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Protein

FYVE, RhoGEF and PH domain-containing protein 3

Gene

FGD3

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

Functioni

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).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri532 – 58857FYVE-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Guanine-nucleotide releasing factor

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_11051. Rho GTPase cycle.
REACT_13638. NRAGE signals death through JNK.
REACT_18407. G alpha (12/13) signalling events.

Names & Taxonomyi

Protein namesi
Recommended name:
FYVE, RhoGEF and PH domain-containing protein 3
Alternative name(s):
Zinc finger FYVE domain-containing protein 5
Gene namesi
Name:FGD3
Synonyms:ZFYVE5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:16027. FGD3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA28104.

Polymorphism and mutation databases

BioMutaiFGD3.
DMDMi61213216.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 725725FYVE, RhoGEF and PH domain-containing protein 3PRO_0000080944Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei128 – 1281Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ5JSP0.
PaxDbiQ5JSP0.
PRIDEiQ5JSP0.

PTM databases

PhosphoSiteiQ5JSP0.

Expressioni

Gene expression databases

BgeeiQ5JSP0.
CleanExiHS_FGD3.
ExpressionAtlasiQ5JSP0. baseline and differential.
GenevestigatoriQ5JSP0.

Organism-specific databases

HPAiHPA020963.
HPA021018.

Interactioni

Protein-protein interaction databases

BioGridi124618. 3 interactions.
STRINGi9606.ENSP00000336914.

Structurei

Secondary structure

1
725
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi605 – 61814Combined sources
Beta strandi620 – 6267Combined sources
Beta strandi635 – 6384Combined sources
Beta strandi644 – 6463Combined sources
Beta strandi648 – 6503Combined sources
Helixi652 – 6543Combined sources
Beta strandi656 – 6583Combined sources
Beta strandi662 – 6643Combined sources
Beta strandi667 – 67610Combined sources
Beta strandi679 – 6879Combined sources
Helixi688 – 70215Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2COCNMR-A605-703[»]
ProteinModelPortaliQ5JSP0.
SMRiQ5JSP0. Positions 161-472, 528-584, 606-703.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5JSP0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini157 – 341185DHPROSITE-ProRule annotationAdd
BLAST
Domaini370 – 469100PH 1PROSITE-ProRule annotationAdd
BLAST
Domaini604 – 703100PH 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 DH (DBL-homology) domain.PROSITE-ProRule annotation
Contains 1 FYVE-type zinc finger.PROSITE-ProRule annotation
Contains 2 PH domains.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri532 – 58857FYVE-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5422.
GeneTreeiENSGT00750000117280.
HOGENOMiHOG000220866.
HOVERGENiHBG007506.
InParanoidiQ5JSP0.
KOiK05722.
OMAiTPHEEAD.
OrthoDBiEOG7C2R0M.
PhylomeDBiQ5JSP0.
TreeFamiTF316247.

