Ras-related protein SEC4 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P07560 (SEC4_YEAST)

Last modified June 16, 2009. Version 114. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
Ras-related protein SEC4
Alternative name(s):
Suppressor of RHO3 protein 6

Gene names

Name:	SEC4
Synonyms:	SRO6
Ordered Locus Names:	YFL005W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	215 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Involved in exocytosis. Maybe by regulating the binding and fusion of secretory vesicles with the cell surface. The GTP-bound form of SEC4 may interact with an effector, thereby stimulating its activity and leading to exocytotic fusion. SEC4 may be an upstream activator of the 19.5S SEC8/SEC15 particle. SEC4 probably interacts directly with SEC8; it could serve as the attachment site for the SEC8/SEC15 particle.
Subunit structure	Interacts with the guanyl-nucleotide exchange factor SEC2. Interacts with YIF1, YIP3, YIP4 and YIP5. Ref.5 Ref.6 Ref.7
Subcellular location	Cytoplasmic vesicle › secretory vesicle membrane; Lipid-anchor; Cytoplasmic side. Cell membrane; Lipid-anchor; Cytoplasmic side. Cytoplasm. Note: A small fraction is soluble.
Sequence similarities	Belongs to the small GTPase superfamily. Rab family.

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Ontologies

Keywords
Biological process	Exocytosis Protein transport Transport
Cellular component	Cell membrane Cytoplasm Cytoplasmic vesicle Membrane
Ligand	GTP-binding Nucleotide-binding
PTM	Lipoprotein Palmitate Phosphoprotein Prenylation
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	Golgi to plasma membrane transport Inferred from mutant phenotype. Source: SGD ascospore-type prospore formation Inferred from mutant phenotype. Source: SGD bipolar cellular bud site selection Traceable author statement. Source: SGD exocytosis Inferred from direct assay. Source: SGD membrane addition at site of cytokinesis Inferred from expression pattern. Source: SGD protein transport Inferred from electronic annotation. Source: UniProtKB-KW small GTPase mediated signal transduction Traceable author statement. Source: SGD vesicle fusion Inferred from mutant phenotype. Source: SGD
Cellular component	actin cap Traceable author statement. Source: SGD incipient cellular bud site Inferred from direct assay. Source: SGD mitochondrial outer membrane Inferred from direct assay. Source: SGD plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane enriched fraction Inferred from direct assay. Source: SGD secretory granule membrane Inferred from electronic annotation. Source: UniProtKB-SubCell transport vesicle Traceable author statement. Source: SGD
Molecular function	GTP binding Inferred from direct assay. Source: SGD GTPase activity Inferred from direct assay. Source: SGD protein binding Ref.6 Ref.7 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
	P38845	1	EBI-16858,EBI-24770
	Q04322	1	EBI-16858,EBI-27427
AGP1	P25376	1	EBI-16858,EBI-2357
ALO1	P54783	1	EBI-16858,EBI-2519
CHO1	P08456	1	EBI-16858,EBI-14055
GAP1	P19145	1	EBI-16858,EBI-7314
GDI1	P39958	1	EBI-16858,EBI-7517
HXT1	P32465	1	EBI-16858,EBI-8759
MRS6	P32864	1	EBI-16858,EBI-14799
OST1	P41543	1	EBI-16858,EBI-12651
PEX11	Q12462	1	EBI-16858,EBI-13198
PMP2	P40975	1	EBI-16858,EBI-2043041
PMP3	P87284	1	EBI-16858,EBI-13555
YIF1	P53845	1	EBI-16858,EBI-28230
YIP3	P53633	1	EBI-16858,EBI-25301
YIP4	P53093	1	EBI-16858,EBI-24124

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 215

215

Ras-related protein SEC4

PRO_0000121330

Regions

Nucleotide binding

27 – 34

GTP

Nucleotide binding

75 – 79

GTP

Nucleotide binding

133 – 136

GTP By similarity

Motif

49 – 57

Effector region Probable

Amino acid modifications

Modified residue

Phosphoserine Ref.8

Modified residue

Phosphoserine Ref.8

Modified residue

201

Phosphoserine Ref.8 Ref.9 Ref.10

Modified residue

204

Phosphoserine Ref.8 Ref.9 Ref.10

Lipidation

214

S-palmitoyl cysteine By similarity

Lipidation

215

S-geranylgeranyl cysteine By similarity

Secondary structure

215

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P07560-1 [UniParc].

