Q5JSP0 (FGD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
FYVE, RhoGEF and PH domain-containing protein 3

Alternative name(s):
Zinc finger FYVE domain-containing protein 5

Gene names

Name:	FGD3
Synonyms:	ZFYVE5

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	725 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Promotes the formation of filopodia. May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape By similarity.
Subcellular location	Cytoplasm Probable. Cytoplasm › cytoskeleton Probable.
Sequence similarities	Contains 1 DH (DBL-homology) domain. Contains 1 FYVE-type zinc finger. Contains 2 PH domains.

Ontologies

Keywords
Cellular component	Cytoplasm Cytoskeleton
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Guanine-nucleotide releasing factor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	actin cytoskeleton organization Inferred from sequence or structural similarity. Source: UniProtKB apoptotic process Traceable author statement. Source: Reactome filopodium assembly Inferred from sequence or structural similarity. Source: UniProtKB nerve growth factor receptor signaling pathway Traceable author statement. Source: Reactome regulation of Cdc42 GTPase activity Inferred from sequence or structural similarity. Source: UniProtKB regulation of cell shape Inferred from sequence or structural similarity. Source: UniProtKB small GTPase mediated signal transduction Traceable author statement. Source: Reactome
Cellular_component	Golgi apparatus Inferred from sequence or structural similarity. Source: UniProtKB cytoskeleton Inferred from electronic annotation. Source: UniProtKB-SubCell cytosol Traceable author statement. Source: Reactome lamellipodium Inferred from sequence or structural similarity. Source: UniProtKB ruffle Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	Rho guanyl-nucleotide exchange factor activity Inferred from electronic annotation. Source: InterPro guanyl-nucleotide exchange factor activity Inferred from sequence or structural similarity. Source: UniProtKB metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phospholipid binding Inferred from electronic annotation. Source: InterPro small GTPase binding Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Alternative products

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

Isoform 1 (identifier: Q5JSP0-1)

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: Q5JSP0-2)

The sequence of this isoform differs from the canonical sequence as follows:
     596-634: KTPTADPQPS...AAIPMSDPQV → VGAPSSCSPP...SAFGVSLGPG
     635-725: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 725

725

FYVE, RhoGEF and PH domain-containing protein 3

PRO_0000080944

Regions

Domain

157 – 341

185

DH

Domain

370 – 469

100

PH 1

Domain

604 – 703

100

PH 2

Zinc finger

532 – 588

57

FYVE-type

Amino acid modifications

Modified residue

128

1

Phosphoserine Ref.4 Ref.5

Natural variations

Alternative sequence

596 – 634

39

KTPTA…SDPQV → VGAPSSCSPPGGAAEPPDTC SCAPAAPAASAFGVSLGPG in isoform 2.

VSP_013074

Alternative sequence

635 – 725

91

Missing in isoform 2.

VSP_013075

Natural variant

275

1

V → I. Ref.3
Corresponds to variant rs3802384 [ dbSNP | Ensembl ].

VAR_021492

Secondary structure

1

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725

Helix Strand Turn

Details...

