Q54S40 (GBPD_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cyclic GMP-binding protein D

Alternative name(s):
Guanine nucleotide exchange factor for rap1
Ras guanine nucleotide exchange factor U
RasGEF domain-containing protein U

Gene names

Name:	gbpD
Synonyms:	gefU, rapgef
ORF Names:	DDB_G0282373

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1312 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Promotes the exchange of Ras-bound GDP by GTP By similarity. Induces the formation of substrate-attached pseudopodia, that leads to increased adhesion and thereby negatively influencing cell speed and polarity. Ref.3 Ref.5
Developmental stage	Increases after starvation is initiated with a peak between 8-12 hours of starvation. Ref.1 Ref.4
Sequence similarities	Contains 3 cyclic nucleotide-binding domains. Contains 1 GRAM domain. Contains 1 N-terminal Ras-GEF domain. Contains 1 Ras-GEF domain.

Ontologies

Keywords
Domain	Repeat
Ligand	Nucleotide-binding cGMP cGMP-binding
Molecular function	Guanine-nucleotide releasing factor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell-substrate adhesion Inferred from mutant phenotype Ref.5. Source: dictyBase establishment or maintenance of cell polarity Inferred from mutant phenotype Ref.5. Source: dictyBase positive regulation of cellular component movement Traceable author statement PubMed 15473840. Source: dictyBase regulation of chemotaxis Inferred from mutant phenotype Ref.5. Source: dictyBase regulation of lateral pseudopodium assembly Inferred from mutant phenotype Ref.5. Source: dictyBase regulation of small GTPase mediated signal transduction Inferred from electronic annotation. Source: InterPro small GTPase mediated signal transduction Inferred from electronic annotation. Source: InterPro
Cellular_component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular_function	Rap guanyl-nucleotide exchange factor activity Inferred from direct assay PubMed 16769729. Source: dictyBase nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1312	1312	Cyclic GMP-binding protein D		PRO_0000353104
Regions
	Domain	26 – 155	130	N-terminal Ras-GEF
	Domain	353 – 582	230	Ras-GEF
	Domain	940 – 1006	67	GRAM
	Nucleotide binding	698 – 857	160	cNMP 1
	Nucleotide binding	1105 – 1218	114	cNMP 2
	Nucleotide binding	1182 – 1303	122	cNMP 3
	Compositional bias	216 – 227	12	Poly-Asn
	Compositional bias	267 – 272	6	Poly-Gly
	Compositional bias	311 – 326	16	Poly-Asn
	Compositional bias	604 – 607	4	Poly-Ser
	Compositional bias	613 – 624	12	Poly-Gly
	Compositional bias	666 – 670	5	Poly-Ser
	Compositional bias	759 – 766	8	Poly-Gly
	Compositional bias	893 – 898	6	Poly-Gly
	Compositional bias	1047 – 1062	16	Poly-Gln
	Compositional bias	1167 – 1201	35	Poly-Asn
Experimental info
	Sequence conflict	621	1	G → A in AAM34042. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q54S40 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: 044A4E51DBA2192E	FASTA	1,312	143,659
	10 20 30 40 50 60 MTDYPFYKPD DETNIIYNIN INKKEGFSAI KSCSLAKLIE KLTSTKQLHT YFSSAFFLTY 70 80 90 100 110 120 RDFTTPLEII NLLISRYTGP PPDSSKDSLR LFEIEVDIVQ ANVLSIFRTL IGTLIQVDFD 130 140 150 160 170 180 TPKLSSSIIE FFNSLPESVK NELFLEFFKA KKMARPPGSI PKPVNSNIIS SAASTMRFSY 190 200 210 220 230 240 SVSPKTQSPN STNNVLSGLL SNNGSNTMNG INGTSNNNVN SNNNNNNGTT NISSPNFDPS 250 260 270 280 290 300 RSSMKMGKGI MKLLQSNIAN FNNQQNGGGG GGSNNGTSPQ SSPSSTLSST NSLFNQQPSL 310 320 330 340 350 360 SMLNDDGSVQ NNNNNNNNNN NNNNVNEIST INVQLPPSTP PINGIPGEKT AFLPEAIAKE 370 380 390 400 410 420 LTIMEWELIT ALSVSDITSK EWNKSVNIQN LTTWFNRISS WVSTKIISKE TPEERAIIIE 430 440 450 460 470 480 AFINIANFAK ELKNYNCVME ILGSLHGSSI SRLKSSWALL SQKTNDMFQI LNNLMTTDGN 490 500 510 520 530 540 FKNYRKILTT VLPNEPCIPY LGLFLTDYTY LDESNPSLST DSNLINIDRI FLISTRVQEF 550 560 570 580 590 600 FQLFTNCNYT FISNMSVRDA ILGEKVWDEN EIFRLSKIRE ETSSLQSLKE SNGIGNSNST 610 620 630 640 650 660 SGGSSSSLVN KDGSGGGGGS GGGGSVNSKG DGKGDGKDNR DGRGDGNSNC GNGSGISSKD 670 680 690 700 710 720 KDLLLSSSSS AASHTVRRKN FVTKYRMSFT GNDPLPSVSS TLSEREWKIL TTNSKTIIYP 