GM4D_ECOLI
ID GM4D_ECOLI Reviewed; 373 AA.
AC P0AC88; P32054; P77687;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=GDP-mannose 4,6-dehydratase {ECO:0000255|HAMAP-Rule:MF_00955};
DE EC=4.2.1.47 {ECO:0000255|HAMAP-Rule:MF_00955};
DE AltName: Full=GDP-D-mannose dehydratase {ECO:0000255|HAMAP-Rule:MF_00955};
GN Name=gmd {ECO:0000255|HAMAP-Rule:MF_00955}; Synonyms=yefA, yefN;
GN OrderedLocusNames=b2053, JW2038;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 50-373.
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 [6]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND PATHWAY.
RX PubMed=9257704; DOI=10.1016/s0014-5793(97)00762-x;
RA Sturla L., Bisso A., Zanardi D., Benatti U., de Flora A., Tonetti M.;
RT "Expression, purification and characterization of GDP-D-mannose 4,6-
RT dehydratase from Escherichia coli.";
RL FEBS Lett. 412:126-130(1997).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), COFACTOR, SUBUNIT, MUTAGENESIS OF
RP THR-133; GLU-135; TYR-157 AND LYS-161, AND ACTIVE SITE.
RX PubMed=10673432; DOI=10.1016/s0969-2126(00)00088-5;
RA Somoza J.R., Menon S., Schmidt H., Joseph-McCarthy D., Dessen A.,
RA Stahl M.L., Somers W.S., Sullivan F.X.;
RT "Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6
RT dehydratase provides insights into the enzyme's catalytic mechanism and
RT regulation by GDP-fucose.";
RL Structure 8:123-135(2000).
CC -!- FUNCTION: Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-
CC deoxy-D-mannose. {ECO:0000255|HAMAP-Rule:MF_00955,
CC ECO:0000269|PubMed:9257704}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O;
CC Xref=Rhea:RHEA:23820, ChEBI:CHEBI:15377, ChEBI:CHEBI:57527,
CC ChEBI:CHEBI:57964; EC=4.2.1.47; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00955, ECO:0000269|PubMed:9257704};
CC -!- COFACTOR:
CC Name=NADP(+); Xref=ChEBI:CHEBI:58349;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00955,
CC ECO:0000269|PubMed:10673432, ECO:0000269|PubMed:9257704};
CC -!- PATHWAY: Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via
CC de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2.
CC {ECO:0000269|PubMed:9257704}.
CC -!- PATHWAY: Exopolysaccharide biosynthesis; colanic acid biosynthesis.
CC {ECO:0000269|PubMed:9257704}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10673432}.
CC -!- SIMILARITY: Belongs to the NAD(P)-dependent epimerase/dehydratase
CC family. GDP-mannose 4,6-dehydratase subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_00955}.
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DR EMBL; U38473; AAC77842.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75114.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15909.1; -; Genomic_DNA.
DR PIR; D64971; D64971.
DR RefSeq; NP_416557.1; NC_000913.3.
DR RefSeq; WP_000048190.1; NZ_STEB01000002.1.
DR PDB; 1DB3; X-ray; 2.30 A; A=2-373.
DR PDBsum; 1DB3; -.
DR AlphaFoldDB; P0AC88; -.
DR SMR; P0AC88; -.
DR BioGRID; 4259690; 193.
DR DIP; DIP-48216N; -.
DR IntAct; P0AC88; 2.
DR STRING; 511145.b2053; -.
DR PaxDb; P0AC88; -.
DR PRIDE; P0AC88; -.
DR EnsemblBacteria; AAC75114; AAC75114; b2053.
DR EnsemblBacteria; BAA15909; BAA15909; BAA15909.
DR GeneID; 66674049; -.
DR GeneID; 946562; -.
DR KEGG; ecj:JW2038; -.
DR KEGG; eco:b2053; -.
DR PATRIC; fig|1411691.4.peg.198; -.
DR EchoBASE; EB1735; -.
DR eggNOG; COG1089; Bacteria.
DR HOGENOM; CLU_007383_14_0_6; -.
