Gmd (PA5453) is the GDP-mannose 4,6-dehydratase (EC 4.2.1.47) of Pseudomonas aeruginosa, an NADP(+)-dependent enzyme of the extended short-chain dehydratase/reductase (SDR) family that converts GDP-alpha-D-mannose to GDP-4-dehydro-6-deoxy-alpha-D-mannose (GDP-4-keto-6-deoxy-D-mannose), releasing water. This is the first committed step toward GDP-D-rhamnose, the sugar donor for the D-rhamnose homopolymer of A-band (common antigen) O polysaccharide; the second step is carried out by Rmd. The purified P. aeruginosa enzyme is bifunctional and can also catalyse the subsequent reduction to GDP-D-rhamnose. P. aeruginosa has no GDP-L-fucose synthase and does not make GDP-L-fucose, so Gmd here feeds D-rhamnose, not fucose, biosynthesis. gmd mutants are impaired in A-band LPS.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008446 GDP-mannose 4,6-dehydratase activity | EXP PMID:9781879 Synthesis of the A-band polysaccharide sugar D-rhamnose requ... | ACCEPT | Summary: PseudoCAP EXP seed row for PTN008684430 (154 leaves, 98 taxa). Seed verdict SOUND: GMD activity is firmly established; the cited PMID:9781879 treats gmd as a previously reported A-band enzyme, and the direct enzyme assay is in PMID:19459932. Reason: Core activity, directly demonstrated for the P. aeruginosa enzyme. Supporting Evidence: PMID:19459932 P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. PMID:9781879 Gmd, a previously reported A-band enzyme, and Rmd are predicted to perform the two-step conversion of GDP-D-Man to GDP-D-Rha. |
| GO:0008446 GDP-mannose 4,6-dehydratase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008684430; eleven seeds, all GMD enzymes (worm, mouse Gmds, E. coli Gmd P0AC88, human GMDS O60547, Arabidopsis, fly, Dictyostelium, Trypanosoma, and Gmd itself). Stands without this seed. Reason: Conserved GMD activity across the clade. Supporting Evidence: PMID:19459932 P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. |
| GO:0008446 GDP-mannose 4,6-dehydratase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC/Rhea/UniRule mapping to the same activity. Reason: Consistent with the experimental rows. Supporting Evidence: PMID:19459932 P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. |
| GO:0009103 lipopolysaccharide biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping to lipopolysaccharide biosynthetic process. Gmd makes the GDP-D-rhamnose donor for A-band LPS. Reason: Core pathway role: A-band O-polysaccharide (LPS) biosynthesis. Supporting Evidence: PMID:19459932 Genes encoding GMD and RMD are present in P. aeruginosa, and genetic evidence indicates they act in A-band O-polysaccharide biosynthesis. |
| GO:0009103 lipopolysaccharide biosynthetic process | IMP PMID:8548534 Prevalence of gca, a gene involved in synthesis of A-band co... | ACCEPT | Summary: PseudoCAP IMP: A-band gca/gmd gene in LPS synthesis. Reason: Genetic and sequence evidence for the LPS role. Supporting Evidence: PMID:8548534 this protein may be functioning as a dehydratase or as a bifunctional enzyme, facilitating the conversion of GDP-D-mannose to GDP-D-rhamnose |
| GO:0009243 O antigen biosynthetic process | IDA PMID:19459932 The structural basis for catalytic function of GMD and RMD, ... | ACCEPT | Summary: PseudoCAP IDA: GMD supplies GDP-D-rhamnose for A-band O polysaccharide. Reason: Direct role in O antigen biosynthesis. Supporting Evidence: PMID:19459932 Genes encoding GMD and RMD are present in P. aeruginosa, and genetic evidence indicates they act in A-band O-polysaccharide biosynthesis. |
| GO:0019306 GDP-D-rhamnose biosynthetic process | EXP PMID:19459932 The structural basis for catalytic function of GMD and RMD, ... | ACCEPT | Summary: PseudoCAP EXP: the purified bifunctional P. aeruginosa GMD produces GDP-D-rhamnose. Reason: Core: first (and, for PaGMD, also second) step of GDP-D-rhamnose biosynthesis. Supporting Evidence: PMID:19459932 P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. |
| GO:0019673 GDP-mannose metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro mapping to GDP-mannose metabolic process. GMD consumes GDP-mannose. Reason: True: GDP-mannose is the substrate. Peripheral to the informative role, which is GDP-D-rhamnose biosynthesis (accepted). Not entailed by it, so kept rather than removed. Supporting Evidence: PMID:9781879 The D-mannuronic acid residues of alginate and the D-rhamnose (D-Rha) residues of A-band polysaccharide are both derived from the common sugar nucleotide precursor GDP-D-mannose (D-Man). |
| GO:0042351 'de novo' GDP-L-fucose biosynthetic process | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN008684430 for 'de novo' GDP-L-fucose biosynthetic process. Seeded by fucose-producing organisms (Arabidopsis, human GMDS, fly, Trypanosoma, Dictyostelium); Gmd is not a seed here. Reason: GMD is the shared first step; the pathway identity is set downstream. P. aeruginosa makes GDP-D-rhamnose (via Rmd), not GDP-L-fucose, and has no GDP-L-fucose synthase. The GDP-L-fucose process term is wrong for this gene; see the GO_CENTRAL note. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN008684430 · PTN008684430 SUPPORTS SOURCE BUT NOT TARGET The GDP-L-fucose process IBD is right for fucose-producing seeds but not for P. aeruginosa, which makes GDP-D-rhamnose. Supporting Evidence: PMID:19459932 P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. |
| GO:0070401 NADP+ binding | IEA GO_REF:0000104 | ACCEPT | Summary: UniRule mapping to NADP+ binding (the GMD cofactor). Reason: NADP(+) is the catalytic cofactor of GMD. Supporting Evidence: PMID:19459932 P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. |
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Download this section (compressed HTML)Q: Should the PTN008684430 GDP-L-fucose process IBD be restricted to lineages that encode a GDP-L-fucose synthase (fcl/GER), so that GMD orthologs in GDP-D-rhamnose producers such as P. aeruginosa are not annotated to GDP-L-fucose biosynthesis?
Experiment: Confirm the absence of GDP-L-fucose and of a GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase in P. aeruginosa by metabolite profiling of a gmd/rmd background.
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