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Phosphoserine phosphatase SerB2 (PSP) (PSPase) (EC 3.1.3.3) (O-phosphoserine phosphohydrolase) (Protein-serine/threonine phosphatase) (EC 3.1.3.16)

 SERB2_MYCTU             Reviewed;         409 AA.
O53289; I6X638;
02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
01-JUN-1998, sequence version 1.
28-FEB-2018, entry version 116.
RecName: Full=Phosphoserine phosphatase SerB2 {ECO:0000303|PubMed:25037224, ECO:0000303|PubMed:25521849};
Short=PSP {ECO:0000303|PubMed:25037224, ECO:0000303|PubMed:25521849};
Short=PSPase;
EC=3.1.3.3 {ECO:0000269|PubMed:25037224, ECO:0000269|PubMed:25521849};
AltName: Full=O-phosphoserine phosphohydrolase {ECO:0000303|PubMed:25521849};
AltName: Full=Protein-serine/threonine phosphatase {ECO:0000305|PubMed:26984196};
EC=3.1.3.16 {ECO:0000269|PubMed:26984196};
Name=serB2 {ECO:0000303|PubMed:25037224, ECO:0000303|PubMed:25521849,
ECO:0000312|EMBL:CCP45851.1};
OrderedLocusNames=Rv3042c {ECO:0000312|EMBL:CCP45851.1};
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
DISRUPTION PHENOTYPE.
STRAIN=H37Rv;
PubMed=12657046; DOI=10.1046/j.1365-2958.2003.03425.x;
Sassetti C.M., Boyd D.H., Rubin E.J.;
"Genes required for mycobacterial growth defined by high density
mutagenesis.";
Mol. Microbiol. 48:77-84(2003).
[3]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[4]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
SUBSTRATE SPECIFICITY, ENZYME REGULATION, PATHWAY, 3D-STRUCTURE
MODELING, AND MUTAGENESIS OF ASP-185; VAL-186; SER-188; SER-273;
LYS-318 AND ASP-341.
STRAIN=ATCC 27294 / TMC 102 / H37Rv;
PubMed=25037224; DOI=10.1074/jbc.M114.597682;
Arora G., Tiwari P., Mandal R.S., Gupta A., Sharma D., Saha S.,
Singh R.;
"High throughput screen identifies small molecule inhibitors specific
for Mycobacterium tuberculosis phosphoserine phosphatase.";
J. Biol. Chem. 289:25149-25165(2014).
[5]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT, 3D-STRUCTURE
MODELING, DOMAIN, AND MUTAGENESIS OF GLY-18; GLY-108; ASP-185;
ASP-187; SER-273; LYS-318; ASP-341 AND ASP-345.
PubMed=25521849; DOI=10.1371/journal.pone.0115409;
Yadav G.P., Shree S., Maurya R., Rai N., Singh D.K., Srivastava K.K.,
Ramachandran R.;
"Characterization of M. tuberculosis SerB2, an essential HAD-family
phosphatase, reveals novel properties.";
PLoS ONE 9:E115409-E115409(2014).
[6]
FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, ENZYME REGULATION,
DRUG TARGET, AND MUTAGENESIS OF ASP-341 AND ASP-345.
PubMed=26984196; DOI=10.1007/s00018-016-2177-2;
Shree S., Singh A.K., Saxena R., Kumar H., Agarwal A., Sharma V.K.,
Srivastava K., Srivastava K.K., Sanyal S., Ramachandran R.;
"The M. tuberculosis HAD phosphatase (Rv3042c) interacts with host
proteins and is inhibited by Clofazimine.";
Cell. Mol. Life Sci. 73:3401-3417(2016).
-!- FUNCTION: Catalyzes the dephosphorylation of O-phospho-L-serine
into L-serine, a step in the L-serine biosynthetic pathway
(PubMed:25037224, PubMed:25521849). Exhibits high specificity for
L-phophoserine compared to substrates like L-phosphothreonine (5%
relative activity) and L-phosphotyrosine (1.7% relative activity)
(PubMed:25521849). {ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849}.
-!- FUNCTION: In the host, induces significant cytoskeleton
rearrangements through cofilin dephosphorylation and its
subsequent activation, and affects the expression of genes that
regulate actin dynamics. It specifically interacts with HSP90,
HSP70 and HSP27 that block apoptotic pathways but not with other
HSPs. Also interacts with GAPDH. It actively dephosphorylates MAP
kinase p38 and NF-kappa B p65 (specifically at Ser-536) that play
crucial roles in inflammatory and immune responses. This in turn
leads to down-regulation of Interleukin 8, a chemotactic and
inflammatory cytokine. Thus might help the pathogen to evade the
host's immune response (PubMed:26984196). Exogenous addition of
purified SerB2 protein to human THP-1 cells (that can be
differentiated into macrophage-like cells) induces microtubule
rearrangements; the phosphatase activity is co-related to the
elicited rearrangements, while addition of the ACT-domains alone
elicits no rearrangements (PubMed:25521849).
{ECO:0000269|PubMed:25521849, ECO:0000269|PubMed:26984196}.
-!- CATALYTIC ACTIVITY: O-phospho-L(or D)-serine + H(2)O = L(or D)-
serine + phosphate. {ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849}.
-!- CATALYTIC ACTIVITY: [a protein]-serine/threonine phosphate + H(2)O
= [a protein]-serine/threonine + phosphate.
{ECO:0000269|PubMed:26984196}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849};
Note=Binds 1 Mg(2+) ion per subunit (By similarity). Can also use
Mn(2+) (PubMed:25037224, PubMed:25521849).
{ECO:0000250|UniProtKB:Q58989, ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849};
-!- ENZYME REGULATION: Clofazimine, a drug being evaluated for XDR and
MDR tuberculosis, inhibits SerB2 phosphatase activity and reverses
the various functional effects described above and interactions
with host proteins (PubMed:26984196). Is inhibited by known PSP
inhibitors such as chlorpromazine, DL-AP3 and sodium
orthovanadate, but not by okadaic acid (PubMed:25037224,
PubMed:25521849). By binding to the ACT domains, amino-acids have
various effects on enzyme activity: L-serine and L-glycine act as
inhibitors, whereas L-lysine, L-tyrosine and L-phenylalanine are
activators (PubMed:25521849). High throughput screen has been
performed to identify specific PSP inhibitors with activity
against intracellular bacteria; the two best hits identified in
this screen, clorobiocin and rosaniline, are bactericidal and kill
bacteria in infected macrophages in a dose-dependent manner
(PubMed:25037224). {ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849, ECO:0000269|PubMed:26984196}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=92.68 uM for O-phospho-L-serine
{ECO:0000269|PubMed:25037224};
KM=135.9 uM for O-phospho-L-serine
{ECO:0000269|PubMed:25521849};
Vmax=14250 nmol/min/mg enzyme {ECO:0000269|PubMed:25521849};
Note=kcat is 8.83 min(-1) (PubMed:25037224). kcat is 25400 sec(-
1) (PubMed:25521849). {ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849};
pH dependence:
Optimum pH is 7.5 (PubMed:25037224, PubMed:25521849). Activity
declines progressively before pH 7.5 and is almost abolished at
6.0 while at higher pH the enzyme remains active till pH 9.0
(PubMed:25521849). {ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849};
Temperature dependence:
Optimum temperature is 37 degrees Celsius. Activity declines at
higher temperatures and is completely abolished by 50 degrees
Celsius. {ECO:0000269|PubMed:25521849};
-!- PATHWAY: Amino-acid biosynthesis; L-serine biosynthesis; L-serine
from 3-phospho-D-glycerate: step 3/3.
{ECO:0000305|PubMed:25037224}.
-!- SUBUNIT: Homodimer. The dimeric population shifts to a tetramer in
the presence of L-serine, which inactivates the enzyme.
{ECO:0000269|PubMed:25521849}.
-!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:26984196}. Host
cytoplasm, host cytosol {ECO:0000269|PubMed:26984196}. Note=Is
secreted into the cytosol of infected macrophages and is found in
bronchoalveolar lavage samples of tuberculosis patients. Co-
localizes with host tubulin. {ECO:0000269|PubMed:26984196}.
-!- DOMAIN: Folds into three domains, i.e. two ACT domains occurring
in tandem at the N-terminus followed by the classical phosphatase
(PSP) domain. The PSP domain alone is capable of hydrolyzing L-
phosphoserine, albeit with much reduced efficacy. The ACT domains
are involved in amino acid binding and play an important role in
modulating enzymatic activity. {ECO:0000269|PubMed:25521849}.
-!- DISRUPTION PHENOTYPE: Transposon mutagenesis experiments have
identified that SerB2 is essential for the pathogen's viability
while SerB1 is not. {ECO:0000269|PubMed:12657046}.
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. SerB
family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL123456; CCP45851.1; -; Genomic_DNA.
RefSeq; NP_217558.1; NC_000962.3.
RefSeq; WP_003912067.1; NZ_KK339370.1.
ProteinModelPortal; O53289; -.
SMR; O53289; -.
STRING; 83332.Rv3042c; -.
PaxDb; O53289; -.
EnsemblBacteria; CCP45851; CCP45851; Rv3042c.
GeneID; 887815; -.
KEGG; mtu:Rv3042c; -.
KEGG; mtv:RVBD_3042c; -.
PATRIC; fig|83332.111.peg.3389; -.
TubercuList; Rv3042c; -.
eggNOG; ENOG4105EAC; Bacteria.
eggNOG; COG0560; LUCA.
eggNOG; COG3830; LUCA.
HOGENOM; HOG000231114; -.
KO; K01079; -.
OMA; LMGFRDR; -.
PhylomeDB; O53289; -.
UniPathway; UPA00135; UER00198.
Proteomes; UP000001584; Chromosome.
GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
GO; GO:0044164; C:host cell cytosol; IEA:UniProtKB-SubCell.
GO; GO:0016597; F:amino acid binding; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004647; F:phosphoserine phosphatase activity; IDA:UniProtKB.
GO; GO:0004722; F:protein serine/threonine phosphatase activity; IDA:UniProtKB.
GO; GO:0016311; P:dephosphorylation; IDA:UniProtKB.
GO; GO:0040007; P:growth; IMP:MTBBASE.
GO; GO:0006564; P:L-serine biosynthetic process; IEA:UniProtKB-KW.
GO; GO:0006470; P:protein dephosphorylation; IDA:UniProtKB.
Gene3D; 1.10.150.210; -; 1.
Gene3D; 3.40.50.1000; -; 2.
InterPro; IPR002912; ACT_dom.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR023214; HAD_sf.
InterPro; IPR023190; Pser_Pase_dom_2.
SUPFAM; SSF56784; SSF56784; 1.
PROSITE; PS51671; ACT; 1.
1: Evidence at protein level;
Amino-acid biosynthesis; Complete proteome; Host cytoplasm; Hydrolase;
Magnesium; Metal-binding; Reference proteome; Secreted;
Serine biosynthesis.
CHAIN 1 409 Phosphoserine phosphatase SerB2.
/FTId=PRO_0000437672.
DOMAIN 8 86 ACT 1. {ECO:0000255|PROSITE-
ProRule:PRU01007}.
DOMAIN 102 174 ACT 2. {ECO:0000305|PubMed:25521849}.
REGION 273 274 Substrate binding.
{ECO:0000250|UniProtKB:Q58989}.
ACT_SITE 185 185 Nucleophile.
{ECO:0000250|UniProtKB:Q58989}.
ACT_SITE 187 187 Proton donor.
{ECO:0000250|UniProtKB:Q58989}.
METAL 185 185 Magnesium.
{ECO:0000250|UniProtKB:Q58989}.
METAL 187 187 Magnesium; via carbonyl oxygen.
