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Protein

Protein-arginine-phosphatase

Gene

ywlE

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the specific dephosphorylation of phosphoarginine residues in a large number of proteins. Counteracts the protein arginine kinase McsB in vivo. Can dephosphorylate CtsR-P; thus, can restore the DNA-binding ability of the CtsR repressor by reversing the McsB-mediated phosphorylation. Is the only active pArg phosphatase present in B.subtilis. Exhibits almost no activity against pSer, pThr, or pTyr peptides. Appears to play a role in B.subtilis stress resistance. Protein arginine phosphorylation has a physiologically important role and is involved in the regulation of many critical cellular processes, such as protein homeostasis, motility, competence, and stringent and stress responses, by regulating gene expression and protein activity.3 Publications

Catalytic activityi

A [protein]-N(omega)-phospho-L-arginine + H2O = a [protein]-L-arginine + phosphate.1 Publication

Enzyme regulationi

Efficiently inhibited by Cu2+ ion, Zn2+ ion, sodium pyrophosphate and N-ethylmaleimide, while the addition of Mg2+, Ca2+ or Fe3+ ions has minimal effect. Inhibited in a competitive manner by vanadate.1 Publication

Kineticsi

kcat is 0.010 sec(-1) with pNPP as substrate (at 37 degrees Celsius and pH 5.5) (PubMed:15995210) and 0.13 sec(-1) with pNPP as substrate (at 40 degrees Celsius and pH 8.0) (PubMed:23770242). pNPP is a phospho-tyrosine mimicking compound.2 Publications

  1. KM=0.157 mM for p-nitrophenyl-phosphate (at 37 degrees Celsius and pH 5.5)3 Publications
  2. KM=28 mM for p-nitrophenyl-phosphate (at 55 degrees Celsius)3 Publications
  3. KM=61.41 mM for p-nitrophenyl-phosphate (at 40 degrees Celsius and pH 8.0)3 Publications

pH dependencei

Optimum pH is 5.5 with pNPP as substrate.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei7 – 71Nucleophile1 Publication
Sitei11 – 111Important for substrate discrimination
Active sitei118 – 1181Proton donor/acceptor1 Publication

GO - Molecular functioni

  1. protein tyrosine phosphatase activity Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Enzyme and pathway databases

BioCyciBSUB:BSU36930-MONOMER.
SABIO-RKP39155.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein-arginine-phosphatase (EC:3.9.1.21 Publication)
Short name:
PAP
Alternative name(s):
Phosphoarginine phosphatase
Gene namesi
Name:ywlE
Ordered Locus Names:BSU36930
ORF Names:ipc-31d
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU36930.

Pathology & Biotechi

Disruption phenotypei

Cellular protein arginine phosphorylation is only detectable in a ywlE mutant and not in the wild-type strain, and global gene expression is significantly impacted in the mutant strain (PubMed:22517742 and PubMed:24263382). Cells lacking this gene are impaired in dephosphorylating McsB-P (PubMed:23770242). They also show a reduced resistance to ethanol stress (PubMed:15995210).4 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi7 – 71C → S: Complete loss of phosphatase activity. 1 Publication
Mutagenesisi11 – 111T → I: 18-fold reduction in p-Arg phosphatase activity and 22-fold increase in p-Tyr phosphatase activity. 1 Publication
Mutagenesisi11 – 111T → V: 18-fold reduction in p-Arg phosphatase activity and 11-fold increase in p-Tyr phosphatase activity. 1 Publication
Mutagenesisi13 – 131R → K: Completely loss of phosphatase activity. 1 Publication
Mutagenesisi118 – 1181D → A: Completely loss of phosphatase activity. 2 Publications
Mutagenesisi120 – 1201F → A: 60-fold reduction in p-Arg phosphatase activity and 4-fold reduction in p-Tyr phosphatase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 150150Protein-arginine-phosphatasePRO_0000046579Add
BLAST

Proteomic databases

PaxDbiP39155.

Expressioni

Inductioni

Expression is up-regulated in the exponential phase of growth, followed by a significant and gradual reduction in the stationary/sporulation phase. Is not up-regulated during ethanol stress.1 Publication

Interactioni

Protein-protein interaction databases

MINTiMINT-7148489.
STRINGi224308.BSU36930.

Structurei

Secondary structure

150
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 1212Combined sources
Helixi13 – 2816Combined sources
Beta strandi32 – 387Combined sources
Helixi49 – 579Combined sources
Helixi71 – 766Combined sources
Beta strandi78 – 847Combined sources
Helixi85 – 9410Combined sources
Helixi96 – 1016Combined sources
Beta strandi102 – 1043Combined sources
Helixi105 – 1106Combined sources
Beta strandi111 – 1133Combined sources
Helixi124 – 14522Combined sources
Turni146 – 1483Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZGGNMR-A1-150[»]
4ETIX-ray1.80A1-150[»]
4ETNX-ray1.10A1-150[»]
4KK3X-ray1.70A1-150[»]
4KK4X-ray1.80A1-150[»]
ProteinModelPortaliP39155.
SMRiP39155. Positions 1-150.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39155.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 136Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0394.
HOGENOMiHOG000273091.
InParanoidiP39155.
KOiK01104.
OMAiEYVTGSH.
OrthoDBiEOG6MH5JB.
PhylomeDBiP39155.

Family and domain databases

InterProiIPR023485. Ptyr_pPase_SF.
IPR000106. Tyr_phospatase/Ars_reductase.
IPR017867. Tyr_phospatase_low_mol_wt.
[Graphical view]
PANTHERiPTHR11717:SF14. PTHR11717:SF14. 1 hit.
PfamiPF01451. LMWPc. 1 hit.
[Graphical view]
PRINTSiPR00719. LMWPTPASE.
SMARTiSM00226. LMWPc. 1 hit.
[Graphical view]
SUPFAMiSSF52788. SSF52788. 1 hit.

