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D,L-glycerol 3-phosphate phosphatase (G3P phosphatase) (EC 3.1.3.21)

 G3PP_MYCTU              Reviewed;         353 AA.
O33194; F2GK45; I6XYN9; Q7D849;
13-APR-2016, integrated into UniProtKB/Swiss-Prot.
01-JAN-1998, sequence version 1.
23-MAY-2018, entry version 123.
RecName: Full=D,L-glycerol 3-phosphate phosphatase {ECO:0000303|PubMed:23801751};
Short=G3P phosphatase {ECO:0000303|PubMed:23801751};
EC=3.1.3.21 {ECO:0000269|PubMed:23801751};
OrderedLocusNames=Rv1692 {ECO:0000312|EMBL:CCP44457.1},
LH57_09220 {ECO:0000312|EMBL:AIR14443.1};
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]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 27294 / TMC 102 / H37Rv;
Hazbon M.H., Riojas M.A., Damon A.M., Alalade R.O., Cantwell B.J.,
Monaco A., King S., Sohrabi A.;
"Phylogenetic analysis of Mycobacterial species using whole genome
sequences.";
Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases.
[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]
X-RAY CRYSTALLOGRAPHY (3.25 ANGSTROMS) IN COMPLEX WITH MAGNESIUM,
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE, PATHWAY, SUBUNIT, AND
DOMAIN.
STRAIN=H37Rv;
PubMed=23801751; DOI=10.1073/pnas.1221597110;
Larrouy-Maumus G., Biswas T., Hunt D.M., Kelly G., Tsodikov O.V.,
de Carvalho L.P.;
"Discovery of a glycerol 3-phosphate phosphatase reveals
glycerophospholipid polar head recycling in Mycobacterium
tuberculosis.";
Proc. Natl. Acad. Sci. U.S.A. 110:11320-11325(2013).
-!- FUNCTION: Glycerol-phosphate phosphatase with a preference for D-
glycerol 3-phosphate (sn-glycerol 1-phosphate) over L-glycerol 3-
phosphate (sn-glycerol 3-phosphate). Is the final enzyme involved
in the recycling/catabolism of glycerophospholipid polar heads. To
a lesser extent, is also able to act on glycerol 2-phosphate and
D-ribulose 5-phosphate, but cannot use D-glyceraldehyde 3-
phosphate, dihydroxyacetone-phosphate, UMP or GMP as substrates.
{ECO:0000269|PubMed:23801751}.
-!- CATALYTIC ACTIVITY: Glycerol 1-phosphate + H(2)O = glycerol +
phosphate. {ECO:0000269|PubMed:23801751}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:23801751};
Name=Co(2+); Xref=ChEBI:CHEBI:48828;
Evidence={ECO:0000269|PubMed:23801751};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:23801751};
Note=Although Co(2+) and Mn(2+) support eight- and fourfold higher
catalytic efficiency than Mg(2+), respectively, Mg(2+) is likely
the physiologically relevant catalytic divalent metal ion.
{ECO:0000269|PubMed:23801751};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.89 mM for D,L-glycerol 3-phosphate
{ECO:0000269|PubMed:23801751};
KM=1.30 mM for D-ribulose 5-phosphate
{ECO:0000269|PubMed:23801751};
KM=2.01 mM for glycerol 2-phosphate
{ECO:0000269|PubMed:23801751};
KM=19.30 mM for p-nitrophenyl 3-phosphate
{ECO:0000269|PubMed:23801751};
KM=1.10 mM for L-glycerol 3-phosphate
{ECO:0000269|PubMed:23801751};
Note=kcat is 0.77 sec(-1) with D,L-glycerol 3-phosphate as
substrate. kcat is 0.18 sec(-1) with D-ribulose 5-phosphate as
substrate. kcat is 0.18 sec(-1) with glycerol 2-phosphate as
substrate. kcat is 1.00 sec(-1) with p-nitrophenyl 3-phosphate
as substrate. kcat is 0.02 sec(-1) with L-glycerol 3-phosphate
as substrate. {ECO:0000269|PubMed:23801751};
-!- PATHWAY: Glycerolipid metabolism. {ECO:0000269|PubMed:23801751}.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23801751}.
-!- DOMAIN: Crystal structures of Rv1692 reveal a unique architecture,
a fusion of a predicted haloacid dehalogenase fold with a
previously unidentified GCN5-related N-acetyltransferase (GNAT)
region. Although not directly involved in acetyl transfer, or
regulation of enzymatic activity in vitro, the GNAT region is
critical for the solubility of the phosphatase.
{ECO:0000269|PubMed:23801751}.
-!- DISRUPTION PHENOTYPE: Deletion of this gene results in an
accumulation of G3P and G3P-containing lipid polar heads.
{ECO:0000269|PubMed:23801751}.
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL123456; CCP44457.1; -; Genomic_DNA.
EMBL; CP009480; AIR14443.1; -; Genomic_DNA.
RefSeq; NP_216208.1; NC_000962.3.
RefSeq; WP_003408380.1; NZ_KK339370.1.
PDB; 4I9G; X-ray; 3.25 A; A/B=1-353.
