ID GMM_ECOLI Reviewed; 159 AA.
AC P32056;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 27-MAR-2002, sequence version 2.
DT 24-JAN-2024, entry version 163.
DE RecName: Full=GDP-mannose mannosyl hydrolase {ECO:0000255|HAMAP-Rule:MF_00941};
DE Short=GDPMH {ECO:0000255|HAMAP-Rule:MF_00941};
DE EC=3.6.1.- {ECO:0000255|HAMAP-Rule:MF_00941, ECO:0000269|PubMed:23481913};
DE AltName: Full=Colanic acid biosynthesis protein WcaH;
GN Name=gmm {ECO:0000255|HAMAP-Rule:MF_00941}; Synonyms=nudD, wcaH, yefC;
GN OrderedLocusNames=b2051, JW5335;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7815923; DOI=10.1093/oxfordjournals.molbev.a040166;
RA Aoyama K., Haase A.M., Reeves P.R.;
RT "Evidence for effect of random genetic drift on G+C content after lateral
RT transfer of fucose pathway genes to Escherichia coli K-12.";
RL Mol. Biol. Evol. 11:829-838(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=8759852; DOI=10.1128/jb.178.16.4885-4893.1996;
RA Stevenson G., Andrianopoulos K., Hobbs M., Reeves P.R.;
RT "Organization of the Escherichia coli K-12 gene cluster responsible for
RT production of the extracellular polysaccharide colanic acid.";
RL J. Bacteriol. 178:4885-4893(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 33694 / HB101;
RX PubMed=7592609; DOI=10.1074/jbc.270.41.24086;
RA Frick D.N., Townsend B.D., Bessman M.J.;
RT "A novel GDP-mannose mannosyl hydrolase shares homology with the MutT
RT family of enzymes.";
RL J. Biol. Chem. 270:24086-24091(1995).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND MASS SPECTROMETRY.
RC STRAIN=ATCC 33694 / HB101;
RX PubMed=10913267; DOI=10.1021/bi000537p;
RA Legler P.M., Massiah M.A., Bessman M.J., Mildvan A.S.;
RT "GDP-mannose mannosyl hydrolase catalyzes nucleophilic substitution at
RT carbon, unlike all other Nudix hydrolases.";
RL Biochemistry 39:8603-8608(2000).
RN [8]
RP MUTAGENESIS OF ARG-51; ARG-64; HIS-87; HIS-101 AND HIS-123, AND COFACTOR.
RX PubMed=12196023; DOI=10.1021/bi020362e;
RA Legler P.M., Massiah M.A., Mildvan A.S.;
RT "Mutational, kinetic, and NMR studies of the mechanism of E. coli GDP-
RT mannose mannosyl hydrolase, an unusual Nudix enzyme.";
RL Biochemistry 41:10834-10848(2002).
RN [9]
RP MUTAGENESIS OF ASP-21; ARG-36 AND TYR-102.
RX PubMed=15966723; DOI=10.1021/bi050583v;
RA Xia Z., Azurmendi H.F., Lairson L.L., Withers S.G., Gabelli S.B.,
RA Bianchet M.A., Amzel L.M., Mildvan A.S.;
RT "Mutational, structural, and kinetic evidence for a dissociative mechanism
RT in the GDP-mannose mannosyl hydrolase reaction.";
RL Biochemistry 44:8989-8997(2005).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=23481913; DOI=10.1016/j.ab.2013.02.023;
RA Xu A., Desai A.M., Brenner S.E., Kirsch J.F.;
RT "A continuous fluorescence assay for the characterization of Nudix
RT hydrolases.";
RL Anal. Biochem. 437:178-184(2013).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
RP MAGNESIUM, COFACTOR, AND SUBUNIT.
RX PubMed=15274914; DOI=10.1016/j.str.2004.03.028;
RA Gabelli S.B., Bianchet M.A., Azurmendi H.F., Xia Z., Sarawat V.,
RA Mildvan A.S., Amzel L.M.;
RT "Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme
RT that cleaves at carbon instead of phosphorus.";
RL Structure 12:927-935(2004).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT PHE-102 IN COMPLEX WITH
RP SUBSTRATE AND MAGNESIUM.
RX PubMed=16981689; DOI=10.1021/bi061239g;
RA Gabelli S.B., Azurmendi H.F., Bianchet M.A., Amzel L.M., Mildvan A.S.;
RT "X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-
RT mannose mannosyl hydrolase reaction.";
RL Biochemistry 45:11290-11303(2006).