Last modified August 1, 1988. Version 1.
Checksum: 7DEDF7DCC7533BA7
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FASTA

215

23,506

        10         20         30         40         50         60 
MSGLRTVSAS SGNGKSYDSI MKILLIGDSG VGKSCLLVRF VEDKFNPSFI TTIGIDFKIK 

        70         80         90        100        110        120 
TVDINGKKVK LQLWDTAGQE RFRTITTAYY RGAMGIILVY DVTDERTFTN IKQWFKTVNE 

       130        140        150        160        170        180 
HANDEAQLLL VGNKSDMETR VVTADQGEAL AKELGIPFIE SSAKNDDNVN EIFFTLAKLI 

       190        200        210 
QEKIDSNKLV GVGNGKEGNI SINSGSGNSS KSNCC

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A ras-like protein is required for a post-Golgi event in yeast secretion." Salminen A., Novick P.J. Cell 49:527-538(1987) [PubMed: 3552249] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae." Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T. Nat. Genet. 10:261-268(1995) [PubMed: 7670463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI." Naitou M., Ozawa M., Sasanuma S., Kobayashi M., Hagiwara H., Shibata T., Hanaoka F., Watanabe K., Ono A., Yamazaki M., Tashiro H., Eki T., Murakami Y. Yeast 12:77-84(1996) [PubMed: 8789262] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Sec2p mediates nucleotide exchange on Sec4p and is involved in polarized delivery of post-Golgi vesicles." Walch-Solimena C., Collins R.N., Novick P.J. J. Cell Biol. 137:1495-1509(1997) [PubMed: 9199166] [Abstract] Cited for: INTERACTION WITH SEC2.
[6]	"Saccharomyces cerevisiae Pra1p/Yip3p interacts with Yip1p and Rab proteins." Calero M., Collins R.N. Biochem. Biophys. Res. Commun. 290:676-681(2002) [PubMed: 11785952] [Abstract] Cited for: INTERACTION WITH YIP3.
[7]	"Identification of the novel proteins Yip4p and Yip5p as Rab GTPase interacting factors." Calero M., Winand N.J., Collins R.N. FEBS Lett. 515:89-98(2002) [PubMed: 11943201] [Abstract] Cited for: INTERACTION WITH YIF1; YIP4 AND YIP5.
[8]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed: 11875433] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-8; SER-11; SER-201 AND SER-204, MASS SPECTROMETRY.
[9]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201 AND SER-204, MASS SPECTROMETRY.
[10]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201 AND SER-204, MASS SPECTROMETRY.
[11]	"Crystal structures of a Rab protein in its inactive and active conformations." Stroupe C., Brunger A.T. J. Mol. Biol. 304:585-598(2000) [PubMed: 11099382] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 18-187 IN COMPLEX WITH GDP AND GTP ANALOG.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

M16507 Genomic DNA. Translation: AAA35032.1.
D50617 Genomic DNA. Translation: BAA09233.1.
AY692843 Genomic DNA. Translation: AAT92862.1.

PIR

TVBYQ4. A25959.

RefSeq

NP_116650.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G16	X-ray	1.80	A/B/C/D	18-187	[»]
1G17	X-ray	2.00	A/B	18-187	[»]
2EQB	X-ray	2.70	A	19-187	[»]
2OCY	X-ray	3.30	C	18-187	[»]
3CPH	X-ray	2.90	A	1-213	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2492N.

IntAct

P07560. 24 interactions.

Proteomic databases

PeptideAtlas

P07560.

PRIDE

P07560.

Genome annotation databases

Ensembl

YFL005W. Saccharomyces cerevisiae. [Contig view]

GeneID

850543.

GenomeReviews

Gene locus YFL005W in contig D50617_GR.

KEGG

sce:YFL005W.

NMPDR

fig|4932.3.peg.2280.

Organism-specific databases

CYGD

YFL005w.

SGD

S000001889. SEC4.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P07560.

OMA

P07560. NEHANDE.

Gene expression databases

GermOnline

YFL005W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR003579. GTPase_Rab.
IPR013753. Ras.
IPR001806. Ras_GTPase.
IPR005225. Small_GTP_bd.
[Graphical view]

Pfam

PF00071. Ras. 1 hit.
[Graphical view]

PRINTS

PR00449. RASTRNSFRMNG.

SMART

SM00175. RAB. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00231. small_GTP. 1 hit.

PROSITE

PS51419. RAB. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

966307.

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Entry information

Entry name

SEC4_YEAST

Accession

Primary (citable) accession number: P07560

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1988
Last modified:	June 16, 2009
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VI

Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents