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GDP-mannose mannosyl hydrolase (GDPMH) (EC 3.6.1.-) (Colanic acid biosynthesis protein WcaH)

 GMM_ECOLI               Reviewed;         159 AA.
P32056;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
27-MAR-2002, sequence version 2.
22-NOV-2017, entry version 135.
RecName: Full=GDP-mannose mannosyl hydrolase {ECO:0000255|HAMAP-Rule:MF_00941};
Short=GDPMH {ECO:0000255|HAMAP-Rule:MF_00941};
EC=3.6.1.- {ECO:0000255|HAMAP-Rule:MF_00941};
AltName: Full=Colanic acid biosynthesis protein WcaH;
Name=gmm {ECO:0000255|HAMAP-Rule:MF_00941}; Synonyms=nudD, wcaH, yefC;
OrderedLocusNames=b2051, JW5335;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=7815923;
Aoyama K., Haase A.M., Reeves P.R.;
"Evidence for effect of random genetic drift on G+C content after
lateral transfer of fucose pathway genes to Escherichia coli K-12.";
Mol. Biol. Evol. 11:829-838(1994).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=8759852; DOI=10.1128/jb.178.16.4885-4893.1996;
Stevenson G., Andrianopoulos K., Hobbs M., Reeves P.R.;
"Organization of the Escherichia coli K-12 gene cluster responsible
for production of the extracellular polysaccharide colanic acid.";
J. Bacteriol. 178:4885-4893(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9097040; DOI=10.1093/dnares/3.6.379;
Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C.,
Yamamoto Y., Horiuchi T.;
"A 460-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 40.1-50.0 min region on the linkage map.";
DNA Res. 3:379-392(1996).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
STRAIN=ATCC 33694 / HB101;
PubMed=7592609; DOI=10.1074/jbc.270.41.24086;
Frick D.N., Townsend B.D., Bessman M.J.;
"A novel GDP-mannose mannosyl hydrolase shares homology with the MutT
family of enzymes.";
J. Biol. Chem. 270:24086-24091(1995).
[7]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND MASS
SPECTROMETRY.
STRAIN=ATCC 33694 / HB101;
PubMed=10913267; DOI=10.1021/bi000537p;
Legler P.M., Massiah M.A., Bessman M.J., Mildvan A.S.;
"GDP-mannose mannosyl hydrolase catalyzes nucleophilic substitution at
carbon, unlike all other Nudix hydrolases.";
Biochemistry 39:8603-8608(2000).
[8]
MUTAGENESIS OF ARG-51; ARG-64; HIS-87; HIS-101 AND HIS-123, AND
COFACTOR.
PubMed=12196023; DOI=10.1021/bi020362e;
Legler P.M., Massiah M.A., Mildvan A.S.;
"Mutational, kinetic, and NMR studies of the mechanism of E. coli GDP-
mannose mannosyl hydrolase, an unusual Nudix enzyme.";
Biochemistry 41:10834-10848(2002).
[9]
MUTAGENESIS OF ASP-21; ARG-36 AND TYR-102.
PubMed=15966723; DOI=10.1021/bi050583v;
Xia Z., Azurmendi H.F., Lairson L.L., Withers S.G., Gabelli S.B.,
Bianchet M.A., Amzel L.M., Mildvan A.S.;
"Mutational, structural, and kinetic evidence for a dissociative
mechanism in the GDP-mannose mannosyl hydrolase reaction.";
Biochemistry 44:8989-8997(2005).
[10]
X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
MAGNESIUM, COFACTOR, AND SUBUNIT.
PubMed=15274914; DOI=10.1016/j.str.2004.03.028;
Gabelli S.B., Bianchet M.A., Azurmendi H.F., Xia Z., Sarawat V.,
Mildvan A.S., Amzel L.M.;
"Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix
enzyme that cleaves at carbon instead of phosphorus.";
Structure 12:927-935(2004).
[11]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT PHE-102 IN COMPLEX
WITH SUBSTRATE AND MAGNESIUM.
PubMed=16981689; DOI=10.1021/bi061239g;
Gabelli S.B., Azurmendi H.F., Bianchet M.A., Amzel L.M., Mildvan A.S.;
"X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-
mannose mannosyl hydrolase reaction.";
Biochemistry 45:11290-11303(2006).
-!- FUNCTION: Hydrolyzes both GDP-mannose and GDP-glucose. Could
participate in the regulation of cell wall biosynthesis by
influencing the concentration of GDP-mannose or GDP-glucose in the
cell. Might also be involved in the biosynthesis of the slime
polysaccharide colanic acid. {ECO:0000269|PubMed:10913267,
ECO:0000269|PubMed:7592609}.
-!- CATALYTIC ACTIVITY: GDP-D-mannose + H(2)O = GDP + D-mannose.