CC -!- FUNCTION: Hydrolyzes both GDP-mannose and GDP-glucose (PubMed:7592609,
CC PubMed:10913267, PubMed:23481913). Could participate in the regulation
CC of cell wall biosynthesis by influencing the concentration of GDP-
CC mannose or GDP-glucose in the cell. Might also be involved in the
CC biosynthesis of the slime polysaccharide colanic acid (PubMed:7592609,
CC PubMed:10913267). {ECO:0000269|PubMed:10913267,
CC ECO:0000269|PubMed:23481913, ECO:0000269|PubMed:7592609}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-mannose + H2O = D-mannose + GDP + H(+);
CC Xref=Rhea:RHEA:28102, ChEBI:CHEBI:4208, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57527, ChEBI:CHEBI:58189;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00941,
CC ECO:0000269|PubMed:10913267, ECO:0000269|PubMed:23481913,
CC ECO:0000269|PubMed:7592609};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00941,
CC ECO:0000269|PubMed:10913267, ECO:0000269|PubMed:12196023,
CC ECO:0000269|PubMed:15274914};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00941,
CC ECO:0000269|PubMed:10913267, ECO:0000269|PubMed:12196023,
CC ECO:0000269|PubMed:15274914};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.3 mM for GDP-mannose {ECO:0000269|PubMed:7592609};
CC KM=1.9 mM for GDP-glucose {ECO:0000269|PubMed:7592609};
CC KM=220 uM for GDP-mannose (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:23481913};
CC Vmax=1.6 umol/min/mg enzyme with GDP-mannose as substrate
CC {ECO:0000269|PubMed:7592609};
CC Vmax=7.5 umol/min/mg enzyme with GDP-glucose as substrate
CC {ECO:0000269|PubMed:7592609};
CC Note=GDP-alpha-D-mannose is likely to be the biological substrate,
CC but the kcat/KM obtained with GDP-alpha-D-glucose is very similar to
CC that with GDP-alpha-D-mannose (PubMed:7592609). kcat is 0.35 sec(-1)
CC for GDP-mannose (PubMed:23481913). {ECO:0000269|PubMed:23481913,
CC ECO:0000269|PubMed:7592609};
CC pH dependence:
CC Optimum pH is 9.3. {ECO:0000269|PubMed:7592609};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00941,
CC ECO:0000269|PubMed:10913267, ECO:0000269|PubMed:15274914,
CC ECO:0000269|PubMed:16981689}.
CC -!- MASS SPECTROMETRY: Mass=18472; Mass_error=67; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:10913267};
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000255|HAMAP-
CC Rule:MF_00941}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC77844.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U38473; AAC77844.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC75112.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA15907.2; -; Genomic_DNA.
DR PIR; E55239; E55239.
DR RefSeq; NP_416555.2; NC_000913.3.
DR RefSeq; WP_001393539.1; NZ_LN832404.1.
DR PDB; 1RYA; X-ray; 1.30 A; A/B=1-159.
DR PDB; 2GT2; X-ray; 2.00 A; A/B/C/D=1-159.
DR PDB; 2GT4; X-ray; 2.30 A; A/B/C=1-159.
DR PDBsum; 1RYA; -.
DR PDBsum; 2GT2; -.
DR PDBsum; 2GT4; -.
DR AlphaFoldDB; P32056; -.
DR SMR; P32056; -.
DR BioGRID; 4261145; 369.
DR STRING; 511145.b2051; -.
DR DrugBank; DB04315; Guanosine-5'-Diphosphate.
DR PaxDb; 511145-b2051; -.
DR EnsemblBacteria; AAC75112; AAC75112; b2051.
DR GeneID; 946559; -.
DR KEGG; ecj:JW5335; -.
DR KEGG; eco:b2051; -.
DR PATRIC; fig|511145.12.peg.2128; -.
DR EchoBASE; EB1737; -.
DR eggNOG; COG1051; Bacteria.
DR HOGENOM; CLU_037162_12_0_6; -.
DR InParanoid; P32056; -.
DR OMA; HDNSRAY; -.
DR OrthoDB; 542521at2; -.
DR PhylomeDB; P32056; -.
DR BioCyc; EcoCyc:GDPMANMANHYDRO-MONOMER; -.
DR BioCyc; MetaCyc:GDPMANMANHYDRO-MONOMER; -.
DR SABIO-RK; P32056; -.
DR EvolutionaryTrace; P32056; -.
DR PRO; PR:P32056; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0047917; F:GDP-glucosidase activity; IDA:EcoCyc.
DR GO; GO:0008727; F:GDP-mannose mannosyl hydrolase activity; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IMP:EcoCyc.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0009103; P:lipopolysaccharide biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd03430; GDPMH; 1.
DR Gene3D; 3.90.79.10; Nucleoside Triphosphate Pyrophosphohydrolase; 1.
DR HAMAP; MF_00941; GDPMH_gmm; 1.
DR InterPro; IPR033715; GDPMH.
DR InterPro; IPR028613; GDPMH_Gmm.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR PANTHER; PTHR43046; GDP-MANNOSE MANNOSYL HYDROLASE; 1.
