G3PP_MYCTU
ID G3PP_MYCTU Reviewed; 353 AA.
AC O33194; F2GK45; I6XYN9; Q7D849;
DT 13-APR-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=D-glycerol 3-phosphate phosphatase {ECO:0000305};
DE AltName: Full=D,L-glycerol 3-phosphate phosphatase {ECO:0000303|PubMed:23801751};
DE Short=G3P phosphatase {ECO:0000303|PubMed:23801751};
GN OrderedLocusNames=Rv1692 {ECO:0000312|EMBL:CCP44457.1},
GN LH57_09220 {ECO:0000312|EMBL:AIR14443.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27294 / TMC 102 / H37Rv;
RA Hazbon M.H., Riojas M.A., Damon A.M., Alalade R.O., Cantwell B.J.,
RA Monaco A., King S., Sohrabi A.;
RT "Phylogenetic analysis of Mycobacterial species using whole genome
RT sequences.";
RL Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases.
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 X-RAY CRYSTALLOGRAPHY (3.25 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, DISRUPTION PHENOTYPE, PATHWAY, SUBUNIT, AND DOMAIN.
RC STRAIN=H37Rv;
RX PubMed=23801751; DOI=10.1073/pnas.1221597110;
RA Larrouy-Maumus G., Biswas T., Hunt D.M., Kelly G., Tsodikov O.V.,
RA de Carvalho L.P.;
RT "Discovery of a glycerol 3-phosphate phosphatase reveals
RT glycerophospholipid polar head recycling in Mycobacterium tuberculosis.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:11320-11325(2013).
CC -!- FUNCTION: Dephosphorylates D-glycerol 3-phosphate (sn-glycerol 1-
CC phosphate). Is the final enzyme involved in the recycling/catabolism of
CC glycerophospholipid polar heads. To a lesser extent, is also able to
CC act on glycerol 2-phosphate and D-ribulose 5-phosphate, but cannot use
CC D-glyceraldehyde 3-phosphate, dihydroxyacetone-phosphate, UMP or GMP as
CC substrates. {ECO:0000269|PubMed:23801751}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + sn-glycerol 1-phosphate = glycerol + phosphate;
CC Xref=Rhea:RHEA:46084, ChEBI:CHEBI:15377, ChEBI:CHEBI:17754,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57685;
CC Evidence={ECO:0000269|PubMed:23801751};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:46085;
CC Evidence={ECO:0000269|PubMed:23801751};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:23801751};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:23801751};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:23801751};
CC Note=Although Co(2+) and Mn(2+) support eight- and fourfold higher
CC catalytic efficiency than Mg(2+), respectively, Mg(2+) is likely the
CC physiologically relevant catalytic divalent metal ion.
CC {ECO:0000269|PubMed:23801751};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.89 mM for D,L-glycerol 3-phosphate
CC {ECO:0000269|PubMed:23801751};
CC KM=1.30 mM for D-ribulose 5-phosphate {ECO:0000269|PubMed:23801751};
CC KM=2.01 mM for glycerol 2-phosphate {ECO:0000269|PubMed:23801751};
CC KM=19.30 mM for p-nitrophenyl 3-phosphate
CC {ECO:0000269|PubMed:23801751};
CC KM=1.10 mM for L-glycerol 3-phosphate {ECO:0000269|PubMed:23801751};
CC Note=kcat is 0.77 sec(-1) with D,L-glycerol 3-phosphate as substrate.
CC kcat is 0.18 sec(-1) with D-ribulose 5-phosphate as substrate. kcat
CC is 0.18 sec(-1) with glycerol 2-phosphate as substrate. kcat is 1.00
CC sec(-1) with p-nitrophenyl 3-phosphate as substrate. kcat is 0.02
CC sec(-1) with L-glycerol 3-phosphate as substrate.
CC {ECO:0000269|PubMed:23801751};
CC -!- PATHWAY: Glycerolipid metabolism. {ECO:0000269|PubMed:23801751}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23801751}.
CC -!- DOMAIN: Crystal structures of Rv1692 reveal a unique architecture, a
CC fusion of a predicted haloacid dehalogenase fold with a previously
CC unidentified GCN5-related N-acetyltransferase (GNAT) region. Although
CC not directly involved in acetyl transfer, or regulation of enzymatic
CC activity in vitro, the GNAT region is critical for the solubility of
CC the phosphatase. {ECO:0000269|PubMed:23801751}.
CC -!- DISRUPTION PHENOTYPE: Deletion of this gene results in an accumulation
CC of G3P and G3P-containing lipid polar heads.
