WbpI (PA3148) is a cytoplasmic nucleotide-sugar 2-epimerase of Pseudomonas aeruginosa that makes a precursor of the B-band (O-specific) O antigen of serotype O5. It converts UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate (UDP-GlcNAc3NAcA) to the manno configuration (UDP-ManNAc3NAcA, EC 5.1.3.23), the last step of a five-enzyme pathway from UDP-GlcNAc that supplies the di-N-acetylated mannosaminuronic acid residues of the O-antigen repeat. Although it belongs to the UDP-N-acetylglucosamine 2-epimerase (WecB) family, the purified enzyme does not act on UDP-GlcNAc or on the mono- or non-oxidized intermediates, and E. coli WecB cannot replace it. wbpI knockouts make no B-band LPS.
Definition: Catalysis of the reaction: UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate = UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronate.
Justification: EC 5.1.3.23 (RHEA:24764) has no GO term. WbpI and B. pertussis WlbD catalyse it and do not use UDP-GlcNAc, so GO:0008761 is wrong for them; current annotations use GO:0008761 or the unrelated 4-epimerase GO:0050378.
Parent term: racemase and epimerase activity, acting on carbohydrates and derivatives
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000271 polysaccharide biosynthetic process | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from the two-seed PTN001056041 IBD (E. coli WecB and this gene's own PseudoCAP row, which is expected). Reason: True, but GO:0009243 O antigen biosynthetic process, accepted in this review, is_a GO:0000271. The node term suits the clade and the IBD stands on WecB as well. Supporting Evidence: PMID:10930727 Specific knockout mutations in the putative UDP-D-N-acetylglucosamine (UDP-D-GlcNAc) epimerase gene, wbpI, or the putative UDP-D-N-acetylmannosamine dehydrogenase gene, wbpA, resulted in strains that no longer produced B-band lipopolysaccharide, confirming the essential roles of these genes in B-band O antigen synthesis. |
| GO:0000271 polysaccharide biosynthetic process | IMP PMID:10930727 Pseudomonas aeruginosa B-band lipopolysaccharide genes wbpA ... | TOO GENERAL | Summary: PseudoCAP row and a seed of PTN001056041. The knockout makes no B-band LPS. Reason: Seed verdict SOUND: WbpI performs a step of O-antigen precursor synthesis, so the claim is right, but GO:0009243 (accepted, from the same paper) is the specific term and is_a GO:0000271. Supporting Evidence: PMID:10930727 Specific knockout mutations in the putative UDP-D-N-acetylglucosamine (UDP-D-GlcNAc) epimerase gene, wbpI, or the putative UDP-D-N-acetylmannosamine dehydrogenase gene, wbpA, resulted in strains that no longer produced B-band lipopolysaccharide, confirming the essential roles of these genes in B-band O antigen synthesis. |
| GO:0003824 catalytic activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA root-term catalytic activity. Reason: Correct but uninformative. The activity is the EC 5.1.3.23 2-epimerase, which has no GO term; the proposed term is the replacement (existing closest parent GO:0016857). Proposed replacements: UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 2-epimerase activity Supporting Evidence: PMID:17346239 Data collected from one- and two-dimensional NMR experiments showed that His6-WbpI catalysed the 2-epimerization of UDP-alpha-D-GlcNAc3NAcA, converting it into UDP-alpha-D-ManNAc3NAcA. |
| GO:0008761 UDP-N-acetylglucosamine 2-epimerase activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN001056041, seeded by E. coli WecB (IDA) and by WbpI itself through two wrong-term rows. GO:0008761 is UDP-GlcNAc = UDP-ManNAc; purified WbpI does not use UDP-GlcNAc. Reason: The family assignment and 2-epimerase chemistry are right, but the substrate in the term is wrong for WbpI. The IBD is sound for the WecB/MnaA-type leaves on the strength of WecB, but WbpI has diverged in substrate, so the node term does not hold for this leaf. Replace with the proposed EC 5.1.3.23 term. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE SOURCE MISCITATION Sources checked: PANTHER:PTN001056041 · PTN001056041 SUPPORTS SOURCE BUT NOT TARGET Mostly WecB/MnaA-type UDP-GlcNAc 2-epimerases (41 leaves); WbpI is a divergent member with a di-N-acetylated uronic acid substrate. UniProtKB:P27828 · E. coli WecB (EcoCyc IDA PMID:15210128) SUPPORTS SOURCE BUT NOT TARGET Sound for WecB. UniProtKB:G3XD61 · wbpI (self; PseudoCAP IMP PMID:10930727, UniProt IDA PMID:17346239) SOURCE BAD Both self-seed rows use GO:0008761 for an enzyme shown not to use UDP-GlcNAc. Proposed replacements: UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 2-epimerase activity Supporting Evidence: PMID:17346239 Neither enzyme utilized UDP-alpha-D-GlcNAc, UDP-alpha-D-GlcNAcA (UDP-2-acetamido-2,3-dideoxy-alpha-D-glucuronic acid) or UDP-alpha-D-GlcNAc3NAc (UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucose) as substrates. PMID:17346239 Data collected from one- and two-dimensional NMR experiments showed that His6-WbpI catalysed the 2-epimerization of UDP-alpha-D-GlcNAc3NAcA, converting it into UDP-alpha-D-ManNAc3NAcA. |