Family and domain databases

Gene3Di1.20.900.10. 1 hit.
2.30.29.30. 2 hits.
3.30.40.10. 1 hit.
InterProiIPR000219. DH-domain.
IPR001849. PH_domain.
IPR011993. PH_like_dom.
IPR000306. Znf_FYVE.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF01363. FYVE. 1 hit.
PF00169. PH. 1 hit.
PF00621. RhoGEF. 1 hit.
[Graphical view]
SMARTiSM00064. FYVE. 1 hit.
SM00233. PH. 2 hits.
SM00325. RhoGEF. 1 hit.
[Graphical view]
SUPFAMiSSF48065. SSF48065. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS50010. DH_2. 1 hit.
PS50003. PH_DOMAIN. 2 hits.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5JSP0-1) [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
MESGRGSSTP PGPIAALGMP DTGPGSSSLG KLQALPVGPR AHCGDPVSLA
60 70 80 90 100
AAGDGSPDIG PTGELSGSLK IPNRDSGIDS PSSSVAGENF PCEEGLEAGP
110 120 130 140 150
SPTVLGAHAE MALDSQVPKV TPQEEADSDV GEEPDSENTP QKADKDAGLA
160 170 180 190 200
QHSGPQKLLH IAQELLHTEE TYVKRLHLLD QVFCTRLTDA GIPPEVIMGI
210 220 230 240 250
FSNISSIHRF HGQFLLPELK TRITEEWDTN PRLGDILQKL APFLKMYGEY
260 270 280 290 300
VKNFDRAVGL VSTWTQRSPL FKDVVHSIQK QEVCGNLTLQ HHMLEPVQRV
310 320 330 340 350
PRYELLLKDY LKRLPQDAPD RKDAERSLEL ISTAANHSNA AIRKVEKMHK
360 370 380 390 400
LLEVYEQLGG EEDIVNPANE LIKEGQIQKL SAKNGTPQDR HLFLFNSMIL
410 420 430 440 450
YCVPKLRLMG QKFSVREKMD ISGLQVQDIV KPNTAHTFII TGRKRSLELQ
460 470 480 490 500
TRTEEEKKEW IQIIQATIEK HKQNSETFKA FGGAFSQDED PSLSPDMPIT
510 520 530 540 550
STSPVEPVVT TEGSSGAAGL EPRKLSSKTR RDKEKQSCKS CGETFNSITK
560 570 580 590 600
RRHHCKLCGA VICGKCSEFK AENSRQSRVC RDCFLTQPVA PESTEKTPTA
610 620 630 640 650
DPQPSLLCGP LRLSESGETW SEVWAAIPMS DPQVLHLQGG SQDGRLPRTI
660 670 680 690 700
PLPSCKLSVP DPEERLDSGH VWKLQWAKQS WYLSASSAEL QQQWLETLST
710 720
AAHGDTAQDS PGALQLQVPM GAAAP
Length:725
Mass (Da):79,401
Last modified:February 15, 2005 - v1
Checksum:i665A7FF5BE16B44B
GO
Isoform 2 (identifier: Q5JSP0-2) [UniParc]FASTAAdd to basket

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.

Show »
Length:634
Mass (Da):68,794
Checksum:i6EC385CE5B2CB426
GO
Isoform 3 (identifier: Q5JSP0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     596-596: Missing.

Note: No experimental confirmation available.

Show »
Length:724
Mass (Da):79,273
Checksum:i4D87C3D1D8FAB9B4
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti275 – 2751V → I.1 Publication
Corresponds to variant rs3802384 [ dbSNP | Ensembl ].
VAR_021492

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei596 – 63439KTPTA…SDPQV → VGAPSSCSPPGGAAEPPDTC SCAPAAPAASAFGVSLGPG in isoform 2. 1 PublicationVSP_013074Add
BLAST
Alternative sequencei596 – 5961Missing in isoform 3. CuratedVSP_055703
Alternative sequencei635 – 72591Missing in isoform 2. 1 PublicationVSP_013075Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY211386 mRNA. Translation: AAP20645.1.
AL389924 Genomic DNA. No translation available.
AL451065 Genomic DNA. No translation available.
BC032429 mRNA. Translation: AAH32429.1.
BC111054 mRNA. Translation: AAI11055.1.
CCDSiCCDS43849.1. [Q5JSP0-1]
CCDS69619.1. [Q5JSP0-3]
RefSeqiNP_001077005.1. NM_001083536.1. [Q5JSP0-1]
NP_001273922.1. NM_001286993.1. [Q5JSP0-3]
NP_149077.2. NM_033086.2. [Q5JSP0-1]
UniGeneiHs.411081.

Genome annotation databases

EnsembliENST00000337352; ENSP00000336914; ENSG00000127084. [Q5JSP0-1]
ENST00000375482; ENSP00000364631; ENSG00000127084. [Q5JSP0-1]
ENST00000416701; ENSP00000413833; ENSG00000127084. [Q5JSP0-3]
ENST00000467786; ENSP00000432310; ENSG00000127084. [Q5JSP0-2]
GeneIDi89846.
KEGGihsa:89846.
UCSCiuc004asw.2. human. [Q5JSP0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY211386 mRNA. Translation: AAP20645.1.
AL389924 Genomic DNA. No translation available.
AL451065 Genomic DNA. No translation available.
BC032429 mRNA. Translation: AAH32429.1.
BC111054 mRNA. Translation: AAI11055.1.
CCDSiCCDS43849.1. [Q5JSP0-1]
CCDS69619.1. [Q5JSP0-3]
RefSeqiNP_001077005.1. NM_001083536.1. [Q5JSP0-1]
NP_001273922.1. NM_001286993.1. [Q5JSP0-3]
NP_149077.2. NM_033086.2. [Q5JSP0-1]
UniGeneiHs.411081.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2COCNMR-A605-703[»]
ProteinModelPortaliQ5JSP0.
SMRiQ5JSP0. Positions 161-472, 528-584, 606-703.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124618. 3 interactions.
STRINGi9606.ENSP00000336914.

PTM databases

PhosphoSiteiQ5JSP0.

Polymorphism and mutation databases

BioMutaiFGD3.
DMDMi61213216.

Proteomic databases

MaxQBiQ5JSP0.
PaxDbiQ5JSP0.
PRIDEiQ5JSP0.

Protocols and materials databases

DNASUi89846.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000337352; ENSP00000336914; ENSG00000127084. [Q5JSP0-1]
ENST00000375482; ENSP00000364631; ENSG00000127084. [Q5JSP0-1]
ENST00000416701; ENSP00000413833; ENSG00000127084. [Q5JSP0-3]
ENST00000467786; ENSP00000432310; ENSG00000127084. [Q5JSP0-2]
GeneIDi89846.
KEGGihsa:89846.
UCSCiuc004asw.2. human. [Q5JSP0-1]

Organism-specific databases

CTDi89846.
GeneCardsiGC09P095709.
HGNCiHGNC:16027. FGD3.
HPAiHPA020963.
HPA021018.
neXtProtiNX_Q5JSP0.
PharmGKBiPA28104.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5422.
GeneTreeiENSGT00750000117280.
HOGENOMiHOG000220866.
HOVERGENiHBG007506.
InParanoidiQ5JSP0.
KOiK05722.
OMAiTPHEEAD.
OrthoDBiEOG7C2R0M.
PhylomeDBiQ5JSP0.
TreeFamiTF316247.

Enzyme and pathway databases

ReactomeiREACT_11051. Rho GTPase cycle.
REACT_13638. NRAGE signals death through JNK.
REACT_18407. G alpha (12/13) signalling events.

Miscellaneous databases

ChiTaRSiFGD3. human.
EvolutionaryTraceiQ5JSP0.
GeneWikiiFGD3.
GenomeRNAii89846.
NextBioi35512812.
PROiQ5JSP0.

Gene expression databases

BgeeiQ5JSP0.
CleanExiHS_FGD3.
ExpressionAtlasiQ5JSP0. baseline and differential.
GenevestigatoriQ5JSP0.

Family and domain databases

Gene3Di1.20.900.10. 1 hit.
2.30.29.30. 2 hits.
3.30.40.10. 1 hit.
InterProiIPR000219. DH-domain.
IPR001849. PH_domain.
IPR011993. PH_like_dom.
IPR000306. Znf_FYVE.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF01363. FYVE. 1 hit.
PF00169. PH. 1 hit.
PF00621. RhoGEF. 1 hit.
[Graphical view]
SMARTiSM00064. FYVE. 1 hit.
SM00233. PH. 2 hits.
SM00325. RhoGEF. 1 hit.
[Graphical view]
SUPFAMiSSF48065. SSF48065. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS50010. DH_2. 1 hit.
PS50003. PH_DOMAIN. 2 hits.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-128, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    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, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    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.

Entry informationi

Entry nameiFGD3_HUMAN
AccessioniPrimary (citable) accession number: Q5JSP0
Secondary accession number(s): F8W7P2
, Q4VX84, Q7Z7D9, Q8N5G1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: February 15, 2005
Last modified: April 29, 2015
This is version 106 of the entry and version 1 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 9
    Human chromosome 9: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.