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Protein

V-type proton ATPase catalytic subunit A

Gene

VMA1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic subunit of the peripheral V1 complex of vacuolar ATPase. V-ATPase (vacuolar ATPase) is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mV, inside positive and acidic, in the vacuolar membrane vesicles. It may participate in maintenance of cytoplasmic Ca2+ homeostasis. This is a catalytic subunit.1 Publication
PI-SceI is an endonuclease that can cleave at a site present in a VMA1 allele that lacks the derived endonuclease segment of the open reading frame; cleavage at this site only occurs during meiosis and initiates "homing", a genetic event that converts a VMA1 allele lacking VDE into one that contains it.1 Publication

Catalytic activityi

ATP + H2O + H+(In) = ADP + phosphate + H+(Out).PROSITE-ProRule annotation

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi257 – 264ATPBy similarity8

GO - Molecular functioni

GO - Biological processi

  • ATP metabolic process Source: InterPro
  • cellular protein metabolic process Source: SGD
  • intein-mediated protein splicing Source: InterPro
  • intron homing Source: UniProtKB-KW
  • vacuolar acidification Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Hydrogen ion transport, Intron homing, Ion transport, Transport

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29571-MONOMER.
ReactomeiR-SCE-1222556. ROS, RNS production in response to bacteria.
R-SCE-77387. Insulin receptor recycling.
R-SCE-917977. Transferrin endocytosis and recycling.

Protein family/group databases

MEROPSiN09.001.
REBASEi2615. PI-SceI.
TCDBi3.A.2.2.3. the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
V-type proton ATPase catalytic subunit A (EC:3.6.3.14)
Short name:
V-ATPase subunit A
Alternative name(s):
Vacuolar proton pump subunit A
Cleaved into the following chain:
Alternative name(s):
Sce VMA intein
VMA1-derived endonuclease
Short name:
VDE
Gene namesi
Name:VMA1
Synonyms:CLS8, TFP1
Ordered Locus Names:YDL185W
ORF Names:D1286
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL185W.
SGDiS000002344. VMA1.

Subcellular locationi

GO - Cellular componenti

  • endomembrane system Source: UniProtKB-SubCell
  • fungal-type vacuole membrane Source: UniProtKB
  • plasma membrane Source: GO_Central
  • vacuolar proton-transporting V-type ATPase, V1 domain Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Vacuole

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi284C → S: Reduces splicing reaction speed. Inhibits splicing; when associated with N-362; S-737 and S-738 in X10SSS VDE. 3 Publications1
Mutagenesisi362H → N: Inhibits splicing; when associated with S-284; S-737 and S-738 in X10SSS VDE. 1 Publication1
Mutagenesisi737N → S: Inhibits splicing; when associated with S-284; N-362 and S-738 in X10SSS VDE. 2 Publications1
Mutagenesisi738C → S: Reduces splicing reaction speed. Inhibits splicing; when associated with S-284; N-362 and S-737 in X10SSS VDE. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources2 Publications
ChainiPRO_00000024582 – 283V-type proton ATPase catalytic subunit A, 1st partAdd BLAST282
ChainiPRO_0000002459284 – 737Endonuclease PI-SceIAdd BLAST454
ChainiPRO_0000002460738 – 1071V-type proton ATPase catalytic subunit A, 2nd partAdd BLAST334

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1 Publication1
Modified residuei131PhosphothreonineCombined sources1
Modified residuei858PhosphoserineCombined sources1
Modified residuei928PhosphoserineCombined sources1

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the VDE intervening region (intein) followed by peptide ligation.

Keywords - PTMi

Acetylation, Autocatalytic cleavage, Phosphoprotein, Protein splicing

Proteomic databases

MaxQBiP17255.
PRIDEiP17255.

2D gel databases

UCD-2DPAGEP17255.

PTM databases

iPTMnetiP17255.

Miscellaneous databases

PMAP-CutDBP17255.

Interactioni

Subunit structurei

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 with RAV1 and RAV2 components of the RAVE complex, which are essential for the stability and assembly of V-ATPase.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RAV1P471042EBI-20245,EBI-25471
VMA6P323662EBI-20245,EBI-20201

Protein-protein interaction databases

BioGridi31859. 377 interactors.
DIPiDIP-2293N.
IntActiP17255. 75 interactors.
MINTiMINT-641889.

