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Information on EC 3.9.1.2 - protein arginine phosphatase
for references in articles please use BRENDA:EC3.9.1.2
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EC Tree 3 Hydrolases
3.9 Acting on phosphorus-nitrogen bonds
3.9.1 Acting on phosphorus-nitrogen bonds (only sub-subclass identified to date)
3.9.1.2 protein arginine phosphatase
IUBMB Comments
The enzyme, characterized from Gram-positive bacteria, hydrolyses the phosphoramidate (P-N) bond of Nω-phospho-L-arginine residues in proteins and peptides that were phosphorylated by EC 2.7.14.1, protein arginine kinase.
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
showSynonyms
protein arginine phosphatase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
LMW-PAP
low-molecular-weight protein arginine phosphatase
PtpB
YwlE
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a [protein]-Nomega-phospho-L-arginine + H2O = a [protein]-L-arginine + phosphate
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
[protein]-Nomega-phospho-L-arginine phosphohydrolase
The enzyme, characterized from Gram-positive bacteria, hydrolyses the phosphoramidate (P-N) bond of Nomega-phospho-L-arginine residues in proteins and peptides that were phosphorylated by EC 2.7.14.1, protein arginine kinase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(N-omega-phospho Arg)n + H2O
(Arg)n + n phosphate
-
Substrates: -
Products: -
Products: -
?
(Nomega-phospho-Arg-Gly-Glu)6 + H2O
(Arg-Gly-Glu)6 + 6 phosphate
-
Substrates: -
Products: -
Products: -
?
(Nomega-phospho-Arg-Gly-Phe)6 + H2O
(Arg-Gly-Phe)6 + 6 phosphate
-
Substrates: -
Products: -
Products: -
?
4-nitrophenyl phosphate + H2O
4-nitrophenol + phosphate
Substrates: -
Products: -
Products: -
?
4-nitrophenyl phosphate + H2O
nitrophenol + phosphate
-
Substrates: -
Products: -
Products: -
?
KpRGGGGYIKIIKV + H2O
KRGGGGYIKIIKV + phosphate
Substrates: hydrolysis of the phosphoramidate bond of phospho-arginine residues in peptides
Products: -
Products: -
?
[culpeine]-Nomega-phospho-L-arginine + H2O
[culpeine]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[histone VIII]-Nomega-phospho-L-arginine + H2O
[histone VIII]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[histone V]-Nomega-phospho-L-arginine + H2O
[histone V]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[protein]-Nomega-phospho-L-arginine + H2O
[protein]-L-arginine + phosphate
Substrates: -
Products: -
Products: -
?
[protein]-tyrosine phosphate + H2O
[protein]-tyrosine + phosphate
Substrates: very low activity
Products: -
Products: -
?
[salmine]-Nomega-phospho-L-arginine + H2O
[salmine]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
a [protein]-Nomega-phospho-L-arginine + H2O
a [protein]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
a [protein]-Nomega-phospho-L-arginine + H2O
a [protein]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
a [protein]-Nomega-phospho-L-arginine + H2O
a [protein]-L-arginine + phosphate
Staphylococcus aureus SA564
-
Substrates: -
Products: -
Products: -
?
phospho-L-arginine + H2O
L-arginine + phosphate
Substrates: -
Products: -
Products: -
?
phospho-L-arginine + H2O
L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[chaperone Tig]-Nomega-phospho-L-arginine + H2O
[chaperone Tig]-L-arginine + phosphate
-
Substrates: during germination, the enzyme (YwlE) dephosphorylates an Arg site on the ribosome associated chaperone Tig, enabling its association with the ribosome to reestablish translation
Products: -
Products: -
?
[chaperone Tig]-Nomega-phospho-L-arginine + H2O
[chaperone Tig]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[chaperone Tig]-Nomega-phospho-L-arginine + H2O
[chaperone Tig]-L-arginine + phosphate
-
Substrates: during germination, the enzyme (YwlE) dephosphorylates an Arg site on the ribosome associated chaperone Tig, enabling its association with the ribosome to reestablish translation
Products: -
Products: -
?
[chaperone Tig]-Nomega-phospho-L-arginine + H2O
[chaperone Tig]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[sigma factor A]-Nomega-phospho-L-arginine + H2O
[sigma factor A]-L-arginine + phosphate
-
Substrates: Arg dephosphorylation of the housekeeping sigma factor A (SigA), mediated by the enzyme (YwlE), facilitates germination by activating the transcriptional machinery
Products: -
Products: -
?