{ECO:0000255|HAMAP-Rule:MF_00941, ECO:0000269|PubMed:10913267,
ECO:0000269|PubMed:7592609}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|HAMAP-Rule:MF_00941,
ECO:0000269|PubMed:10913267, ECO:0000269|PubMed:12196023,
ECO:0000269|PubMed:15274914};
Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-
Rule:MF_00941, ECO:0000269|PubMed:10913267,
ECO:0000269|PubMed:12196023, ECO:0000269|PubMed:15274914};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.3 mM for GDP-mannose {ECO:0000269|PubMed:7592609};
KM=1.9 mM for GDP-glucose {ECO:0000269|PubMed:7592609};
Vmax=1.6 umol/min/mg enzyme with GDP-mannose as substrate
{ECO:0000269|PubMed:7592609};
Vmax=7.5 umol/min/mg enzyme with GDP-glucose as substrate
{ECO:0000269|PubMed:7592609};
Note=GDP-alpha-D-mannose is likely to be the biological
substrate, but the Kcat/KM obtained with GDP-alpha-D-glucose is
very similar to that with GDP-alpha-D-mannose.;
pH dependence:
Optimum pH is 9.3. {ECO:0000269|PubMed:7592609};
-!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00941,
ECO:0000269|PubMed:10913267, ECO:0000269|PubMed:15274914,
ECO:0000269|PubMed:16981689}.
-!- MASS SPECTROMETRY: Mass=18472; Mass_error=67; Method=MALDI;
Range=1-159; Evidence={ECO:0000269|PubMed:10913267};
-!- SIMILARITY: Belongs to the Nudix hydrolase family.
{ECO:0000255|HAMAP-Rule:MF_00941}.
-!- SEQUENCE CAUTION:
Sequence=AAC77844.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; U38473; AAC77844.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC75112.2; -; Genomic_DNA.
EMBL; AP009048; BAA15907.2; -; Genomic_DNA.
PIR; E55239; E55239.
RefSeq; NP_416555.2; NC_000913.3.
RefSeq; WP_001393539.1; NZ_LN832404.1.
PDB; 1RYA; X-ray; 1.30 A; A/B=1-159.
PDB; 2GT2; X-ray; 2.00 A; A/B/C/D=1-159.
PDB; 2GT4; X-ray; 2.30 A; A/B/C=1-159.
PDBsum; 1RYA; -.
PDBsum; 2GT2; -.
PDBsum; 2GT4; -.
ProteinModelPortal; P32056; -.
SMR; P32056; -.
BioGrid; 4261145; 369.
STRING; 316385.ECDH10B_2201; -.
DrugBank; DB04315; Guanosine-5'-Diphosphate.
PaxDb; P32056; -.
PRIDE; P32056; -.
EnsemblBacteria; AAC75112; AAC75112; b2051.
EnsemblBacteria; BAA15907; BAA15907; BAA15907.
GeneID; 946559; -.
KEGG; ecj:JW5335; -.
KEGG; eco:b2051; -.
PATRIC; fig|511145.12.peg.2128; -.
EchoBASE; EB1737; -.
EcoGene; EG11789; gmm.
eggNOG; ENOG4105FGF; Bacteria.
eggNOG; COG0494; LUCA.
HOGENOM; HOG000280400; -.
InParanoid; P32056; -.
KO; K03207; -.
PhylomeDB; P32056; -.
BioCyc; EcoCyc:GDPMANMANHYDRO-MONOMER; -.
BioCyc; MetaCyc:GDPMANMANHYDRO-MONOMER; -.
SABIO-RK; P32056; -.
EvolutionaryTrace; P32056; -.
PRO; PR:P32056; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0047917; F:GDP-glucosidase activity; IDA:EcoCyc.
GO; GO:0008727; F:GDP-mannose mannosyl hydrolase activity; IEA:InterPro.
GO; GO:0000287; F:magnesium ion binding; IMP:EcoCyc.
GO; GO:0030145; F:manganese ion binding; IMP:EcoCyc.
GO; GO:0009103; P:lipopolysaccharide biosynthetic process; IEA:UniProtKB-KW.
CDD; cd03430; GDPMH; 1.
HAMAP; MF_00941; GDPMH_gmm; 1.
InterPro; IPR033715; GDPMH.
InterPro; IPR028613; GDPMH_Gmm.
InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
InterPro; IPR020084; NUDIX_hydrolase_CS.
InterPro; IPR000086; NUDIX_hydrolase_dom.
Pfam; PF00293; NUDIX; 1.
PIRSF; PIRSF037599; GDPMH; 1.
SUPFAM; SSF55811; SSF55811; 1.
PROSITE; PS51462; NUDIX; 1.
PROSITE; PS00893; NUDIX_BOX; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Hydrolase;
Lipopolysaccharide biosynthesis; Magnesium; Metal-binding;
Reference proteome.
CHAIN 1 159 GDP-mannose mannosyl hydrolase.
/FTId=PRO_0000056983.
DOMAIN 13 153 Nudix hydrolase. {ECO:0000255|HAMAP-
Rule:MF_00941}.