DR PANTHER; PTHR43046:SF12; GDP-MANNOSE MANNOSYL HYDROLASE; 1.
DR Pfam; PF00293; NUDIX; 1.
DR PIRSF; PIRSF037599; GDPMH; 1.
DR SUPFAM; SSF55811; Nudix; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Lipopolysaccharide biosynthesis; Magnesium;
KW Metal-binding; Reference proteome.
FT CHAIN 1..159
FT /note="GDP-mannose mannosyl hydrolase"
FT /id="PRO_0000056983"
FT DOMAIN 13..153
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00941"
FT MOTIF 50..71
FT /note="Nudix box"
FT BINDING 2..3
FT /ligand="substrate"
FT BINDING 8
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00941,
FT ECO:0000269|PubMed:15274914, ECO:0000269|PubMed:16981689"
FT BINDING 36
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00941,
FT ECO:0000269|PubMed:15274914, ECO:0000269|PubMed:16981689"
FT BINDING 49
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00941,
FT ECO:0000269|PubMed:15274914, ECO:0000269|PubMed:16981689"
FT BINDING 69
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00941,
FT ECO:0000269|PubMed:15274914, ECO:0000269|PubMed:16981689"
FT BINDING 122
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00941,
FT ECO:0000269|PubMed:15274914, ECO:0000269|PubMed:16981689"
FT SITE 123
FT /note="Critical for catalysis"
FT MUTAGEN 21
FT /note="D->A: Increases Km for GDP-mannose 5-fold. Reduces
FT activity 120-fold."
FT /evidence="ECO:0000269|PubMed:15966723"
FT MUTAGEN 21
FT /note="D->N: Increases Km for GDP-mannose 9-fold. Reduces
FT activity 400-fold."
FT /evidence="ECO:0000269|PubMed:15966723"
FT MUTAGEN 36
FT /note="R->Q: Increases Km for GDP-mannose 9-fold. Reduces
FT activity 24-fold."
FT /evidence="ECO:0000269|PubMed:15966723"
FT MUTAGEN 51
FT /note="R->K: Increases Km for GDP-mannose 40-fold. Reduces
FT activity 10-fold."
FT /evidence="ECO:0000269|PubMed:12196023"
FT MUTAGEN 51
FT /note="R->Q: Increases Km for GDP-mannose 40-fold. Reduces
FT activity 300-fold."
FT /evidence="ECO:0000269|PubMed:12196023"
FT MUTAGEN 64
FT /note="R->Q: Increases Km for GDP-mannose 80-fold. Reduces
FT activity 24-fold."
FT /evidence="ECO:0000269|PubMed:12196023"
FT MUTAGEN 69
FT /note="E->Q: Increases Km for GDP-mannose 10-fold.
FT Increases Km for magnesium 40-fold. Reduces activity 150-
FT fold."
FT MUTAGEN 87
FT /note="H->Q: Increases Km for GDP-mannose 4-fold. Reduces
FT activity 200-fold."
FT /evidence="ECO:0000269|PubMed:12196023"
FT MUTAGEN 101
FT /note="H->Q: Increases Km for GDP-mannose 14-fold. Reduces
FT activity 7-fold."
FT /evidence="ECO:0000269|PubMed:12196023"
FT MUTAGEN 102
FT /note="Y->F: Increases Km for GDP-mannose 7-fold. Reduces
FT activity 100-fold."
FT /evidence="ECO:0000269|PubMed:15966723"
FT MUTAGEN 123
FT /note="H->Q: Increases Km for GDP-mannose 5-fold. Reduces
FT activity 2000-fold."
FT /evidence="ECO:0000269|PubMed:12196023"
FT HELIX 5..14
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 17..25
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 31..36
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 49..51
FT /evidence="ECO:0007829|PDB:1RYA"
FT HELIX 58..70
FT /evidence="ECO:0007829|PDB:1RYA"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 79..92
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 100..110
FT /evidence="ECO:0007829|PDB:1RYA"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 120..129
FT /evidence="ECO:0007829|PDB:1RYA"
FT HELIX 131..136
FT /evidence="ECO:0007829|PDB:1RYA"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:2GT2"
FT HELIX 142..145
FT /evidence="ECO:0007829|PDB:1RYA"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:1RYA"
FT HELIX 150..153
FT /evidence="ECO:0007829|PDB:1RYA"
SQ SEQUENCE 159 AA; 18273 MW; C7ADFFC56AD6B32A CRC64;
MFLRQEDFAT VVRSTPLVSL DFIVENSRGE FLLGKRTNRP AQGYWFVPGG RVQKDETLEA
AFERLTMAEL GLRLPITAGQ FYGVWQHFYD DNFSGTDFTT HYVVLGFRFR VSEEELLLPD
EQHDDYRWLT SDALLASDNV HANSRAYFLA EKRTGVPGL
//