[sigma factor A]-Nomega-phospho-L-arginine + H2O
[sigma factor A]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
[sigma factor A]-Nomega-phospho-L-arginine + H2O
[sigma factor A]-L-arginine + phosphate
-
Substrates: Arg dephosphorylation of the housekeeping sigma factor A (SigA), mediated by the enzyme (YwlE), facilitates germination by activating the transcriptional machinery
Products: -
Products: -
?
[sigma factor A]-Nomega-phospho-L-arginine + H2O
[sigma factor A]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
additional information
?
-
Substrates: recombinant DARP is only active on phosphoarginine, no or poor activity with phosphotyrosine, phosphoserine, and phosphothreonine
Products: -
Products: -
-
additional information
?
-
-
Substrates: enzyme releases phosphate from Nomega-phosphoarginine residues of phosphopeptides
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
[protein]-Nomega-phospho-L-arginine + H2O
[protein]-L-arginine + phosphate
Substrates: -
Products: -
Products: -
?
a [protein]-Nomega-phospho-L-arginine + H2O
a [protein]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
a [protein]-Nomega-phospho-L-arginine + H2O
a [protein]-L-arginine + phosphate
-
Substrates: -
Products: -
Products: -
?
a [protein]-Nomega-phospho-L-arginine + H2O
a [protein]-L-arginine + phosphate
Staphylococcus aureus SA564
-
Substrates: -
Products: -
Products: -
?
[chaperone Tig]-Nomega-phospho-L-arginine + H2O
[chaperone Tig]-L-arginine + phosphate
-
Substrates: during germination, the enzyme (YwlE) dephosphorylates an Arg site on the ribosome associated chaperone Tig, enabling its association with the ribosome to reestablish translation
Products: -
Products: -
?
[chaperone Tig]-Nomega-phospho-L-arginine + H2O
[chaperone Tig]-L-arginine + phosphate
-
Substrates: during germination, the enzyme (YwlE) dephosphorylates an Arg site on the ribosome associated chaperone Tig, enabling its association with the ribosome to reestablish translation
Products: -
Products: -
?
[sigma factor A]-Nomega-phospho-L-arginine + H2O
[sigma factor A]-L-arginine + phosphate
-
Substrates: Arg dephosphorylation of the housekeeping sigma factor A (SigA), mediated by the enzyme (YwlE), facilitates germination by activating the transcriptional machinery
Products: -
Products: -
?
[sigma factor A]-Nomega-phospho-L-arginine + H2O
[sigma factor A]-L-arginine + phosphate
-
Substrates: Arg dephosphorylation of the housekeeping sigma factor A (SigA), mediated by the enzyme (YwlE), facilitates germination by activating the transcriptional machinery
Products: -
Products: -
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
N-{(2S)-1-amino-5-[(2-imino-2,5-dihydro-1,3-selenazol-4-yl)amino]-1-oxopentan-2-yl}benzamide
irreversible inhibition, kinact/KI is 310 per M and min, by inducing disulfide bond formation between the two active site cysteine residues
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
calculation of kinetics, Michaelis-Menten curves and Lineweaver-Burk plots, overview
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00169
4-nitrophenyl phosphate
mutant C14S, pH 7.6, 25°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the Drosophila melanogaster genome contains four low molecular weight protein tyrosine phosphatase (LMW-PTP) members: Primo-1, Primo-2, CG14297, and CG31469 (DARP)
malfunction
physiological function
additional information
the enzyme protein adopts the typical LMW-PTP fold and has a canonically arranged P-loop, crystal structure analysis. CG31469 is unique as it contains a threonine residue at the fifth position of the P-loop motif instead of highly conserved isoleucine and a characteristically narrow active site pocket, which should facilitate the accommodation of phosphoarginine. CG31469 is enzymatically active on phosphoarginine. The catalytic motif of DARP is composed of C7IGNTCR13 and is located at the beta1-alpha1 loop, which is called the phosphate-binding loop or simply P-loop. The P-loop motif contains the catalytic serine, which functions as a nucleophile, and the conserved arginine residue (Arg13 in DARP), which anchors the phosphate group of the substrate during dephosphorylation, structural analysis of the catalytic pocket, catalytic loop arrangement and substrate binding, overview. DARP has a characteristically narrow catalytic pocket compared to that of low molecular weight-protein tyrosine phosphatases (LMW-PTPs). The accessibility of the catalytic pocket region, which is controlled by the presence of nonconserved threonine in the P-loop region and the pocket size, determines the substrate preference of DARP. The threonine residue at position 5 of the P-loop significantly contributes to the substrate specificity of DARP. DARP is a cysteine-based phosphatase
malfunction
-