Beta strand

605 – 618

14

Beta strand

620 – 626

7

Beta strand

635 – 638

4

Beta strand

644 – 646

3

Beta strand

648 – 650

3

Helix

652 – 654

3

Beta strand

656 – 658

3

Beta strand

662 – 664

3

Beta strand

667 – 676

10

Beta strand

679 – 687

9

Helix

688 – 702

15

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified February 15, 2005. Version 1. Checksum: 665A7FF5BE16B44B	FASTA	725	79,401
	10 20 30 40 50 60 MESGRGSSTP PGPIAALGMP DTGPGSSSLG KLQALPVGPR AHCGDPVSLA AAGDGSPDIG 70 80 90 100 110 120 PTGELSGSLK IPNRDSGIDS PSSSVAGENF PCEEGLEAGP SPTVLGAHAE MALDSQVPKV 130 140 150 160 170 180 TPQEEADSDV GEEPDSENTP QKADKDAGLA QHSGPQKLLH IAQELLHTEE TYVKRLHLLD 190 200 210 220 230 240 QVFCTRLTDA GIPPEVIMGI FSNISSIHRF HGQFLLPELK TRITEEWDTN PRLGDILQKL 250 260 270 280 290 300 APFLKMYGEY VKNFDRAVGL VSTWTQRSPL FKDVVHSIQK QEVCGNLTLQ HHMLEPVQRV 310 320 330 340 350 360 PRYELLLKDY LKRLPQDAPD RKDAERSLEL ISTAANHSNA AIRKVEKMHK LLEVYEQLGG 370 380 390 400 410 420 EEDIVNPANE LIKEGQIQKL SAKNGTPQDR HLFLFNSMIL YCVPKLRLMG QKFSVREKMD 430 440 450 460 470 480 ISGLQVQDIV KPNTAHTFII TGRKRSLELQ TRTEEEKKEW IQIIQATIEK HKQNSETFKA 490 500 510 520 530 540 FGGAFSQDED PSLSPDMPIT STSPVEPVVT TEGSSGAAGL EPRKLSSKTR RDKEKQSCKS 550 560 570 580 590 600 CGETFNSITK RRHHCKLCGA VICGKCSEFK AENSRQSRVC RDCFLTQPVA PESTEKTPTA 610 620 630 640 650 660 DPQPSLLCGP LRLSESGETW SEVWAAIPMS DPQVLHLQGG SQDGRLPRTI PLPSCKLSVP 670 680 690 700 710 720 DPEERLDSGH VWKLQWAKQS WYLSASSAEL QQQWLETLST AAHGDTAQDS PGALQLQVPM GAAAP
	Isoform 2 [UniParc]. Checksum: 6EC385CE5B2CB426	FASTA	634	68,794
	10 20 30 40 50 60 MESGRGSSTP PGPIAALGMP DTGPGSSSLG KLQALPVGPR AHCGDPVSLA AAGDGSPDIG 70 80 90 100 110 120 PTGELSGSLK IPNRDSGIDS PSSSVAGENF PCEEGLEAGP SPTVLGAHAE MALDSQVPKV 130 140 150 160 170 180 TPQEEADSDV GEEPDSENTP QKADKDAGLA QHSGPQKLLH IAQELLHTEE TYVKRLHLLD 190 200 210 220 230 240 QVFCTRLTDA GIPPEVIMGI FSNISSIHRF HGQFLLPELK TRITEEWDTN PRLGDILQKL 250 260 270 280 290 300 APFLKMYGEY VKNFDRAVGL VSTWTQRSPL FKDVVHSIQK QEVCGNLTLQ HHMLEPVQRV 310 320 330 340 350 360 PRYELLLKDY LKRLPQDAPD RKDAERSLEL ISTAANHSNA AIRKVEKMHK LLEVYEQLGG 370 380 390 400 410 420 EEDIVNPANE LIKEGQIQKL SAKNGTPQDR HLFLFNSMIL YCVPKLRLMG QKFSVREKMD 430 440 450 460 470 480 ISGLQVQDIV KPNTAHTFII TGRKRSLELQ TRTEEEKKEW IQIIQATIEK HKQNSETFKA 490 500 510 520 530 540 FGGAFSQDED PSLSPDMPIT STSPVEPVVT TEGSSGAAGL EPRKLSSKTR RDKEKQSCKS 550 560 570 580 590 600 CGETFNSITK RRHHCKLCGA VICGKCSEFK AENSRQSRVC RDCFLTQPVA PESTEVGAPS 610 620 630 SCSPPGGAAE PPDTCSCAPA APAASAFGVS LGPG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of a human FGD3 gene: a novel faciogenital dysplasia (FGD1; Aarskog syndrome) gene homolog." Shan Y.X., Yu L. Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
[2]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT ILE-275. Tissue: Brain.
[4]	"Phosphoproteome of resting human platelets." Zahedi R.P., Lewandrowski U., Wiesner J., Wortelkamp S., Moebius J., Schuetz C., Walter U., Gambaryan S., Sickmann A. J. Proteome Res. 7:526-534(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-128, MASS SPECTROMETRY. Tissue: Platelet.
[5]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-128, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[6]	"Solution structure of the C-terminal PH domain of FYVE, RhoGEF and PH domain containing protein 3 (FGD3) from human." RIKEN structural genomics initiative (RSGI) Submitted (NOV-2005) to the PDB data bank Cited for: STRUCTURE BY NMR OF 605-703.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY211386 mRNA. Translation: AAP20645.1.
AL389924, AL451065 Genomic DNA. Translation: CAI41118.1.
AL451065, AL389924 Genomic DNA. Translation: CAI95107.1.
BC032429 mRNA. Translation: AAH32429.1.
BC111054 mRNA. Translation: AAI11055.1.

