P31412 (VATC_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
V-type proton ATPase subunit C
Short name=V-ATPase subunit C

Alternative name(s):
V-ATPase 42 kDa subunit
Vacuolar proton pump subunit C

Gene names

Name:	VMA5
Synonyms:	VAT3, VATC
Ordered Locus Names:	YKL080W
ORF Names:	YKL410

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	392 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C acts as a flexible stator that holds together the catalytic and the membrane sectors of the enzyme. Reversibly leaves the enzyme after glucose depletion, causing the catalytic subcomplex V1 to detach from the V0 section. Binds ATP and is likely to have a specific function in the catalytic activity of the catalytic sector. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. Ref.8
Subunit structure	V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex (components: a, c, c', c'', d and e). Interacts directly with VMA4. Ref.1 Ref.12
Subcellular location	Vacuole membrane; Peripheral membrane protein Ref.10.
Miscellaneous	Present with 21114 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the V-ATPase C subunit family.
Sequence caution	The sequence AAA34440.1 differs from that shown. Reason: Frameshift at position 25.

Ontologies

Keywords
Biological process	Hydrogen ion transport Ion transport Transport
Cellular component	Membrane Vacuole
Ligand	ATP-binding Nucleotide-binding
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	ATP hydrolysis coupled proton transport Inferred from electronic annotation. Source: InterPro vacuolar acidification Traceable author statement PubMed 10224039PubMed 9442887. Source: SGD
Cellular_component	fungal-type vacuole membrane Traceable author statement PubMed 11717306. Source: SGD integral to membrane Inferred from sequence model PubMed 12192589. Source: SGD vacuolar proton-transporting V-type ATPase, V1 domain Traceable author statement PubMed 10224039PubMed 9442887. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW proton-transporting ATPase activity, rotational mechanism Traceable author statement PubMed 10224039PubMed 9442887. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6

Chain

2 – 392

391

V-type proton ATPase subunit C

PRO_0000209358

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.6

Experimental info

Mutagenesis

255

1

F → A: Is rapidly degraded and disrupts stable ATPase assembly. Ref.9

Secondary structure

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392

Helix Strand Turn

Details...