enzyme inactivation significantly decreases the capacity of the mutant to degrade extracellular DNA, to hydrolyze proteins in the extracellular milieu, and to withstand Triton X-100 induced autolysis. Enzyme-deficient mutant cells are additionally ingested faster by polymorphonuclear leukocytes in a whole blood phagocytosis assay
malfunction
Staphylococcus aureus SA564
-
enzyme inactivation significantly decreases the capacity of the mutant to degrade extracellular DNA, to hydrolyze proteins in the extracellular milieu, and to withstand Triton X-100 induced autolysis. Enzyme-deficient mutant cells are additionally ingested faster by polymorphonuclear leukocytes in a whole blood phagocytosis assay
-
physiological function
a mutant lacking the YwlE arginine phosphatase accumulates a strikingly large number of arginine phosphorylations i.e. 217 sites in 134 proteins, however only a minor fraction of these sites is increasingly modified during heat shock or oxidative stress. The main proteins accumulating comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine
physiological function
-
an enzyme deletion strain accumulates arginine phosphorylated proteins and allows for identification of 121 phosphorylation sites for 87 proteins. Protein arginine phosphorylation has a functional role and is involved in the regulation of many critical cellular processes, such as protein degradation, motility, competence, and stringent and stress responses
physiological function
-
during germination, the enzyme (YwlE) dephosphorylates an Arg site on the ribosome associated chaperone Tig, enabling its association with the ribosome to reestablish translation. Arg dephosphorylation of the housekeeping sigma factor A (SigA), mediated by the enzyme (YwlE), facilitates germination by activating the transcriptional machinery
physiological function
-
the enzyme negatively regulates arginine phosphorylation and consequently induces the expression of stress-response genes that are crucial for bacterial stress tolerance and pathogenic homolog Staphylococcus aureus virulence
physiological function
-
the enzyme contributes positively to the ability of Staphylococcus aureus to evade host innate immunity. The enzyme promotes the transcription and secretion of nuclease, the transcription of the aureolysin encoding gene, and reduces the autolytic activity of Staphylococcus aureus
physiological function
-
a mutant lacking the YwlE arginine phosphatase accumulates a strikingly large number of arginine phosphorylations i.e. 217 sites in 134 proteins, however only a minor fraction of these sites is increasingly modified during heat shock or oxidative stress. The main proteins accumulating comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine
-
physiological function
-
during germination, the enzyme (YwlE) dephosphorylates an Arg site on the ribosome associated chaperone Tig, enabling its association with the ribosome to reestablish translation. Arg dephosphorylation of the housekeeping sigma factor A (SigA), mediated by the enzyme (YwlE), facilitates germination by activating the transcriptional machinery
-
physiological function
Staphylococcus aureus SA564
-
the enzyme contributes positively to the ability of Staphylococcus aureus to evade host innate immunity. The enzyme promotes the transcription and secretion of nuclease, the transcription of the aureolysin encoding gene, and reduces the autolytic activity of Staphylococcus aureus
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PAP_BACSU
Bacillus subtilis (strain 168)
150
0
16785
Swiss-Prot
Mitochondrion (Reliability: 2)
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged C7S mutant enzyme, sitting drop vapor diffusion method, mixing of 0.001 ml 12 mg/ml protein solution with 0.001 ml of precipitant solution containing 0.1 M HEPES-NaOH, pH 7.47, 1.2 M sodium citrate tribasic, and 9% w/v D-sorbitol, and equilibration against the precipitant solution, at 18°C, X-ray diffraction structure determination and analysis at 2.20 A resolution
in complex with phosphate.The phosphate-binding site is formed by the side chain of Arg13, the backbone amides of the phosphate-loop and the positive end of the macrodipole of helix H1, which together generate a highly positively charged pocket at the bottom of the substrate-binding cleft. The substrate-mimicking Arg149 is sandwiched between Thr11, Asp118, and Phe120 with its guanidinium group hydrogen bonding to Asp118. Structure of mutant C7S in complex with phosphate shows the formation of a covalent phospho-Ser7 adduct indicating that the crystallized mutant mimics the phospho-enzyme intermediate of the dephosphorylation reaction
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C9A
T11I
site-directed mutagenesis, substitution of Thr11 to isoleucine causes a remarkable decrease in the dephosphorylation of phosphoarginine and a noticeable increase in the dephosphorylation of phosphotyrosine
T11I/Y127F
site-directed mutagenesis, the dephosphorylation activity of the double mutant T11I/Y127F toward phosphotyrosine is noticeably higher than that of the T11I single mutant protein