CC {ECO:0000269|PubMed:23801751}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC {ECO:0000305}.
CC -!- CAUTION: Although the enzyme shows affinity to L-glycerol 3-phosphate
CC (sn-glycerol 3-phosphate), it hydrolyzes the substrate with poor
CC efficacy and is therefore not associated with EC 3.1.3.21 / RHEA:11476.
CC {ECO:0000269|PubMed:23801751}.
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DR EMBL; AL123456; CCP44457.1; -; Genomic_DNA.
DR EMBL; CP009480; AIR14443.1; -; Genomic_DNA.
DR RefSeq; NP_216208.1; NC_000962.3.
DR RefSeq; WP_003408380.1; NZ_NVQJ01000010.1.
DR PDB; 4I9G; X-ray; 3.25 A; A/B=1-353.
DR PDBsum; 4I9G; -.
DR AlphaFoldDB; O33194; -.
DR SMR; O33194; -.
DR STRING; 83332.Rv1692; -.
DR SwissLipids; SLP:000001039; -.
DR PaxDb; O33194; -.
DR PRIDE; O33194; -.
DR DNASU; 885241; -.
DR GeneID; 45425661; -.
DR GeneID; 885241; -.
DR KEGG; mtu:Rv1692; -.
DR PATRIC; fig|83332.111.peg.1880; -.
DR TubercuList; Rv1692; -.
DR eggNOG; COG0647; Bacteria.
DR HOGENOM; CLU_043473_1_0_11; -.
DR OMA; PPMHRET; -.
DR PhylomeDB; O33194; -.
DR BRENDA; 3.1.3.21; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0050897; F:cobalt ion binding; IDA:UniProtKB.
DR GO; GO:0000121; F:glycerol-1-phosphatase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0006071; P:glycerol metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0046475; P:glycerophospholipid catabolic process; IMP:UniProtKB.
DR Gene3D; 3.40.50.1000; -; 2.
DR InterPro; IPR041065; GNAT-like.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006357; HAD-SF_hydro_IIA.
DR InterPro; IPR023214; HAD_sf.
DR Pfam; PF18407; GNAT_like; 1.
DR Pfam; PF13344; Hydrolase_6; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01460; HAD-SF-IIA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycerol metabolism; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..353
FT /note="D-glycerol 3-phosphate phosphatase"
FT /id="PRO_0000435901"
FT ACT_SITE 14
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q96GD0"
FT ACT_SITE 16
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q96GD0"
FT BINDING 14
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23801751,
FT ECO:0007744|PDB:4I9G"
FT BINDING 16
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23801751,
FT ECO:0007744|PDB:4I9G"
FT BINDING 209
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23801751,
FT ECO:0007744|PDB:4I9G"
FT TURN 4..7
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 9..14
FT /evidence="ECO:0007829|PDB:4I9G"
FT TURN 15..18
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 29..34
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 38..44
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 51..61
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 73..82
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 97..104
FT /evidence="ECO:0007829|PDB:4I9G"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 131..142
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 146..150
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 154..158
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 166..177
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 190..199
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 202..209
FT /evidence="ECO:0007829|PDB:4I9G"
FT TURN 211..213
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 214..220
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 225..228
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 235..239
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 248..253
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 254..258
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 261..264
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 265..267
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 272..276
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 278..285
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 300..311
FT /evidence="ECO:0007829|PDB:4I9G"
FT STRAND 323..328
FT /evidence="ECO:0007829|PDB:4I9G"
FT HELIX 329..337
FT /evidence="ECO:0007829|PDB:4I9G"
SQ SEQUENCE 353 AA; 37011 MW; 5DBE79E0040B5849 CRC64;
MKSIAQEHDC LLIDLDGTVF CGRQPTGGAV QSLSQVRSRK LFVTNNASRS ADEVAAHLCE
LGFTATGEDV VTSAQSAAHL LAGQLAPGAR VLIVGTEALA NEVAAVGLRP VRRFEDRPDA
VVQGLSMTTG WSDLAEAALA IRAGALWVAA NVDPTLPTER GLLPGNGSMV AALRTATGMD
PRVAGKPAPA LMTEAVARGD FRAALVVGDR LDTDIEGANA AGLPSLMVLT GVNSAWDAVY
AEPVRRPTYI GHDLRSLHQD SKLLAVAPQP GWQIDVGGGA VTVCANGDVD DLEFIDDGLS
IVRAVASAVW EARAADLHQR PLRIEAGDER ARAALQRWSL MRSDHPVTSV GTQ
