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Protein

Probable ADP-ribose 1''-phosphate phosphatase YML087W

Gene

YMR087W

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Highly specific phosphatase involved in the metabolism of ADP-ribose 1''-phosphate (Appr1p) which is produced as a consequence of tRNA splicing. + phosphate.

Catalytic activityi

ADP-D-ribose 1''-phosphate + H2O = ADP-D-ribose + phosphate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei23Substrate1
Binding sitei55Substrate1
Active sitei80Sequence analysis1
Binding sitei80Substrate1
Active sitei90Sequence analysis1
Binding sitei90Substrate1
Active sitei145Sequence analysis1
Binding sitei148Substrate1
Binding sitei195Substrate1

GO - Molecular functioni

  • phosphatase activity Source: SGD

GO - Biological processi

  • tRNA splicing, via endonucleolytic cleavage and ligation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BioCyciYEAST:G3O-32787-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable ADP-ribose 1''-phosphate phosphatase YML087W (EC:3.1.3.84)
Gene namesi
Ordered Locus Names:YMR087W
ORF Names:YM9582.12
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR087W.
SGDiS000004693. YMR087W.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002032851 – 284Probable ADP-ribose 1''-phosphate phosphatase YML087WAdd BLAST284

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi128 ↔ 136

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiQ04299.
PRIDEiQ04299.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi35262. 16 interactors.
DIPiDIP-1320N.
IntActiQ04299. 1 interactor.
MINTiMINT-400800.

Structurei

Secondary structure

1284
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi18 – 24Combined sources7
Helixi26 – 35Combined sources10
Beta strandi47 – 52Combined sources6
Helixi54 – 62Combined sources9
Beta strandi73 – 77Combined sources5
Helixi89 – 97Combined sources9
Helixi100 – 109Combined sources10
Turni110 – 112Combined sources3
Beta strandi121 – 124Combined sources4
Helixi125 – 129Combined sources5
Beta strandi140 – 145Combined sources6
Beta strandi152 – 154Combined sources3
Helixi162 – 165Combined sources4
Helixi167 – 179Combined sources13
Beta strandi186 – 190Combined sources5
Beta strandi193 – 196Combined sources4
Helixi202 – 217Combined sources16
Helixi219 – 221Combined sources3
Helixi224 – 234Combined sources11
Helixi240 – 242Combined sources3
Helixi245 – 254Combined sources10
Helixi258 – 262Combined sources5
Turni266 – 268Combined sources3
Helixi271 – 273Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NJRX-ray1.90A1-284[»]
1TXZX-ray2.05A1-284[»]
1TY8X-ray2.10A1-284[»]
ProteinModelPortaliQ04299.
SMRiQ04299.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ04299.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini34 – 230MacroPROSITE-ProRule annotationAdd BLAST197

Sequence similaritiesi

Contains 1 Macro domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000000754.
OMAiPGLCTGY.
OrthoDBiEOG092C49L6.

Family and domain databases

InterProiIPR028071. Macro-like_dom.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF14519. Macro_2. 1 hit.
[Graphical view]
SMARTiSM00506. A1pp. 1 hit.
[Graphical view]
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q04299-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTGSLNRHSL LNGVKKMRII LCDTNEVVTN LWQESIPHAY IQNDKYLCIH
60 70 80 90 100
HGHLQSLMDS MRKGDAIHHG HSYAIVSPGN SYGYLGGGFD KALYNYFGGK
110 120 130 140 150
PFETWFRNQL GGRYHTVGSA TVVDLQRCLE EKTIECRDGI RYIIHVPTVV
160 170 180 190 200
APSAPIFNPQ NPLKTGFEPV FNAMWNALMH SPKDIDGLII PGLCTGYAGV
210 220 230 240 250
PPIISCKSMA FALRLYMAGD HISKELKNVL IMYYLQYPFE PFFPESCKIE
260 270 280
CQKLGIDIEM LKSFNVEKDA IELLIPRRIL TLDL
Length:284
Mass (Da):32,067
Last modified:November 1, 1997 - v1
Checksum:iA8584DBB7B4B0A6B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49259 Genomic DNA. Translation: CAA89234.1.
AY558403 Genomic DNA. Translation: AAS56729.1.
BK006946 Genomic DNA. Translation: DAA09984.1.
PIRiS54463.
RefSeqiNP_013805.1. NM_001182587.1.

Genome annotation databases

EnsemblFungiiYMR087W; YMR087W; YMR087W.
GeneIDi855112.
KEGGisce:YMR087W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49259 Genomic DNA. Translation: CAA89234.1.
AY558403 Genomic DNA. Translation: AAS56729.1.
BK006946 Genomic DNA. Translation: DAA09984.1.
PIRiS54463.
RefSeqiNP_013805.1. NM_001182587.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NJRX-ray1.90A1-284[»]
1TXZX-ray2.05A1-284[»]
1TY8X-ray2.10A1-284[»]
ProteinModelPortaliQ04299.
SMRiQ04299.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35262. 16 interactors.
DIPiDIP-1320N.
IntActiQ04299. 1 interactor.
MINTiMINT-400800.

Proteomic databases

MaxQBiQ04299.
PRIDEiQ04299.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR087W; YMR087W; YMR087W.
GeneIDi855112.
KEGGisce:YMR087W.

Organism-specific databases

EuPathDBiFungiDB:YMR087W.
SGDiS000004693. YMR087W.

Phylogenomic databases

HOGENOMiHOG000000754.
OMAiPGLCTGY.
OrthoDBiEOG092C49L6.

Enzyme and pathway databases

BioCyciYEAST:G3O-32787-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ04299.
PROiQ04299.

Family and domain databases

InterProiIPR028071. Macro-like_dom.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF14519. Macro_2. 1 hit.
[Graphical view]
SMARTiSM00506. A1pp. 1 hit.
[Graphical view]
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYMX7_YEAST
AccessioniPrimary (citable) accession number: Q04299
Secondary accession number(s): D6VZR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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