| GO:0008761 UDP-N-acetylglucosamine 2-epimerase activity | IDA PMID:17346239 Identification and biochemical characterization of two novel... | MODIFY | Summary: UniProt IDA from the purified-enzyme paper. The paper shows 2-epimerization of UDP-GlcNAc3NAcA and no activity on UDP-GlcNAc, so the activity is right in kind but the term names the wrong substrate. It is also one of the two WbpI seeds of PTN001056041. Reason: Lateral correction to the EC 5.1.3.23 activity, for which GO has no term; propose it. The abstract states the substrate exclusion outright. Proposed replacements: UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 2-epimerase activity Supporting Evidence: PMID:17346239 Neither enzyme utilized UDP-alpha-D-GlcNAc, UDP-alpha-D-GlcNAcA (UDP-2-acetamido-2,3-dideoxy-alpha-D-glucuronic acid) or UDP-alpha-D-GlcNAc3NAc (UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucose) as substrates. PMID:17346239 Data collected from one- and two-dimensional NMR experiments showed that His6-WbpI catalysed the 2-epimerization of UDP-alpha-D-GlcNAc3NAcA, converting it into UDP-alpha-D-ManNAc3NAcA. |
| GO:0008761 UDP-N-acetylglucosamine 2-epimerase activity | IMP PMID:10930727 Pseudomonas aeruginosa B-band lipopolysaccharide genes wbpA ... | MODIFY | Summary: PseudoCAP row and a WbpI seed of PTN001056041. The evidence is loss of B-band LPS in the knockout, and the term follows the gene's provisional name. Reason: Seed verdict WRONG. A loss of LPS does not show which reaction the enzyme performs, the cited abstract calls the gene a "putative" UDP-GlcNAc epimerase and proposes a di-N-acetylated substrate, and the purified enzyme does not use UDP-GlcNAc. Replace with the proposed EC 5.1.3.23 term. Proposed replacements: UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 2-epimerase activity Supporting Evidence: PMID:10930727 These results imply that the P. aeruginosa UDP-D-GlcNAc precursor may be di-N-acetylated prior to further modification, preventing the E. coli enzymes from recognizing it as a substrate. PMID:17346239 Neither enzyme utilized UDP-alpha-D-GlcNAc, UDP-alpha-D-GlcNAcA (UDP-2-acetamido-2,3-dideoxy-alpha-D-glucuronic acid) or UDP-alpha-D-GlcNAc3NAc (UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucose) as substrates. |
| GO:0009243 O antigen biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping (LPS O-antigen biosynthesis). Reason: Same claim as the IMP row; WbpI makes an O-antigen precursor sugar. Supporting Evidence: PMID:10930727 Specific knockout mutations in the putative UDP-D-N-acetylglucosamine (UDP-D-GlcNAc) epimerase gene, wbpI, or the putative UDP-D-N-acetylmannosamine dehydrogenase gene, wbpA, resulted in strains that no longer produced B-band lipopolysaccharide, confirming the essential roles of these genes in B-band O antigen synthesis. |
| GO:0009243 O antigen biosynthetic process | IMP PMID:10930727 Pseudomonas aeruginosa B-band lipopolysaccharide genes wbpA ... | ACCEPT | Summary: PseudoCAP row; wbpI knockouts make no B-band O antigen. Reason: WbpI catalyses the last step in making UDP-ManNAc3NAcA, a donor of the O-antigen repeat, so it performs a step of O-antigen biosynthesis; the knockout confirms the role. Supporting Evidence: PMID:10930727 Specific knockout mutations in the putative UDP-D-N-acetylglucosamine (UDP-D-GlcNAc) epimerase gene, wbpI, or the putative UDP-D-N-acetylmannosamine dehydrogenase gene, wbpA, resulted in strains that no longer produced B-band lipopolysaccharide, confirming the essential roles of these genes in B-band O antigen synthesis. PMID:17346239 Data collected from one- and two-dimensional NMR experiments showed that His6-WbpI catalysed the 2-epimerization of UDP-alpha-D-GlcNAc3NAcA, converting it into UDP-alpha-D-ManNAc3NAcA. |
| GO:0050378 UDP-glucuronate 4-epimerase activity | EXP PMID:17346239 Identification and biochemical characterization of two novel... | MODIFY | Summary: PseudoCAP EXP row. GO:0050378 is UDP-alpha-D-glucuronate = UDP-alpha-D-galacturonate, a C4 epimerization of a different substrate; the paper shows a C2 epimerization of UDP-GlcNAc3NAcA. Reason: Wrong term for the measured activity (lateral correction). Replace with the proposed EC 5.1.3.23 term. Not a seed. Proposed replacements: UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate 2-epimerase activity Supporting Evidence: PMID:17346239 Data collected from one- and two-dimensional NMR experiments showed that His6-WbpI catalysed the 2-epimerization of UDP-alpha-D-GlcNAc3NAcA, converting it into UDP-alpha-D-ManNAc3NAcA. |
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