Y127F
site-directed mutagenesis, the mutation abrogates the hydrogen bond between Tyr127 and Asn44, the Y127F mutant is slightly less active on phosphotyrosine than the wild-type enzyme
C14S
mutation of auxiliary cysteine residue present in the active site, significant resuction in kcat value
C7S
structure in complex with phosphate shows the formation of a covalent phospho-Ser7 adduct indicating that the crystallized mutant mimics the phospho-enzyme intermediate of the dephosphorylation reaction
C9S
mutation of active site cysteine, complete loss of activity
T11I
18fold reduction of specific activity with phospho-arginine substrates, marked increasing in the activity toward phospho-tyrosine substrates
T11V
18fold reduction of specific activity with phospho-arginine substrates, marked increasing in the activity toward phospho-tyrosine substrates
C9A
substrate-trapping mutant, retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. Mutant C9A stably binds to arginine-phosphorylated proteins
C9A
-
substrate-trapping mutant, retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. Mutant C9A stably binds to arginine-phosphorylated proteins
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) RIL by nickel affinity chromatography and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene CG31469, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) RIL
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
analysis
development of a substrate-trapping mutant that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. Mutant C9A stably binds to arginine-phosphorylated proteins. The substrate-trapping efficiency is improved by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captures arginine-phosphorylated proteins from complex Bacillus subtilis ywlE- cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications
analysis
-
development of a substrate-trapping mutant that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. Mutant C9A stably binds to arginine-phosphorylated proteins. The substrate-trapping efficiency is improved by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captures arginine-phosphorylated proteins from complex Bacillus subtilis ywlE- cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Elsholz, A.K.; Turgay, K.; Michalik, S.; Hessling, B.; Gronau, K.; Oertel, D.; Mader, U., Bernhardt, J., Becher, D., Hecker, M. and Gerth, U.
Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis
Proc. Natl. Acad. Sci. USA
109
7451-7456
2012
Bacillus subtilis
brenda
Fuhrmann, J.; Subramanian, V.; Thompson, P.R.
Targeting the arginine phosphatase YwlE with a catalytic redox-based inhibitor
ACS Chem. Biol.
8
2024-2032
2013
Geobacillus stearothermophilus (S0F332)
brenda
Fuhrmann, J.; Mierzwa, B.; Trentini, D.B.; Spiess, S.; Lehner, A.; Charpentier, E.; Clausen, T.
Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria
Cell Rep.
3
1832-1839
2013
Geobacillus stearothermophilus (S0F332)
brenda
Kumon, A.; Kodama, H.; Kondo, M.; Yokol, F.; Hiraishi, H.
Nomega-phosphoarginine phosphatase (17 kDa) and alkaline phosphatase as protein arginine phosphatases
J. Biochem.
119
719-724
1996
Rattus norvegicus
brenda
Trentini, D.; Fuhrmann, J.; Mechtler, K.; Clausen, T.
Chasing phosphoarginine proteins: Development of a selective enrichment method using a phosphatase trap
Mol. Cell. Proteomics
13
1953-1964
2014
Bacillus subtilis (P39155), Bacillus subtilis 168 (P39155)
brenda
Schmidt, A.; Trentini, D.B.; Spiess, S.; Fuhrmann, J.; Ammerer, G.; Mechtler, K.; Clausen, T.
Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response
Mol. Cell. Proteomics
13
537-550
2014
Bacillus subtilis (P39155), Bacillus subtilis 168 (P39155)
brenda
Zhou, B.; Semanjski, M.; Orlovetskie, N.; Bhattacharya, S.; Alon, S.; Argaman, L.; Jarrous, N.; Zhang, Y.; Macek, B.; Sinai, L.; Ben-Yehuda, S.
Arginine dephosphorylation propels spore germination in bacteria
Proc. Natl. Acad. Sci. USA
116
14228-14237
2019
Bacillus subtilis, Bacillus subtilis PY79
brenda
Lee, H.; Mo, Y.; Shin, H.; Kim, S.; Ku, B.
Structural and biochemical characterization of the two Drosophila low molecular weight-protein tyrosine phosphatases DARP and Primo-1
Mol. Cells
43
1035-1045
2020
Drosophila melanogaster (Q8ING6)
brenda
Huang, B.; Zhao, Z.; Huang, C.; Zhao, M.; Zhang, Y.; Liu, Y.; Liao, X.; Huang, S.; Zhao, Y.
Role of metal cations and oxyanions in the regulation of protein arginine phosphatase activity of YwlE from Bacillus subtilis
Biochim. Biophys. Acta Gen. Subj.
1864
129698
2020
Bacillus subtilis
brenda
Elhawy, M.I.; Molle, V.; Becker, S.L.; Bischoff, M.
The low-molecular weight protein arginine phosphatase PtpB affects nuclease production, cell wall integrity, and uptake rates of Staphylococcus aureus by polymorphonuclear leukocytes
Int. J. Mol. Sci.
22
5342
2021
Staphylococcus aureus, Staphylococcus aureus SA564
brenda
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