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   04-NOV-2026, entry version 172.
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; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; 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 IN COMPLEX WITH SUBSTRATE AND MAGNESIUM, COFACTOR,
RP   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 OF MUTANT PHE-102 IN COMPLEX WITH SUBSTRATE AND
RP   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:10913267,
CC       PubMed:23481913, PubMed:7592609). 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:10913267,
CC       PubMed:7592609). {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; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00941, ECO:0000269|PubMed:10913267,
CC         ECO:0000269|PubMed:12196023, 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_CP009789.1.
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   AlphaFoldDB; P32056; -.
DR   SMR; P32056; -.
DR   BioGRID; 4261145; 371.
DR   FunCoup; P32056; 16.
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   KEGG; ecoc:C3026_11545; -.
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; ADFSTHY; -.
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; 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   CDD; cd03430; NUDIX_GDPMH_NudD; 1.
DR   FunFam; 3.90.79.10:FF:000064; GDP-mannose mannosyl hydrolase; 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   NCBIfam; NF011963; PRK15434.1; 1.
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
FT                   150-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
//