P07560 (SEC4_YEAST) Reviewed, UniProtKB/Swiss-Prot

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 (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	215 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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. Ref.10
Subunit structure	Interacts with the guanyl-nucleotide exchange factor SEC2. Interacts with SRO7, YIF1, YIP3, YIP4 and YIP5. Ref.6 Ref.7 Ref.8 Ref.10
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.

Ontologies

Keywords
Biological process	Exocytosis Protein transport Transport
Cellular component	Cell membrane Cytoplasm Cytoplasmic vesicle Membrane
Ligand	GTP-binding Nucleotide-binding
PTM	Lipoprotein Phosphoprotein Prenylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	Golgi to plasma membrane transport Inferred from mutant phenotype. Source: SGD ascospore-type prospore assembly Inferred from mutant phenotype. Source: SGD autophagy 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 mutant phenotype. 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 transport vesicle membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	GTP binding Inferred from direct assay. Source: SGD GTPase activity Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction Ref.7Ref.8. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GDI1	P39958	4	EBI-16858,EBI-7517
YIF1	P53845	2	EBI-16858,EBI-28230
YIP3	P53633	2	EBI-16858,EBI-25301
YIP4	P53093	2	EBI-16858,EBI-24124

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

8

GTP

Nucleotide binding

75 – 79

5

GTP

Nucleotide binding

133 – 136

4

GTP By similarity

Motif

49 – 57

9

Effector region Probable

Amino acid modifications

Modified residue

8

1

Phosphoserine Ref.9

Modified residue

11

1

Phosphoserine Ref.9

Modified residue

201

1

Phosphoserine Ref.9 Ref.11 Ref.12

Modified residue

204

1

Phosphoserine Ref.9 Ref.11 Ref.12

Lipidation

214

1

S-geranylgeranyl cysteine By similarity

Lipidation

215

1

S-geranylgeranyl cysteine By similarity

Secondary structure

1

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215

Helix Strand Turn

Details...

Beta strand

20 – 28

9

Helix

33 – 42

10

Beta strand

57 – 66

10

Beta strand

68 – 74

7

Helix

79 – 81

3

Helix

87 – 90

4

Beta strand

93 – 101

9

Helix

105 – 109

5

Helix

111 – 121

11

Beta strand

127 – 133

7

Helix

144 – 154

11

Beta strand

158 – 160

3

Turn

163 – 166

4

Helix

169 – 182

14

Sequences

	Sequence		Length	Mass (Da)
	P07560 [UniParc]. Last modified August 1, 1988. Version 1. Checksum: 7DEDF7DCC7533BA7	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

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]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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.
[5]	"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. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"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.
[7]	"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.
[8]	"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.
[9]	"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. Strain: 2124.
[10]	"The yeast lgl family member Sro7p is an effector of the secretory Rab GTPase Sec4p." Grosshans B.L., Andreeva A., Gangar A., Niessen S., Yates J.R. III, Brennwald P., Novick P. J. Cell Biol. 172:55-66(2006) [PubMed: 16390997] [Abstract] Cited for: FUNCTION, INTERACTION WITH SRO7.
[11]	"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. Strain: ADR376.
[12]	"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.
[13]	"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M16507 Genomic DNA. Translation: AAA35032.1.
D50617 Genomic DNA. Translation: BAA09233.1.
AY692843 Genomic DNA. Translation: AAT92862.1.
BK006940 Genomic DNA. Translation: DAA12434.1.

PIR

TVBYQ4. A25959.

RefSeq

NP_116650.1. NM_001179961.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P07560.

SMR

P07560. Positions 19-187.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2492N.

IntAct

P07560. 19 interactions.

MINT

MINT-689902.

STRING

P07560.

Proteomic databases

PeptideAtlas

P07560.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YFL005W; YFL005W; YFL005W.

GeneID

850543.

KEGG

sce:YFL005W.

NMPDR

fig|4932.3.peg.2280.

Organism-specific databases

CYGD

YFL005w.

SGD

S000001889. SEC4.

Phylogenomic databases

eggNOG

fuNOG06918.

GeneTree

EFGT00050000002458.

HOGENOM

HBG745225.

OMA

KCDINDK.

OrthoDB

EOG4X3M9K.

Gene expression databases

ArrayExpress

P07560.

Genevestigator

P07560.

GermOnline

YFL005W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]

KO

K07976.

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

NextBio

966307.

Entry information

Entry name

SEC4_YEAST

Accession

Primary (citable) accession number: P07560
Secondary accession number(s): D6VTM4

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1988
Last modified:	December 14, 2011
This is version 140 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program