Structurei

Secondary structure

11071
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi290 – 293Combined sources4
Beta strandi298 – 300Combined sources3
Helixi301 – 303Combined sources3
Beta strandi309 – 312Combined sources4
Beta strandi315 – 322Combined sources8
Beta strandi325 – 335Combined sources11
Beta strandi343 – 345Combined sources3
Beta strandi347 – 349Combined sources3
Beta strandi355 – 359Combined sources5
Beta strandi363 – 369Combined sources7
Beta strandi372 – 379Combined sources8
Beta strandi382 – 396Combined sources15
Beta strandi398 – 400Combined sources3
Beta strandi402 – 414Combined sources13
Helixi415 – 417Combined sources3
Helixi420 – 431Combined sources12
Beta strandi434 – 443Combined sources10
Helixi444 – 449Combined sources6
Helixi452 – 457Combined sources6
Beta strandi459 – 462Combined sources4
Turni471 – 474Combined sources4
Beta strandi479 – 481Combined sources3
Beta strandi485 – 487Combined sources3
Helixi488 – 501Combined sources14
Beta strandi506 – 514Combined sources9
Helixi516 – 528Combined sources13
Beta strandi531 – 533Combined sources3
Beta strandi534 – 537Combined sources4
Beta strandi538 – 540Combined sources3
Turni541 – 543Combined sources3
Beta strandi544 – 548Combined sources5
Turni556 – 559Combined sources4
Helixi570 – 575Combined sources6
Beta strandi579 – 584Combined sources6
Helixi588 – 591Combined sources4
Helixi595 – 609Combined sources15
Beta strandi610 – 613Combined sources4
Beta strandi619 – 625Combined sources7
Helixi627 – 639Combined sources13
Beta strandi643 – 650Combined sources8
Helixi654 – 656Combined sources3
Beta strandi657 – 659Combined sources3
Beta strandi661 – 669Combined sources9
Helixi672 – 678Combined sources7
Turni684 – 686Combined sources3
Helixi693 – 695Combined sources3
Beta strandi700 – 702Combined sources3
Beta strandi704 – 719Combined sources16
Beta strandi721 – 723Combined sources3
Beta strandi727 – 729Combined sources3
Beta strandi733 – 735Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DFAX-ray2.00A284-737[»]
1EF0X-ray2.10A/B283-741[»]
1GPPX-ray1.35A284-736[»]
1JVAX-ray2.10A/B274-747[»]
1LWSX-ray3.50A284-737[»]
1LWTX-ray3.20A284-737[»]
1UM2X-ray2.90A/B284-737[»]
C/D274-747[»]
1VDEX-ray2.40A/B284-737[»]
3J9Telectron microscopy6.90A/C/E2-1071[»]
3J9Uelectron microscopy7.60A/C/E2-1071[»]
3J9Velectron microscopy8.30A/C/E2-1071[»]
5BW9X-ray7.00A/B/C/a/b/c1-1071[»]
5D80X-ray6.20A/B/C/a/b/c1-1071[»]
ProteinModelPortaliP17255.
SMRiP17255.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17255.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini494 – 642DOD-type homing endonucleasePROSITE-ProRule annotationAdd BLAST149

Sequence similaritiesi

Belongs to the ATPase alpha/beta chains family.Curated
Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00550000074787.
HOGENOMiHOG000141780.
InParanoidiP17255.
KOiK02145.
OMAiSYHDEAQ.
OrthoDBiEOG092C12O0.

Family and domain databases

Gene3Di1.10.1140.10. 1 hit.
2.170.16.10. 1 hit.
3.10.28.10. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR031686. ATP-synth_a_Xtn.
IPR020003. ATPase_a/bsu_AS.
IPR004100. ATPase_F1/V1/A1_a/bsu_N.
IPR000194. ATPase_F1/V1/A1_a/bsu_nucl-bd.
IPR024034. ATPase_F1/V1_bsu_C.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR007868. Hom_end_hint.
IPR007869. Homing_endonuc_PI-Sce.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00006. ATP-synt_ab. 1 hit.
PF02874. ATP-synt_ab_N. 1 hit.
PF16886. ATP-synt_ab_Xtn. 1 hit.
PF05204. Hom_end. 2 hits.
PF05203. Hom_end_hint. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF50615. SSF50615. 1 hit.
SSF51294. SSF51294. 2 hits.
SSF52540. SSF52540. 2 hits.
SSF55608. SSF55608. 2 hits.
PROSITEiPS00152. ATPASE_ALPHA_BETA. 1 hit.
PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P17255-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV
60 70 80 90 100
KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRTG KPLSVELGPG
110 120 130 140 150
LMETIYDGIQ RPLKAIKEES QSIYIPRGID TPALDRTIKW QFTPGKFQVG
160 170 180 190 200
DHISGGDIYG SVFENSLISS HKILLPPRSR GTITWIAPAG EYTLDEKILE
210 220 230 240 250
VEFDGKKSDF TLYHTWPVRV PRPVTEKLSA DYPLLTGQRV LDALFPCVQG
260 270 280 290 300
GTTCIPGAFG CGKTVISQSL SKYSNSDAII YVGCFAKGTN VLMADGSIEC
310 320 330 340 350
IENIEVGNKV MGKDGRPREV IKLPRGRETM YSVVQKSQHR AHKSDSSREV
360 370 380 390 400
PELLKFTCNA THELVVRTPR SVRRLSRTIK GVEYFEVITF EMGQKKAPDG
410 420 430 440 450
RIVELVKEVS KSYPISEGPE RANELVESYR KASNKAYFEW TIEARDLSLL
460 470 480 490 500
GSHVRKATYQ TYAPILYEND HFFDYMQKSK FHLTIEGPKV LAYLLGLWIG
510 520 530 540 550
DGLSDRATFS VDSRDTSLME RVTEYAEKLN LCAEYKDRKE PQVAKTVNLY
560 570 580 590 600
SKVVRGNGIR NNLNTENPLW DAIVGLGFLK DGVKNIPSFL STDNIGTRET
610 620 630 640 650
FLAGLIDSDG YVTDEHGIKA TIKTIHTSVR DGLVSLARSL GLVVSVNAEP
660 670 680 690 700
AKVDMNGTKH KISYAIYMSG GDVLLNVLSK CAGSKKFRPA PAAAFARECR
710 720 730 740 750
GFYFELQELK EDDYYGITLS DDSDHQFLLA NQVVVHNCGE RGNEMAEVLM
760 770 780 790 800
EFPELYTEMS GTKEPIMKRT TLVANTSNMP VAAREASIYT GITLAEYFRD
810 820 830 840 850
QGKNVSMIAD SSSRWAEALR EISGRLGEMP ADQGFPAYLG AKLASFYERA
860 870 880 890 900
GKAVALGSPD RTGSVSIVAA VSPAGGDFSD PVTTATLGIT QVFWGLDKKL
910 920 930 940 950
AQRKHFPSIN TSVSYSKYTN VLNKFYDSNY PEFPVLRDRM KEILSNAEEL
960 970 980 990 1000
EQVVQLVGKS ALSDSDKITL DVATLIKEDF LQQNGYSTYD AFCPIWKTFD
1010 1020 1030 1040 1050
MMRAFISYHD EAQKAVANGA NWSKLADSTG DVKHAVSSSK FFEPSRGEKE
1060 1070
VHGEFEKLLS TMQERFAEST D
Length:1,071
Mass (Da):118,637
Last modified:January 23, 2007 - v3
Checksum:i2A4C65D2F59426FD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti875G → D in AAB63978 (PubMed:2905423).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05409 Genomic DNA. Translation: AAA34664.1.
X83276 Genomic DNA. Translation: CAA58261.1.
Z74233 Genomic DNA. Translation: CAA98760.1.
Z74233 Genomic DNA. Translation: CAA98761.1. Sequence problems.
Z74233 Genomic DNA. Translation: CAA98762.1.
X58857 Genomic DNA. Translation: CAA41657.1.
M21609 Genomic DNA. Translation: AAB63978.1.
BK006938 Genomic DNA. Translation: DAA11677.1.
PIRiA35746. PXBYVA.
RefSeqiNP_010096.1. NM_001180245.1.

Genome annotation databases

EnsemblFungiiYDL185W; YDL185W; YDL185W.
GeneIDi851342.
KEGGisce:YDL185W.

