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P39155 (PAP_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protein-arginine-phosphatase

Short name=PAP
EC=3.1.3.-
Alternative name(s):
Phosphoarginine phosphatase
Gene names
Name:ywlE
Ordered Locus Names:BSU36930
ORF Names:ipc-31d
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length150 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.5 Ref.9

Catalytic activity

Protein arginine phosphate + H2O = protein arginine + phosphate. Ref.9

Enzyme regulation

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. Ref.3

Induction

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. Ref.3

Disruption phenotype

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 (Ref.4 and Ref.5). Cells lacking this gene are impaired in dephosphorylating McsB-P (Ref.9). They also show a reduced resistance to ethanol stress (Ref.3). Ref.3 Ref.4 Ref.5 Ref.9

Sequence similarities

Belongs to the low molecular weight phosphotyrosine protein phosphatase family.

Caution

Was originally thought to be a protein-tyrosine-phosphatase (Ref.3). Was later shown to function as an arginine phosphatase in vivo and in vitro (Ref.4 and Ref.9).

Biophysicochemical properties

Kinetic parameters:

kcat is 0.010 sec(-1) with pNPP as substrate (at 37 degrees Celsius and pH 5.5) (Ref.3) and 0.13 sec(-1) with pNPP as substrate (at 40 degrees Celsius and pH 8.0) (Ref.9). pNPP is a phospho-tyrosine mimicking compound.

KM=0.157 mM for p-nitrophenyl-phosphate (at 37 degrees Celsius and pH 5.5) (Ref.3) Ref.3 Ref.6 Ref.9

KM=28 mM for p-nitrophenyl-phosphate (at 55 degrees Celsius) (Ref.6)

KM=61.41 mM for p-nitrophenyl-phosphate (at 40 degrees Celsius and pH 8.0) (Ref.9)

pH dependence:

Optimum pH is 5.5 with pNPP as substrate (Ref.3).

Ontologies

Keywords
   Molecular functionHydrolase
Protein phosphatase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Molecular_functionprotein tyrosine phosphatase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 150150Protein-arginine-phosphatase
PRO_0000046579

Regions

Region8 – 136Substrate binding

Sites

Active site71Nucleophile Ref.9
Active site1181Proton donor/acceptor Ref.9
Site111Important for substrate discrimination

Experimental info

Mutagenesis71C → S: Complete loss of phosphatase activity. Ref.3
Mutagenesis111T → I: 18-fold reduction in p-Arg phosphatase activity and 22-fold increase in p-Tyr phosphatase activity. Ref.9
Mutagenesis111T → V: 18-fold reduction in p-Arg phosphatase activity and 11-fold increase in p-Tyr phosphatase activity. Ref.9
Mutagenesis131R → K: Completely loss of phosphatase activity. Ref.3
Mutagenesis1181D → A: Completely loss of phosphatase activity. Ref.3 Ref.9
Mutagenesis1201F → A: 60-fold reduction in p-Arg phosphatase activity and 4-fold reduction in p-Tyr phosphatase activity. Ref.9

Secondary structure

.................... 150
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P39155 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: E1BD5EA5231DED2C

FASTA15016,785
        10         20         30         40         50         60 
MDIIFVCTGN TCRSPMAEAL FKSIAEREGL NVNVRSAGVF ASPNGKATPH AVEALFEKHI 

        70         80         90        100        110        120 
ALNHVSSPLT EELMESADLV LAMTHQHKQI IASQFGRYRD KVFTLKEYVT GSHGDVLDPF 

       130        140        150 
GGSIDIYKQT RDELEELLRQ LAKQLKKDRR 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z38002 Genomic DNA. Translation: CAA86107.1.
AL009126 Genomic DNA. Translation: CAB15710.1.
PIRS49360. I40479.
RefSeqNP_391574.1. NC_000964.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZGGNMR-A1-150[»]
4ETIX-ray1.80A1-150[»]
4ETNX-ray1.10A1-150[»]
4KK3X-ray1.70A1-150[»]
4KK4X-ray1.80A1-150[»]
ProteinModelPortalP39155.
SMRP39155. Positions 1-150.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-7148489.
STRING224308.BSU36930.

Protein family/group databases

PptaseDBP3D0507170.

Proteomic databases

PaxDbP39155.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB15710; CAB15710; BSU36930.
GeneID937021.
KEGGbsu:BSU36930.
PATRIC18979420. VBIBacSub10457_3872.

Organism-specific databases

GenoListBSU36930.

Phylogenomic databases

eggNOGCOG0394.
HOGENOMHOG000273091.
KOK01104.
OMAPMAMALL.
OrthoDBEOG6MH5JB.
PhylomeDBP39155.

Enzyme and pathway databases

BioCycBSUB:BSU36930-MONOMER.
SABIO-RKP39155.

Family and domain databases

InterProIPR023485. Ptyr_pPase_SF.
IPR000106. Tyr_phospatase/Ars_reductase.
IPR017867. Tyr_phospatase_low_mol_wt.
[Graphical view]
PANTHERPTHR11717. PTHR11717. 1 hit.
PfamPF01451. LMWPc. 1 hit.
[Graphical view]
PRINTSPR00719. LMWPTPASE.
SMARTSM00226. LMWPc. 1 hit.
[Graphical view]
SUPFAMSSF52788. SSF52788. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP39155.

Entry information

Entry namePAP_BACSU
AccessionPrimary (citable) accession number: P39155
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList