GPGP_MYCTU
ID GPGP_MYCTU Reviewed; 223 AA.
AC P9WIC7; L0T9S0; P71724; Q7D764;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 43.
DE RecName: Full=Glucosyl-3-phosphoglycerate phosphatase {ECO:0000303|PubMed:22355692};
DE EC=3.1.3.85 {ECO:0000269|PubMed:22355692};
DE AltName: Full=Mannosyl-3-phosphoglycerate phosphatase;
DE EC=3.1.3.70 {ECO:0000269|PubMed:22355692};
GN Name=gpgP {ECO:0000303|PubMed:22355692}; OrderedLocusNames=Rv2419c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP PUPYLATION AT LYS-47, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=20066036; DOI=10.1371/journal.pone.0008589;
RA Festa R.A., McAllister F., Pearce M.J., Mintseris J., Burns K.E.,
RA Gygi S.P., Darwin K.H.;
RT "Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium
RT tuberculosis.";
RL PLoS ONE 5:E8589-E8589(2010).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=22355692; DOI=10.1038/srep00177;
RA Mendes V., Maranha A., Alarico S., da Costa M.S., Empadinhas N.;
RT "Mycobacterium tuberculosis Rv2419c, the missing glucosyl-3-
RT phosphoglycerate phosphatase for the second step in methylglucose
RT lipopolysaccharide biosynthesis.";
RL Sci. Rep. 1:177-177(2011).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) OF APOENZYME AND COMPLEXES WITH
RP PHOSPHATE AND VANADATE, ACTIVE SITE, REACTION MECHANISM, SUBUNIT, AND
RP MUTAGENESIS OF ARG-10; HIS-11; ASN-17; ARG-60; HIS-159 AND LEU-209.
RC STRAIN=H37Rv;
RX PubMed=24914210; DOI=10.1074/jbc.m114.569913;
RA Zheng Q., Jiang D., Zhang W., Zhang Q., Zhao Q., Jin J., Li X., Yang H.,
RA Bartlam M., Shaw N., Zhou W., Rao Z.;
RT "Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a
RT histidine phosphatase.";
RL J. Biol. Chem. 289:21242-21251(2014).
CC -!- FUNCTION: Involved in the biosynthesis of mycobacterial methylglucose
CC lipopolysaccharides (MGLPs). Catalyzes the dephosphorylation of
CC glucosyl-3-phosphoglycerate (GPG) to glucosylglycerate (GG). GPG is the
CC preferred substrate, but GpgP also exhibits low dephosphorylation
CC activity on mannosyl-3-phosphoglycerate (MPG) and mannosylglucosyl-3-
CC phosphoglycerate (MGPG) in vitro. Shows only trace of phosphoglycerate
CC mutase (PGM) activity. {ECO:0000269|PubMed:22355692}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2-O-(alpha-D-glucopyranosyl)-3-phospho-glycerate + H2O =
CC (2R)-2-O-(alpha-D-glucopyranosyl)-glycerate + phosphate;
CC Xref=Rhea:RHEA:31343, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:62510, ChEBI:CHEBI:62600; EC=3.1.3.85;
CC Evidence={ECO:0000269|PubMed:22355692};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:31344;
CC Evidence={ECO:0000269|PubMed:22355692};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-O-(alpha-D-mannosyl)-3-phosphoglycerate + H2O = (2R)-2-O-
CC (alpha-D-mannosyl)-glycerate + phosphate; Xref=Rhea:RHEA:19309,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:57541,
CC ChEBI:CHEBI:57744; EC=3.1.3.70;
CC Evidence={ECO:0000269|PubMed:22355692};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:19310;
CC Evidence={ECO:0000269|PubMed:22355692};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2-O-[alpha-D-mannopyranosyl-(1->2)-alpha-D-
CC glucopyranosyl]-3-phospho-glycerate + H2O = (2R)-2-O-[alpha-D-
CC mannopyranosyl-(1->2)-alpha-D-glucopyranosyl]-glycerate + phosphate;
CC Xref=Rhea:RHEA:47696, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:62602, ChEBI:CHEBI:87836;
CC Evidence={ECO:0000269|PubMed:22355692};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:47697;
CC Evidence={ECO:0000269|PubMed:22355692};
CC -!- ACTIVITY REGULATION: Progressively inhibited by cobalt ions at
CC concentrations between 10-50 mM and by copper ions at any concentration
CC between 1-50 mM. {ECO:0000269|PubMed:22355692}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.35 mM for glucosyl-3-phosphoglycerate (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:22355692};
CC Vmax=67.2 umol/min/mg enzyme with glucosyl-3-phosphoglycerate as
CC substrate (at 37 degrees Celsius) {ECO:0000269|PubMed:22355692};
CC pH dependence:
CC Optimum pH is 7 (at 37 degrees Celsius). Is active between pH 4.0 and
CC 10.0. {ECO:0000269|PubMed:22355692};
CC Temperature dependence:
CC Optimum temperature is 45 degrees Celsius. Is active between 20 and
CC 50 degrees Celsius. {ECO:0000269|PubMed:22355692};
CC -!- SUBUNIT: Homodimer (PubMed:22355692). Dimerization of the enzyme is
CC essential for its dephosphorylation activity (PubMed:24914210).
CC {ECO:0000269|PubMed:22355692, ECO:0000269|PubMed:24914210}.
CC -!- SIMILARITY: Belongs to the phosphoglycerate mutase family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL123456; CCP45210.1; -; Genomic_DNA.
DR PIR; F70685; F70685.
DR RefSeq; NP_216935.1; NC_000962.3.
DR RefSeq; WP_003412388.1; NZ_NVQJ01000054.1.
DR PDB; 4PZ9; X-ray; 1.94 A; A/B=1-223.
DR PDB; 4PZA; X-ray; 1.78 A; A/B=1-223.
DR PDB; 4QIH; X-ray; 2.30 A; A/B=1-223.
DR PDB; 6S2Q; X-ray; 2.50 A; A/B/C/D=1-223.
DR PDB; 6S2R; X-ray; 1.45 A; A/B=1-223.
DR PDBsum; 4PZ9; -.
DR PDBsum; 4PZA; -.
DR PDBsum; 4QIH; -.
DR PDBsum; 6S2Q; -.
DR PDBsum; 6S2R; -.
DR AlphaFoldDB; P9WIC7; -.
DR SMR; P9WIC7; -.
DR STRING; 83332.Rv2419c; -.
DR SwissLipids; SLP:000001399; -.
DR PaxDb; P9WIC7; -.
DR DNASU; 885727; -.
DR GeneID; 45426406; -.
DR GeneID; 885727; -.
DR KEGG; mtu:Rv2419c; -.
DR TubercuList; Rv2419c; -.
DR eggNOG; COG0406; Bacteria.
DR OMA; TEWNVAR; -.
DR PhylomeDB; P9WIC7; -.
DR BRENDA; 3.1.3.85; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0050531; F:mannosyl-3-phosphoglycerate phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0016791; F:phosphatase activity; IDA:UniProtKB.
DR GO; GO:0016311; P:dephosphorylation; IDA:UniProtKB.
DR CDD; cd07067; HP_PGM_like; 1.
DR Gene3D; 3.40.50.1240; -; 1.
DR InterPro; IPR013078; His_Pase_superF_clade-1.
DR InterPro; IPR029033; His_PPase_superfam.
DR InterPro; IPR001345; PG/BPGM_mutase_AS.
DR Pfam; PF00300; His_Phos_1; 1.
DR SMART; SM00855; PGAM; 1.
DR SUPFAM; SSF53254; SSF53254; 1.
DR PROSITE; PS00175; PG_MUTASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Isopeptide bond; Reference proteome;
KW Ubl conjugation.
FT CHAIN 1..223
FT /note="Glucosyl-3-phosphoglycerate phosphatase"
FT /id="PRO_0000396114"
FT ACT_SITE 11
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000269|PubMed:24914210"
FT ACT_SITE 84
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:24914210"
FT BINDING 10
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24914210"
FT BINDING 60
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24914210"
FT BINDING 159
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24914210"
FT CROSSLNK 47
FT /note="Isoglutamyl lysine isopeptide (Lys-Gln) (interchain
FT with Q-Cter in protein Pup)"
FT /evidence="ECO:0000269|PubMed:20066036"
FT MUTAGEN 10
FT /note="R->A: Loss of phosphatase activity."
FT /evidence="ECO:0000269|PubMed:24914210"
FT MUTAGEN 11
FT /note="H->A: Almost completely abolished phosphatase
FT activity."
FT /evidence="ECO:0000269|PubMed:24914210"
FT MUTAGEN 17
FT /note="N->A: About 5% of wild-type phosphatase activity."
FT /evidence="ECO:0000269|PubMed:24914210"
FT MUTAGEN 60
FT /note="R->A: Loss of phosphatase activity."
FT /evidence="ECO:0000269|PubMed:24914210"
FT MUTAGEN 159
FT /note="H->A: About 5% of wild-type phosphatase activity."
FT /evidence="ECO:0000269|PubMed:24914210"
FT MUTAGEN 209
FT /note="L->E: Disrupts dimerization of the enzyme, which
FT exists as a monomer and has lost its ability to perform
FT dephosphorylation."
FT /evidence="ECO:0000269|PubMed:24914210"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 15..18
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 32..46
FT /evidence="ECO:0007829|PDB:6S2R"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:6S2R"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 105..111
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 123..140
FT /evidence="ECO:0007829|PDB:6S2R"
FT TURN 142..145
FT /evidence="ECO:0007829|PDB:6S2R"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:6S2Q"
FT STRAND 154..158
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 160..170
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 175..180
FT /evidence="ECO:0007829|PDB:6S2R"
FT STRAND 189..196
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:6S2R"
FT STRAND 206..214
FT /evidence="ECO:0007829|PDB:6S2R"
FT HELIX 220..223
FT /evidence="ECO:0007829|PDB:6S2R"
SQ SEQUENCE 223 AA; 24174 MW; 1B5FD5DEF80A87A0 CRC64;
MRARRLVMLR HGQTDYNVGS RMQGQLDTEL SELGRTQAVA AAEVLGKRQP LLIVSSDLRR
AYDTAVKLGE RTGLVVRVDT RLRETHLGDW QGLTHAQIDA DAPGARLAWR EDATWAPHGG
ESRVDVAARS RPLVAELVAS EPEWGGADEP DRPVVLVAHG GLIAALSAAL LKLPVANWPA
LGGMGNASWT QLSGHWAPGS DFESIRWRLD VWNASAQVSS DVL