PDBsum; 4I9G; -.
ProteinModelPortal; O33194; -.
SMR; O33194; -.
STRING; 83332.Rv1692; -.
SwissLipids; SLP:000001039; -.
PaxDb; O33194; -.
EnsemblBacteria; AIR14443; AIR14443; LH57_09220.
EnsemblBacteria; CCP44457; CCP44457; Rv1692.
GeneID; 885241; -.
KEGG; mtu:Rv1692; -.
KEGG; mtv:RVBD_1692; -.
PATRIC; fig|83332.111.peg.1880; -.
TubercuList; Rv1692; -.
eggNOG; ENOG4105DSU; Bacteria.
eggNOG; COG0647; LUCA.
HOGENOM; HOG000068103; -.
OMA; VFGTAYC; -.
PhylomeDB; O33194; -.
Proteomes; UP000001584; Chromosome.
Proteomes; UP000031768; Chromosome.
GO; GO:0050897; F:cobalt ion binding; IDA:UniProtKB.
GO; GO:0000121; F:glycerol-1-phosphatase activity; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0006071; P:glycerol metabolic process; IEA:UniProtKB-KW.
GO; GO:0046475; P:glycerophospholipid catabolic process; IMP:UniProtKB.
Gene3D; 3.40.50.1000; -; 3.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR006357; HAD-SF_hydro_IIA.
InterPro; IPR023214; HAD_sf.
Pfam; PF13344; Hydrolase_6; 1.
PIRSF; PIRSF000915; PGP-type_phosphatase; 1.
SUPFAM; SSF56784; SSF56784; 1.
TIGRFAMs; TIGR01460; HAD-SF-IIA; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Glycerol metabolism; Hydrolase;
Magnesium; Metal-binding; Reference proteome.
CHAIN 1 353 D,L-glycerol 3-phosphate phosphatase.
/FTId=PRO_0000435901.
ACT_SITE 14 14 Nucleophile.
{ECO:0000250|UniProtKB:Q96GD0}.
ACT_SITE 16 16 Proton donor.
{ECO:0000250|UniProtKB:Q96GD0}.
METAL 14 14 Magnesium. {ECO:0000244|PDB:4I9G,
ECO:0000269|PubMed:23801751}.
METAL 16 16 Magnesium; via carbonyl oxygen.
{ECO:0000244|PDB:4I9G,
ECO:0000269|PubMed:23801751}.
METAL 209 209 Magnesium. {ECO:0000244|PDB:4I9G,
ECO:0000269|PubMed:23801751}.
TURN 4 7 {ECO:0000244|PDB:4I9G}.
STRAND 9 14 {ECO:0000244|PDB:4I9G}.
TURN 15 18 {ECO:0000244|PDB:4I9G}.
STRAND 19 21 {ECO:0000244|PDB:4I9G}.
HELIX 29 34 {ECO:0000244|PDB:4I9G}.
STRAND 38 44 {ECO:0000244|PDB:4I9G}.
HELIX 51 61 {ECO:0000244|PDB:4I9G}.
HELIX 67 69 {ECO:0000244|PDB:4I9G}.
STRAND 70 72 {ECO:0000244|PDB:4I9G}.
HELIX 73 82 {ECO:0000244|PDB:4I9G}.
STRAND 90 95 {ECO:0000244|PDB:4I9G}.
HELIX 97 104 {ECO:0000244|PDB:4I9G}.
TURN 105 107 {ECO:0000244|PDB:4I9G}.
STRAND 109 111 {ECO:0000244|PDB:4I9G}.
STRAND 119 123 {ECO:0000244|PDB:4I9G}.
HELIX 131 142 {ECO:0000244|PDB:4I9G}.
STRAND 146 150 {ECO:0000244|PDB:4I9G}.
STRAND 154 158 {ECO:0000244|PDB:4I9G}.
STRAND 161 164 {ECO:0000244|PDB:4I9G}.
HELIX 166 177 {ECO:0000244|PDB:4I9G}.
HELIX 190 199 {ECO:0000244|PDB:4I9G}.
STRAND 202 209 {ECO:0000244|PDB:4I9G}.
TURN 211 213 {ECO:0000244|PDB:4I9G}.
HELIX 214 220 {ECO:0000244|PDB:4I9G}.
STRAND 225 228 {ECO:0000244|PDB:4I9G}.
HELIX 235 239 {ECO:0000244|PDB:4I9G}.
HELIX 243 245 {ECO:0000244|PDB:4I9G}.
STRAND 248 253 {ECO:0000244|PDB:4I9G}.
HELIX 254 258 {ECO:0000244|PDB:4I9G}.
HELIX 261 264 {ECO:0000244|PDB:4I9G}.
STRAND 265 267 {ECO:0000244|PDB:4I9G}.
STRAND 272 276 {ECO:0000244|PDB:4I9G}.
STRAND 278 285 {ECO:0000244|PDB:4I9G}.
HELIX 300 311 {ECO:0000244|PDB:4I9G}.
STRAND 323 328 {ECO:0000244|PDB:4I9G}.
HELIX 329 337 {ECO:0000244|PDB:4I9G}.
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


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