{ECO:0000250|UniProtKB:Q58989}.
METAL 341 341 Magnesium.
{ECO:0000250|UniProtKB:Q58989}.
BINDING 194 194 Substrate.
{ECO:0000250|UniProtKB:Q58989}.
BINDING 230 230 Substrate.
{ECO:0000250|UniProtKB:Q58989}.
BINDING 318 318 Substrate.
{ECO:0000250|UniProtKB:Q58989}.
BINDING 344 344 Substrate.
{ECO:0000250|UniProtKB:Q58989}.
MUTAGEN 18 18 G->A: Does not bind L-serine and
correspondingly no oligomeric transitions
is observed in the presence of L-serine.
{ECO:0000269|PubMed:25521849}.
MUTAGEN 108 108 G->A: Does not bind L-serine and
correspondingly no oligomeric transitions
is observed in the presence of L-serine.
{ECO:0000269|PubMed:25521849}.
MUTAGEN 185 185 D->G: Completely abolishes enzymatic
activity. {ECO:0000269|PubMed:25037224}.
MUTAGEN 185 185 D->N: Completely abolishes enzymatic
activity. {ECO:0000269|PubMed:25521849}.
MUTAGEN 186 186 V->Q: Decreases enzymatic activity by
50%. {ECO:0000269|PubMed:25037224}.
MUTAGEN 187 187 D->N: Decreases enzymatic activity by
15%. {ECO:0000269|PubMed:25521849}.
MUTAGEN 188 188 S->A: No effect on enzymatic activity.
{ECO:0000269|PubMed:25037224}.
MUTAGEN 273 273 S->A: Completely abolishes enzymatic
activity (PubMed:25521849). Decreases
enzymatic activity by 60%
(PubMed:25037224).
{ECO:0000269|PubMed:25037224,
ECO:0000269|PubMed:25521849}.
MUTAGEN 318 318 K->A: Decreases enzymatic activity by
50%. {ECO:0000269|PubMed:25521849}.
MUTAGEN 318 318 K->E: Completely abolishes enzymatic
activity. {ECO:0000269|PubMed:25037224}.
MUTAGEN 341 341 D->G: Decreases enzymatic activity by
80%. {ECO:0000269|PubMed:25037224}.
MUTAGEN 341 341 D->N: Decreases enzymatic activity by
85%. Completely abolishes enzymatic
activity, does not elicit cytoskeletal
rearrangements, and does not suppress IL-
8 production after TNF-alpha stimulation;
when associated with N-345.
{ECO:0000269|PubMed:25521849}.
MUTAGEN 345 345 D->N: Decreases enzymatic activity by
55%. Completely abolishes enzymatic
activity, does not elicit cytoskeletal
rearrangements, and does not suppress IL-
8 production after TNF-alpha stimulation;
when associated with N-341.
{ECO:0000269|PubMed:25521849}.
SEQUENCE 409 AA; 43059 MW; A2D5C6A741A2EF89 CRC64;
MPAKVSVLIT VTGMDQPGVT SALFEVLAQH GVELLNVEQV VIRGRLTLGV LVSCPLDVAD
GTALRDDVAA AIHGVGLDVA IERSDDLPII RQPSTHTIFV LGRPITAGAF SAVARGVAAL
GVNIDFIRGI SDYPVTGLEL RVSVPPGCVG PLQIALTKVA AEEHVDVAVE DYGLAWRTKR
LIVFDVDSTL VQGEVIEMLA ARAGAQGQVA AITEAAMRGE LDFAESLQRR VATLAGLPAT
VIDDVAEQLE LMPGARTTIR TLRRLGFRCG VVSGGFRRII EPLARELMLD FVASNELEIV
DGILTGRVVG PIVDRPGKAK ALRDFASQYG VPMEQTVAVG DGANDIDMLG AAGLGIAFNA
KPALREVADA SLSHPYLDTV LFLLGVTRGE IEAADAGDCG VRRVEIPAD


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