REGION 2 3 Substrate binding.
MOTIF 50 71 Nudix box.
METAL 49 49 Magnesium; via carbonyl oxygen.
{ECO:0000255|HAMAP-Rule:MF_00941,
ECO:0000269|PubMed:15274914,
ECO:0000269|PubMed:16981689}.
METAL 69 69 Magnesium. {ECO:0000255|HAMAP-
Rule:MF_00941,
ECO:0000269|PubMed:15274914,
ECO:0000269|PubMed:16981689}.
METAL 122 122 Magnesium. {ECO:0000255|HAMAP-
Rule:MF_00941,
ECO:0000269|PubMed:15274914,
ECO:0000269|PubMed:16981689}.
BINDING 8 8 Substrate. {ECO:0000255|HAMAP-
Rule:MF_00941,
ECO:0000269|PubMed:15274914,
ECO:0000269|PubMed:16981689}.
BINDING 36 36 Substrate. {ECO:0000255|HAMAP-
Rule:MF_00941,
ECO:0000269|PubMed:15274914,
ECO:0000269|PubMed:16981689}.
SITE 123 123 Critical for catalysis.
MUTAGEN 21 21 D->A: Increases Km for GDP-mannose 5-
fold. Reduces activity 120-fold.
{ECO:0000269|PubMed:15966723}.
MUTAGEN 21 21 D->N: Increases Km for GDP-mannose 9-
fold. Reduces activity 400-fold.
{ECO:0000269|PubMed:15966723}.
MUTAGEN 36 36 R->Q: Increases Km for GDP-mannose 9-
fold. Reduces activity 24-fold.
{ECO:0000269|PubMed:15966723}.
MUTAGEN 51 51 R->K: Increases Km for GDP-mannose 40-
fold. Reduces activity 10-fold.
{ECO:0000269|PubMed:12196023}.
MUTAGEN 51 51 R->Q: Increases Km for GDP-mannose 40-
fold. Reduces activity 300-fold.
{ECO:0000269|PubMed:12196023}.
MUTAGEN 64 64 R->Q: Increases Km for GDP-mannose 80-
fold. Reduces activity 24-fold.
{ECO:0000269|PubMed:12196023}.
MUTAGEN 69 69 E->Q: Increases Km for GDP-mannose 10-
fold. Increases Km for magnesium 40-fold.
Reduces activity 150-fold.
MUTAGEN 87 87 H->Q: Increases Km for GDP-mannose 4-
fold. Reduces activity 200-fold.
{ECO:0000269|PubMed:12196023}.
MUTAGEN 101 101 H->Q: Increases Km for GDP-mannose 14-
fold. Reduces activity 7-fold.
{ECO:0000269|PubMed:12196023}.
MUTAGEN 102 102 Y->F: Increases Km for GDP-mannose 7-
fold. Reduces activity 100-fold.
{ECO:0000269|PubMed:15966723}.
MUTAGEN 123 123 H->Q: Increases Km for GDP-mannose 5-
fold. Reduces activity 2000-fold.
{ECO:0000269|PubMed:12196023}.
HELIX 5 14 {ECO:0000244|PDB:1RYA}.
STRAND 17 25 {ECO:0000244|PDB:1RYA}.
STRAND 31 36 {ECO:0000244|PDB:1RYA}.
STRAND 38 41 {ECO:0000244|PDB:1RYA}.
STRAND 44 46 {ECO:0000244|PDB:1RYA}.
STRAND 49 51 {ECO:0000244|PDB:1RYA}.
HELIX 58 70 {ECO:0000244|PDB:1RYA}.
HELIX 76 78 {ECO:0000244|PDB:1RYA}.
STRAND 79 92 {ECO:0000244|PDB:1RYA}.
STRAND 95 98 {ECO:0000244|PDB:1RYA}.
STRAND 100 110 {ECO:0000244|PDB:1RYA}.
HELIX 113 115 {ECO:0000244|PDB:1RYA}.
STRAND 120 129 {ECO:0000244|PDB:1RYA}.
HELIX 131 136 {ECO:0000244|PDB:1RYA}.
STRAND 138 140 {ECO:0000244|PDB:2GT2}.
HELIX 142 145 {ECO:0000244|PDB:1RYA}.
HELIX 146 148 {ECO:0000244|PDB:1RYA}.
HELIX 150 153 {ECO:0000244|PDB:1RYA}.
SEQUENCE 159 AA; 18273 MW; C7ADFFC56AD6B32A CRC64;
MFLRQEDFAT VVRSTPLVSL DFIVENSRGE FLLGKRTNRP AQGYWFVPGG RVQKDETLEA
AFERLTMAEL GLRLPITAGQ FYGVWQHFYD DNFSGTDFTT HYVVLGFRFR VSEEELLLPD
EQHDDYRWLT SDALLASDNV HANSRAYFLA EKRTGVPGL


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