GM4D_PSEAE
ID GM4D_PSEAE Reviewed; 323 AA.
AC Q51366;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 08-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 143.
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=gca;
GN OrderedLocusNames=PA5453;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PATHWAY.
RC STRAIN=IATS O5;
RX PubMed=8548534; DOI=10.1128/cdli.2.5.554-562.1995;
RA Currie H.L., Lightfoot J., Lam J.S.;
RT "Prevalence of gca, a gene involved in synthesis of A-band common antigen
RT polysaccharide in Pseudomonas aeruginosa.";
RL Clin. Diagn. Lab. Immunol. 2:554-562(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH NADP, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RX PubMed=14739333; DOI=10.1110/ps.03393904;
RA Webb N.A., Mulichak A.M., Lam J.S., Rocchetta H.L., Garavito R.M.;
RT "Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a
RT bacterial GDP-D-rhamnose biosynthetic pathway.";
RL Protein Sci. 13:529-539(2004).
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:14739333}.
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:14739333};
CC -!- COFACTOR:
CC Name=NADP(+); Xref=ChEBI:CHEBI:58349;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00955,
CC ECO:0000269|PubMed:14739333};
CC -!- PATHWAY: Bacterial outer membrane biogenesis; lipopolysaccharide
CC biosynthesis. {ECO:0000269|PubMed:8548534}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:14739333}.
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; U18320; AAC44117.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG08838.1; -; Genomic_DNA.
DR PIR; G82964; G82964.
DR RefSeq; NP_254140.1; NC_002516.2.
DR RefSeq; WP_003096890.1; NZ_QZGE01000012.1.
DR PDB; 1RPN; X-ray; 2.15 A; A/B/C/D=1-323.
DR PDBsum; 1RPN; -.
DR AlphaFoldDB; Q51366; -.
DR SMR; Q51366; -.
DR STRING; 287.DR97_2832; -.
DR DrugBank; DB04315; Guanosine-5'-Diphosphate.
DR PaxDb; Q51366; -.
DR PRIDE; Q51366; -.
DR DNASU; 883089; -.
DR EnsemblBacteria; AAG08838; AAG08838; PA5453.
DR GeneID; 883089; -.
DR KEGG; pae:PA5453; -.
DR PATRIC; fig|208964.12.peg.5716; -.
DR PseudoCAP; PA5453; -.
DR HOGENOM; CLU_007383_14_0_6; -.
DR InParanoid; Q51366; -.
DR OMA; TDCLYLG; -.
DR PhylomeDB; Q51366; -.
DR BioCyc; MetaCyc:MON-12848; -.
DR BioCyc; PAER208964:G1FZ6-5581-MON; -.
DR BRENDA; 4.2.1.47; 5087.
DR UniPathway; UPA00030; -.
DR EvolutionaryTrace; Q51366; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0008446; F:GDP-mannose 4,6-dehydratase activity; EXP:PseudoCAP.
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:0019306; P:GDP-D-rhamnose biosynthetic process; EXP:PseudoCAP.
DR GO; GO:0019673; P:GDP-mannose metabolic process; IBA:GO_Central.
DR GO; GO:0009103; P:lipopolysaccharide biosynthetic process; IMP:PseudoCAP.
DR GO; GO:0009243; P:O antigen biosynthetic process; IDA:PseudoCAP.
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; Lipopolysaccharide biosynthesis; Lyase; NADP;
KW Reference proteome.
FT CHAIN 1..323
FT /note="GDP-mannose 4,6-dehydratase"
FT /id="PRO_0000201715"
FT ACT_SITE 126
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT ACT_SITE 128
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT ACT_SITE 150
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955"
FT BINDING 11..14
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT BINDING 36
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT BINDING 59..60
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT BINDING 81..85
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT BINDING 154
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT BINDING 180
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT BINDING 185
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00955,
FT ECO:0000269|PubMed:14739333"
FT CONFLICT 153
FT /note="A -> V (in Ref. 1; AAC44117)"
FT /evidence="ECO:0000305"
FT CONFLICT 167
FT /note="S -> N (in Ref. 1; AAC44117)"
FT /evidence="ECO:0000305"
FT CONFLICT 216
FT /note="A -> V (in Ref. 1; AAC44117)"
FT /evidence="ECO:0000305"
FT CONFLICT 223
FT /note="A -> G (in Ref. 1; AAC44117)"
FT /evidence="ECO:0000305"
FT CONFLICT 247
FT /note="G -> V (in Ref. 1; AAC44117)"
FT /evidence="ECO:0000305"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:1RPN"
FT TURN 9..11
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 42..46
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 87..90
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 94..101
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 103..115
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 119..126
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 127..130
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 134..138
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 149..168
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 190..202
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 223..235
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 249..251
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 252..261
FT /evidence="ECO:0007829|PDB:1RPN"
FT TURN 262..264
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:1RPN"
FT STRAND 271..273
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 275..277
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 291..297
FT /evidence="ECO:0007829|PDB:1RPN"
FT HELIX 305..322
FT /evidence="ECO:0007829|PDB:1RPN"
SQ SEQUENCE 323 AA; 36399 MW; 6C2BCC27D00D97E0 CRC64;
MTRSALVTGI TGQDGAYLAK LLLEKGYRVH GLVARRSSDT RWRLRELGIE GDIQYEDGDM
ADACSVQRAV IKAQPQEVYN LAAQSFVGAS WNQPVTTGVV DGLGVTHLLE AIRQFSPETR
FYQASTSEMF GLIQAERQDE NTPFYPRSPY GVAKLYGHWI TVNYRESFGL HASSGILFNH
ESPLRGIEFV TRKVTDAVAR IKLGKQQELR LGNVDAKRDW GFAGDYVEAM WLMLQQDKAD
DYVVATGVTT TVRDMCQIAF EHVGLDYRDF LKIDPAFFRP AEVDVLLGNP AKAQRVLGWK
PRTSLDELIR MMVEADLRRV SRE
