51206. SSF51206. 2 hits.
SSF56281. SSF56281. 1 hit.
PROSITEiPS00889. CNMP_BINDING_2. 1 hit.
PS50042. CNMP_BINDING_3. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDE5_DICDI
AccessioniPrimary (citable) accession number: Q8MLZ3
Secondary accession number(s): Q554K9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2008
Last sequence update: October 1, 2002
Last modified: November 2, 2016
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. 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.