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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

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Protein phosphatase

    Enzyme and pathway databases

    BioCyciBSUB:BSU36930-MONOMER.
    BRENDAi3.1.3.48. 658.
    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 Componenti: 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.Bsubs1_010100019966.

    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.
    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.
    WP_003227664.1. NZ_JNCM01000034.1.

    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.
    WP_003227664.1. NZ_JNCM01000034.1.

    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.Bsubs1_010100019966.

    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.
    BRENDAi3.1.3.48. 658.
    SABIO-RKP39155.

    Miscellaneous databases

    EvolutionaryTraceiP39155.

    Family and domain databases

    InterProiIPR023485. Ptyr_pPase_SF.
    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: June 24, 2015
    This is version 115 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.