730 740 750 760 770 780 RGKTVLSVGE TNTNIYRVIS GRVKVETLKS FNSSDADLGA GGGGGGDNRG EDNSLMAIKA 790 800 810 820 830 840 RNRLSLNLPA QDDGYYVEEG EIFGQESFLY TDRPMLSNII VDSGECELME IEKSFVLQLF 850 860 870 880 890 900 ASEHQLSATF YKFIGVIQAQ LLKSIYINFT SNYGNGGSGG SGSNGNGGGS SNGAGGGGLS 910 920 930 940 950 960 SSVSIGNLNS PNINRIDFKR RSTIFETPSS LDILRDGNDS SFRTKFGLSQ DEVIIKRYQC 970 980 990 1000 1010 1020 KHNNMNGTLY ITKHNLCFEG KFLGINKNKT IPFDRTDKIL TVDKNIMTVT TKEKVKKFTF 1030 1040 1050 1060 1070 1080 KSHDDLNEGY GISVQIWANH LNINVKQQLQ LQQQQLQQQQ QQPSQQPSQQ QSQSSQLQQS 1090 1100 1110 1120 1130 1140 VSASSTTPPV PNSPKVGRGE SFSNIKDLPS KDEWNQILKG TKPLTFKKGE ILICEGVEYQ 1150 1160 1170 1180 1190 1200 KMFQIVKGEC SVVKSLLPTP LDQNIFNNIN NNNNNNNNNN NNNNNNNNNN NNNNNNGNNN 1210 1220 1230 1240 1250 1260 NSIFKNNSSI SNTNSNTSID GGVGGGLSPQ TLVDPKNSVI VSKLTHGSIF GEMSFLLPGG 1270 1280 1290 1300 1310 SATSLVVSSD EVEVYIIESY FLHILLKSKP YLASKFYKYL ACVLETRVRN LT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of four candidate cGMP targets in Dictyostelium." Goldberg J.M., Bosgraaf L., Van Haastert P.J.M., Smith J.L. Proc. Natl. Acad. Sci. U.S.A. 99:6749-6754(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DEVELOPMENTAL STAGE.
[2]	"The genome of the social amoeba Dictyostelium discoideum." Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N. , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A. Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
[3]	"A novel cGMP signalling pathway mediating myosin phosphorylation and chemotaxis in Dictyostelium." Bosgraaf L., Russcher H., Smith J.L., Wessels D., Soll D.R., Van Haastert P.J.M. EMBO J. 21:4560-4570(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[4]	"The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles." Wilkins A., Szafranski K., Fraser D.J., Bakthavatsalam D., Mueller R., Fisher P.R., Gloeckner G., Eichinger L., Noegel A.A., Insall R.H. Genome Biol. 6:R68.1-R68.12(2005) [PubMed] [Europe PMC] [Abstract] Cited for: DEVELOPMENTAL STAGE.
[5]	"RasGEF-containing proteins GbpC and GbpD have differential effects on cell polarity and chemotaxis in Dictyostelium." Bosgraaf L., Waijer A., Engel R., Visser A.J.W.G., Wessels D., Soll D., van Haastert P.J.M. J. Cell Sci. 118:1899-1910(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF481924 Genomic DNA. Translation: AAM34042.1. AAFI02000047 Genomic DNA. Translation: EAL66046.1.
RefSeq	XP_640199.1. XM_635107.1.
3D structure databases
HSSP	HSSP built from PDB template 1BKD based on UniProtKB Q07889.
ProteinModelPortal	Q54S40.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDB_0215332.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0215332; DDB0215332; DDB_G0282373.
GeneID	8623739.
KEGG	ddi:DDB_G0282373.
Organism-specific databases
dictyBase	DDB_G0282373. gbpD.
Phylogenomic databases
eggNOG	KOG3417.
OMA	EAFINIA.
Family and domain databases
Gene3D	1.10.840.10. 1 hit. 2.60.120.10. 3 hits.
InterPro	IPR018490. cNMP-bd-like. IPR000595. cNMP-bd_dom. IPR004182. GRAM. IPR000651. Ras-like_Gua-exchang_fac_N. IPR008937. Ras_GEF. IPR023578. Ras_GEF_dom. IPR001895. RasGRF_CDC25. IPR014710. RmlC-like_jellyroll. [Graphical view]
PANTHER	PTHR23113. PTHR23113. 1 hit.
Pfam	PF00027. cNMP_binding. 1 hit. PF02893. GRAM. 1 hit. PF00617. RasGEF. 1 hit. PF00618. RasGEF_N. 1 hit. [Graphical view]
SMART	SM00568. GRAM. 1 hit. SM00147. RasGEF. 1 hit. SM00229. RasGEFN. 1 hit. [Graphical view]
SUPFAM	SSF51206. cNMP_binding. 2 hits. SSF48366. Ras_GEF. 1 hit.
PROSITE	PS00888. CNMP_BINDING_1. False negative. PS00889. CNMP_BINDING_2. False negative. PS50042. CNMP_BINDING_3. 2 hits. PS00720. RASGEF. False negative. PS50009. RASGEF_CAT. 1 hit. PS50212. RASGEF_NTER. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

GBPD_DICDI

Accession

Primary (citable) accession number: Q54S40
Secondary accession number(s): Q8MVR0

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 25, 2008
Last sequence update:	May 24, 2005
Last modified:	May 1, 2013
This is version 55 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)