Sequencei

Sequence statusi: Complete.

P39155-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDIIFVCTGN TCRSPMAEAL FKSIAEREGL NVNVRSAGVF ASPNGKATPH
60 70 80 90 100
AVEALFEKHI ALNHVSSPLT EELMESADLV LAMTHQHKQI IASQFGRYRD
110 120 130 140 150
KVFTLKEYVT GSHGDVLDPF GGSIDIYKQT RDELEELLRQ LAKQLKKDRR
Length:150
Mass (Da):16,785
Last modified:February 1, 1995 - v1
Checksum:iE1BD5EA5231DED2C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38002 Genomic DNA. Translation: CAA86107.1.
AL009126 Genomic DNA. Translation: CAB15710.1.
PIRiI40479. S49360.
RefSeqiNP_391574.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB15710; CAB15710; BSU36930.
GeneIDi937021.
KEGGibsu:BSU36930.
PATRICi18979420. VBIBacSub10457_3872.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38002 Genomic DNA. Translation: CAA86107.1.
AL009126 Genomic DNA. Translation: CAB15710.1.
PIRiI40479. S49360.
RefSeqiNP_391574.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZGGNMR-A1-150[»]
4ETIX-ray1.80A1-150[»]
4ETNX-ray1.10A1-150[»]
4KK3X-ray1.70A1-150[»]
4KK4X-ray1.80A1-150[»]
ProteinModelPortaliP39155.
SMRiP39155. Positions 1-150.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-7148489.
STRINGi224308.BSU36930.

Proteomic databases

PaxDbiP39155.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15710; CAB15710; BSU36930.
GeneIDi937021.
KEGGibsu:BSU36930.
PATRICi18979420. VBIBacSub10457_3872.

Organism-specific databases

GenoListiBSU36930.

Phylogenomic databases

eggNOGiCOG0394.
HOGENOMiHOG000273091.
InParanoidiP39155.
KOiK01104.
OMAiEYVTGSH.
OrthoDBiEOG6MH5JB.
PhylomeDBiP39155.

Enzyme and pathway databases

BioCyciBSUB:BSU36930-MONOMER.
SABIO-RKP39155.

Miscellaneous databases

EvolutionaryTraceiP39155.

Family and domain databases

InterProiIPR023485. Ptyr_pPase_SF.
IPR000106. Tyr_phospatase/Ars_reductase.
IPR017867. Tyr_phospatase_low_mol_wt.
[Graphical view]
PANTHERiPTHR11717:SF14. PTHR11717:SF14. 1 hit.
PfamiPF01451. LMWPc. 1 hit.
[Graphical view]
PRINTSiPR00719. LMWPTPASE.
SMARTiSM00226. LMWPc. 1 hit.
[Graphical view]
SUPFAMiSSF52788. SSF52788. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Two genes encoding uracil phosphoribosyltransferase are present in Bacillus subtilis."
    Martinussen J., Glaser P., Andersen P.S., Saxild H.H.
    J. Bacteriol. 177:271-274(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis."
    Musumeci L., Bongiorni C., Tautz L., Edwards R.A., Osterman A., Perego M., Mustelin T., Bottini N.
    J. Bacteriol. 187:4945-4956(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE, INDUCTION, MUTAGENESIS OF CYS-7; ARG-13 AND ASP-118, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: 168 / JH642.
  4. "Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis."
    Elsholz A.K., Turgay K., Michalik S., Hessling B., Gronau K., Oertel D., Mader U., Bernhardt J., Becher D., Hecker M., Gerth U.
    Proc. Natl. Acad. Sci. U.S.A. 109:7451-7456(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ARGININE PHOSPHATASE, IDENTIFICATION OF SUBSTRATES, DISRUPTION PHENOTYPE.
    Strain: 168.
  5. "Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response."
    Schmidt A., Trentini D.B., Spiess S., Fuhrmann J., Ammerer G., Mechtler K., Clausen T.
    Mol. Cell. Proteomics 13:537-550(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION OF SUBSTRATES, DISRUPTION PHENOTYPE.
    Strain: 168.
  6. "Solution structure of a low-molecular-weight protein tyrosine phosphatase from Bacillus subtilis."
    Xu H., Xia B., Jin C.
    J. Bacteriol. 188:1509-1517(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, KINETIC PARAMETERS.
  7. "Crystal Structure of YwlE from Bacillus subtilis."
    Cao X.F.
    Submitted (APR-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS).
  8. "Crystal structure of YwlE mutant from Bacillus subtilis."
    Cao X.F., Su X.D.
    Submitted (APR-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) OF MUTANT SER-12 IN COMPLEX WITH PHOSPHATE.
  9. "Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria."
    Fuhrmann J., Mierzwa B., Trentini D.B., Spiess S., Lehner A., Charpentier E., Clausen T.
    Cell Rep. 3:1832-1839(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF WILD-TYPE IN COMPLEX WITH PHOSPHATE AND MUTANT PHOSPHO-SER-7, FUNCTION AS AN ARGININE PHOSPHATASE, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, DISRUPTION PHENOTYPE, SUBSTRATE DISCRIMINATION SITE, REACTION MECHANISM, ACTIVE SITES, MUTAGENESIS OF THR-11; ASP-118 AND PHE-120.
    Strain: 168.

Entry informationi

Entry nameiPAP_BACSU
AccessioniPrimary (citable) accession number: P39155
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: March 4, 2015
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to be a protein-tyrosine-phosphatase (PubMed:15995210). Was later shown to function as an arginine phosphatase in vivo and in vitro (PubMed:22517742 and PubMed:23770242).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.