Cross-referencesi

Web resourcesi

Description of Sce VMA in Inbase

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05409 Genomic DNA. Translation: AAA34664.1.
X83276 Genomic DNA. Translation: CAA58261.1.
Z74233 Genomic DNA. Translation: CAA98760.1.
Z74233 Genomic DNA. Translation: CAA98761.1. Sequence problems.
Z74233 Genomic DNA. Translation: CAA98762.1.
X58857 Genomic DNA. Translation: CAA41657.1.
M21609 Genomic DNA. Translation: AAB63978.1.
BK006938 Genomic DNA. Translation: DAA11677.1.
PIRiA35746. PXBYVA.
RefSeqiNP_010096.1. NM_001180245.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DFAX-ray2.00A284-737[»]
1EF0X-ray2.10A/B283-741[»]
1GPPX-ray1.35A284-736[»]
1JVAX-ray2.10A/B274-747[»]
1LWSX-ray3.50A284-737[»]
1LWTX-ray3.20A284-737[»]
1UM2X-ray2.90A/B284-737[»]
C/D274-747[»]
1VDEX-ray2.40A/B284-737[»]
3J9Telectron microscopy6.90A/C/E2-1071[»]
3J9Uelectron microscopy7.60A/C/E2-1071[»]
3J9Velectron microscopy8.30A/C/E2-1071[»]
5BW9X-ray7.00A/B/C/a/b/c1-1071[»]
5D80X-ray6.20A/B/C/a/b/c1-1071[»]
ProteinModelPortaliP17255.
SMRiP17255.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31859. 377 interactors.
DIPiDIP-2293N.
IntActiP17255. 75 interactors.
MINTiMINT-641889.

Protein family/group databases

MEROPSiN09.001.
REBASEi2615. PI-SceI.
TCDBi3.A.2.2.3. the h(+)- or na(+)-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.

PTM databases

iPTMnetiP17255.

2D gel databases

UCD-2DPAGEP17255.

Proteomic databases

MaxQBiP17255.
PRIDEiP17255.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL185W; YDL185W; YDL185W.
GeneIDi851342.
KEGGisce:YDL185W.

Organism-specific databases

EuPathDBiFungiDB:YDL185W.
SGDiS000002344. VMA1.

Phylogenomic databases

GeneTreeiENSGT00550000074787.
HOGENOMiHOG000141780.
InParanoidiP17255.
KOiK02145.
OMAiSYHDEAQ.
OrthoDBiEOG092C12O0.

Enzyme and pathway databases

BioCyciYEAST:G3O-29571-MONOMER.
ReactomeiR-SCE-1222556. ROS, RNS production in response to bacteria.
R-SCE-77387. Insulin receptor recycling.
R-SCE-917977. Transferrin endocytosis and recycling.

Miscellaneous databases

EvolutionaryTraceiP17255.
PMAP-CutDBP17255.
PROiP17255.

Family and domain databases

Gene3Di1.10.1140.10. 1 hit.
2.170.16.10. 1 hit.
3.10.28.10. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR031686. ATP-synth_a_Xtn.
IPR020003. ATPase_a/bsu_AS.
IPR004100. ATPase_F1/V1/A1_a/bsu_N.
IPR000194. ATPase_F1/V1/A1_a/bsu_nucl-bd.
IPR024034. ATPase_F1/V1_bsu_C.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR007868. Hom_end_hint.
IPR007869. Homing_endonuc_PI-Sce.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00006. ATP-synt_ab. 1 hit.
PF02874. ATP-synt_ab_N. 1 hit.
PF16886. ATP-synt_ab_Xtn. 1 hit.
PF05204. Hom_end. 2 hits.
PF05203. Hom_end_hint. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF50615. SSF50615. 1 hit.
SSF51294. SSF51294. 2 hits.
SSF52540. SSF52540. 2 hits.
SSF55608. SSF55608. 2 hits.
PROSITEiPS00152. ATPASE_ALPHA_BETA. 1 hit.
PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVATA_YEAST
AccessioniPrimary (citable) accession number: P17255
Secondary accession number(s): D6VRG7, O74301, Q9Y7W5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 207 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 199895 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

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 one 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.