DR InParanoid; P0AC88; -.
DR OMA; TDCLYLG; -.
DR PhylomeDB; P0AC88; -.
DR BioCyc; EcoCyc:GDPMANDEHYDRA-MON; -.
DR BioCyc; MetaCyc:GDPMANDEHYDRA-MON; -.
DR SABIO-RK; P0AC88; -.
DR UniPathway; UPA00128; UER00190.
DR UniPathway; UPA00980; -.
DR EvolutionaryTrace; P0AC88; -.
DR PRO; PR:P0AC88; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008446; F:GDP-mannose 4,6-dehydratase activity; IDA:EcoCyc.
DR GO; GO:0070401; F:NADP+ binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042351; P:'de novo' GDP-L-fucose biosynthetic process; IBA:GO_Central.
DR GO; GO:0009242; P:colanic acid biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0019673; P:GDP-mannose metabolic process; IBA:GO_Central.
DR HAMAP; MF_00955; GDP_Man_dehydratase; 1.
DR InterPro; IPR006368; GDP_Man_deHydtase.
DR InterPro; IPR016040; NAD(P)-bd_dom.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR43715; PTHR43715; 1.
DR Pfam; PF16363; GDP_Man_Dehyd; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01472; gmd; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; NADP; Reference proteome.
FT CHAIN 1..373
FT /note="GDP-mannose 4,6-dehydratase"
FT /id="PRO_0000201712"
FT ACT_SITE 133
FT /evidence="ECO:0000305|PubMed:10673432"
FT ACT_SITE 135
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:10673432"
FT ACT_SITE 157
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:10673432"
FT BINDING 9..14
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 64..65
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 86..90
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 101
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 161
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000305"
FT BINDING 187
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 192
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT MUTAGEN 133
FT /note="T->V: Strongly reduces activity."
FT /evidence="ECO:0000269|PubMed:10673432"
FT MUTAGEN 135
FT /note="E->Q: Strongly reduces activity."
FT /evidence="ECO:0000269|PubMed:10673432"
FT MUTAGEN 157
FT /note="Y->F: Strongly reduces activity."
FT /evidence="ECO:0000269|PubMed:10673432"
FT MUTAGEN 161
FT /note="K->A: Strongly reduces activity."
FT /evidence="ECO:0000269|PubMed:10673432"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:1DB3"
FT TURN 9..11
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 68..78
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 81..85
FT /evidence="ECO:0007829|PDB:1DB3"
FT TURN 91..96
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 99..106
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 108..119
FT /evidence="ECO:0007829|PDB:1DB3"
FT TURN 123..125
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 127..133
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 134..137
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 142..145
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 156..175
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 179..184
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 197..209
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 216..219
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 230..239
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 242..245
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 249..251
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 259..268
FT /evidence="ECO:0007829|PDB:1DB3"
FT TURN 269..271
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 272..278
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 280..282
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 284..290
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 292..294
FT /evidence="ECO:0007829|PDB:1DB3"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 325..331
FT /evidence="ECO:0007829|PDB:1DB3"
FT HELIX 339..355
FT /evidence="ECO:0007829|PDB:1DB3"
SQ SEQUENCE 373 AA; 42047 MW; 1A9BA2A7C566DE11 CRC64;
MSKVALITGV TGQDGSYLAE FLLEKGYEVH GIKRRASSFN TERVDHIYQD PHTCNPKFHL
HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE YTADVDAMGT LRLLEAIRFL
GLEKKTRFYQ ASTSELYGLV QEIPQKETTP FYPRSPYAVA KLYAYWITVN YRESYGMYAC
NGILFNHESP RRGETFVTRK ITRAIANIAQ GLESCLYLGN MDSLRDWGHA KDYVKMQWMM
LQQEQPEDFV IATGVQYSVR QFVEMAAAQL GIKLRFEGTG VEEKGIVVSV TGHDAPGVKP
GDVIIAVDPR YFRPAEVETL LGDPTKAHEK LGWKPEITLR EMVSEMVAND LEAAKKHSLL
KSHGYDVAIA LES