IPI

IPI00384357.
IPI00413785.

RefSeq

NP_001077005.1. NM_001083536.1.
NP_149077.2. NM_033086.2.

UniGene

Hs.411081.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2COC	NMR	-	A	605-703	[»]

ProteinModelPortal

Q5JSP0.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000336914.

PTM databases

PhosphoSite

Q5JSP0.

Polymorphism databases

DMDM

61213216.

Proteomic databases

PaxDb

Q5JSP0.

PRIDE

Q5JSP0.

Protocols and materials databases

DNASU

89846.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000337352; ENSP00000336914; ENSG00000127084.
ENST00000375482; ENSP00000364631; ENSG00000127084.
ENST00000467786; ENSP00000432310; ENSG00000127084.

GeneID

89846.

KEGG

hsa:89846.

UCSC

uc004asw.2. human.

Organism-specific databases

CTD

89846.

GeneCards

GC09P095709.

HGNC

HGNC:16027. FGD3.

HPA

HPA020963.
HPA021018.

neXtProt

NX_Q5JSP0.

PharmGKB

PA28104.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5422.

HOGENOM

HOG000220866.

HOVERGEN

HBG007506.

InParanoid

Q5JSP0.

KO

K05722.

OMA

VCRECFL.

OrthoDB

EOG44F68Q.

PhylomeDB

Q5JSP0.

Enzyme and pathway databases

Reactome

REACT_111102. Signal Transduction.

Gene expression databases

ArrayExpress

Q5JSP0.

Bgee

Q5JSP0.

CleanEx

HS_FGD3.

Genevestigator

Q5JSP0.

GermOnline

ENSG00000127084. Homo sapiens.

Family and domain databases

Gene3D

1.20.900.10. 1 hit.
2.30.29.30. 2 hits.
3.30.40.10. 1 hit.

InterPro

IPR000219. DH-domain.
IPR011993. PH_like_dom.
IPR001849. Pleckstrin_homology.
IPR000306. Znf_FYVE.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]

Pfam

PF01363. FYVE. 1 hit.
PF00169. PH. 1 hit.
PF00621. RhoGEF. 1 hit.
[Graphical view]

SMART

SM00064. FYVE. 1 hit.
SM00233. PH. 2 hits.
SM00325. RhoGEF. 1 hit.
[Graphical view]

SUPFAM

SSF48065. DH-domain. 1 hit.
SSF57903. FYVE_PHD_ZnF. 1 hit.

PROSITE

PS50010. DH_2. 1 hit.
PS50003. PH_DOMAIN. 2 hits.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

FGD3. human.

EvolutionaryTrace

Q5JSP0.

GenomeRNAi

89846.

NextBio

76332.

Entry information

Entry name

FGD3_HUMAN

Accession

Primary (citable) accession number: Q5JSP0
Secondary accession number(s): Q4VX84, Q7Z7D9, Q8N5G1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	February 15, 2005
Last modified:	May 1, 2013
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

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.