Beta strand

9 – 17

9

Helix

30 – 36

7

Helix

38 – 41

4

Beta strand

43 – 47

5

Helix

58 – 60

3

Helix

61 – 88

28

Beta strand

94 – 96

3

Helix

107 – 112

6

Turn

118 – 120

3

Helix

127 – 165

39

Turn

170 – 172

3

Turn

176 – 178

3

Helix

181 – 183

3

Beta strand

189 – 199

11

Helix

200 – 202

3

Helix

203 – 209

7

Helix

210 – 212

3

Beta strand

213 – 217

5

Beta strand

223 – 227

5

Beta strand

229 – 239

11

Helix

240 – 242

3

Helix

243 – 252

10

Beta strand

256 – 258

3

Helix

264 – 319

56

Beta strand

325 – 332

8

Helix

337 – 348

12

Helix

349 – 352

4

Beta strand

384 – 392

9

Sequences

	Sequence		Length	Mass (Da)
	P31412 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 0CD1B814046C377E	FASTA	392	44,189
	10 20 30 40 50 60 MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT 70 80 90 100 110 120 LIVESEELSK VDNQIGASIG KIIEILQGLN ETSTNAYRTL PINNMPVPEY LENFQWQTRK 130 140 150 160 170 180 FKLDKSIKDL ITLISNESSQ LDADVRATYA NYNSAKTNLA AAERKKTGDL SVRSLHDIVK 190 200 210 220 230 240 PEDFVLNSEH LTTVLVAVPK SLKSDFEKSY ETLSKNVVPA SASVIAEDAE YVLFNVHLFK 250 260 270 280 290 300 KNVQEFTTAA REKKFIPREF NYSEELIDQL KKEHDSAASL EQSLRVQLVR LAKTAYVDVF 310 320 330 340 350 360 INWFHIKALR VYVESVLRYG LPPHFNIKII AVPPKNLSKC KSELIDAFGF LGGNAFMKDK 370 380 390 KGKINKQDTS LHQYASLVDT EYEPFVMYII NL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and mutational analysis of the gene encoding subunit C of yeast vacuolar H(+)-ATPase." Beltran C., Kopecky J., Pan Y.-C.E., Nelson H., Nelson N. J. Biol. Chem. 267:774-779(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 99-117, SUBUNIT.
[2]	"Isolation of vacuolar membrane H(+)-ATPase-deficient yeast mutants; the VMA5 and VMA4 genes are essential for assembly and activity of the vacuolar H(+)-ATPase." Ho M.N., Hill K.J., Lindorfer M.A., Stevens T.H. J. Biol. Chem. 268:221-227(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 99-111; 147-156; 242-251 AND 311-318.
[3]	"Sequence analysis of a 10 kb fragment of yeast chromosome XI identifies the SMY1 locus and reveals sequences related to a pre-mRNA splicing factor and vacuolar ATPase subunit C plus a number of unidentified open reading frames." James C.M., Gent M.E., Indge K.J., Oliver S.G. Yeast 10:247-255(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W. Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	Bienvenut W.V., Peters C. Submitted (JUN-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-70; 82-98; 126-146; 157-164; 209-215; 242-251; 259-285; 319-328 AND 342-358, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, MASS SPECTROMETRY.
[7]	"Evidence for major structural changes in subunit C of the vacuolar ATPase due to nucleotide binding." Armbruester A., Hohn C., Hermesdorf A., Schumacher K., Boersch M., Grueber G. FEBS Lett. 579:1961-1967(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 106-115 AND 358-365, NUCLEOTIDE-BINDING.
[8]	"The H subunit (Vma13p) of the yeast V-ATPase inhibits the ATPase activity of cytosolic V1 complexes." Parra K.J., Keenan K.L., Kane P.M. J. Biol. Chem. 275:21761-21767(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Mutational analysis of the subunit C (Vma5p) of the yeast vacuolar H+-ATPase." Curtis K.K., Francis S.A., Oluwatosin Y., Kane P.M. J. Biol. Chem. 277:8979-8988(2002) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF PHE-255.
[10]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]	"Defined sites of interaction between subunits E (Vma4p), C (Vma5p), and G (Vma10p) within the stator structure of the vacuolar H(+)-ATPase." Jones R.P.O., Durose L.J., Findlay J.B.C., Harrison M.A. Biochemistry 44:3933-3941(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH VMA4.
[13]	Erratum Jones R.P.O., Durose L.J., Findlay J.B.C., Harrison M.A. Biochemistry 44:11924-11924(2005)
[14]	"Crystal structure of yeast V-ATPase subunit C reveals its stator function." Drory O., Frolow F., Nelson N. EMBO Rep. 5:1148-1152(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M77143 Genomic DNA. Translation: AAA34440.1. Frameshift.
X75560 Genomic DNA. Translation: CAA53237.1.
Z28080 Genomic DNA. Translation: CAA81917.1.
BK006944 Genomic DNA. Translation: DAA09077.1.

PIR

S37905.

RefSeq

NP_012843.1. NM_001179646.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U7L	X-ray	1.75	A	1-392	[»]
4DL0	X-ray	2.90	C/I	158-277	[»]
4EFA	X-ray	2.82	C	158-277	[»]

ProteinModelPortal

P31412.

SMR

P31412. Positions 5-392.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4701N.

IntAct

P31412. 17 interactions.

MINT

MINT-496270.

STRING

4932.YKL080W.

Protein family/group databases

TCDB

3.A.2.2.3. H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) superfamily.

Proteomic databases

PaxDb

P31412.

PeptideAtlas

P31412.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKL080W; YKL080W; YKL080W.

GeneID

853782.

KEGG

sce:YKL080W.

Organism-specific databases

SGD

S000001563. VMA5.

Phylogenomic databases

eggNOG

COG5127.

GeneTree

ENSGT00390000004263.

HOGENOM

HOG000207528.

KO

K02148.

OMA

FRINQTQ.

OrthoDB

EOG4DJP54.

Gene expression databases

Genevestigator

P31412.

GermOnline

YKL080W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR004907. ATPase_V1-cplx_csu.
[Graphical view]

PANTHER

PTHR10137. PTHR10137. 1 hit.

Pfam

PF03223. V-ATPase_C. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P31412.

NextBio

974900.

Entry information

Entry name

VATC_YEAST

Accession

Primary (citable) accession number: P31412
Secondary accession number(s): D6VXK7

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 120 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program