WbpE (PA3155) is a 359-residue pyridoxal 5'-phosphate (PLP)-dependent aminotransferase of the DegT/DnrJ/EryC1 family, encoded in the B-band O-antigen gene cluster of Pseudomonas aeruginosa PAO1 (serotype O5). The homodimeric enzyme transfers the amino group of L-glutamate to UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronic acid (UDP-3-keto-GlcNAcA), the product of the WbpB dehydrogenase, giving UDP-2-acetamido-3-amino-2,3-dideoxy-D-glucuronic acid (UDP-GlcNAc3NA; EC 2.6.1.98). WbpB and WbpE work as a coupled dehydrogenase/aminotransferase pair with NAD+ recycling. This is the third step of the WbpA-WbpB-WbpE-WbpD-WbpI pathway that converts UDP-GlcNAc into UDP-ManNAc3NAcA, the donor of the di-N-acetylated mannuronic acid residue of the B-band O-antigen repeat. wbpE knockouts lack B-band O antigen, and the Bordetella pertussis homolog WlbC complements the mutant.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000271 polysaccharide biosynthetic process | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA polysaccharide biosynthetic process from PTN001250039, seeded by E. coli WecE (P27833) and by the PseudoCAP IDA row on WbpE itself. Reason: True for WbpE and for the clade (WecE makes the TDP-Fuc4NAc donor of enterobacterial common antigen; WbpE makes a UDP-sugar donor of the O antigen), so the IBD is sound. For this gene the polysaccharide is known: GO:0009243 O antigen biosynthetic process, accepted in this review, is an is_a descendant of GO:0000271, so this row adds nothing beyond it. WbpE's own appearance in WITH/FROM reflects its own experimental seed and is expected. Supporting Evidence: PMID:19348502 is thought to be produced by five enzymes (WbpA, WbpB, WbpE, WbpD, and WbpI) in a stepwise manner starting from UDP-GlcNAc |
| GO:0000271 polysaccharide biosynthetic process | IDA PMID:19282284 Characterization of WbpB, WbpE, and WbpD and reconstitution ... | TOO GENERAL | Summary: PseudoCAP IDA from the in vitro reconstitution of the UDP-ManNAc3NAcA nucleotide-sugar pathway; one of the two seeds of the PTN001250039 polysaccharide biosynthesis IBD. Reason: Sound as a seed (the reconstituted pathway makes a nucleotide-sugar precursor of the B-band O antigen, and the companion paper shows wbpE knockouts lack B-band O antigen), but GO:0009243 O antigen biosynthetic process, an is_a descendant, is accepted here, so this row is uninformative for WbpE. Supporting Evidence: PMID:19282284 The lipopolysaccharide of Pseudomonas aeruginosa PAO1 contains an unusual sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid (d-ManNAc3NAcA). |
| GO:0006065 UDP-glucuronate biosynthetic process | EXP PMID:19282284 Characterization of WbpB, WbpE, and WbpD and reconstitution ... | MODIFY | Summary: PseudoCAP EXP UDP-glucuronate biosynthetic process from the WbpB/WbpE/WbpD reconstitution. Reason: The process is wrong as stated. GO:0006065 is the formation of UDP-glucuronate (UDP-GlcA). WbpE aminates UDP-3-keto-GlcNAcA to UDP-GlcNAc3NA; UDP-glucuronate is neither substrate nor product of the Wbp pathway, whose first step oxidises UDP-GlcNAc. The products are glucuronic-acid derivatives, which probably explains the choice. The sound essence is nucleotide-sugar biosynthesis; there is no GO term for UDP-ManNAc3NAcA biosynthesis. Same correction as made for the sibling wbpD row from PseudoCAP. Proposed replacements: nucleotide-sugar biosynthetic process Supporting Evidence: PMID:19282284 we identified ions that corresponded to the predicted products of WbpB (UDP-3-keto-d-GlcNAcA) and WbpE (UDP-d-GlcNAc3NA) in the coupled enzyme-substrate reaction PMID:19348502 WbpB and WbpE are a dehydrogenase/aminotransferase pair that converts UDP-GlcNAcA to UDP-GlcNAc(3NH(2))A in a coupled reaction |
| GO:0008483 transaminase activity | EXP PMID:19282284 Characterization of WbpB, WbpE, and WbpD and reconstitution ... | ACCEPT | Summary: PseudoCAP EXP transaminase activity; purified His6-WbpE produced UDP-GlcNAc3NA when coupled with WbpB. A seed of the PTN001250039 transaminase IBD. Reason: Direct biochemistry with purified protein, confirmed independently by PMID:19348502 (IDA) and by the PLP/product external-aldimine structure (PMID:20604544). No more specific GO term exists for EC 2.6.1.98. Supporting Evidence: PMID:19282284 Activities of His(6)-WbpB and His(6)-WbpE were detected only when both proteins were combined in the same reaction. |
| GO:0008483 transaminase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA transaminase activity from PTN001250039, seeded by six characterised sugar aminotransferases (WecE, ArnB x2, NtdA, Pat, WbpE). Reason: Every seed is a characterised nucleotide-sugar or sugar-phosphate aminotransferase, so the node term suits the clade and WbpE's own biochemistry confirms it. Supporting Evidence: PMID:19348502 WbpB and WbpE are a dehydrogenase/aminotransferase pair that converts UDP-GlcNAcA to UDP-GlcNAc(3NH(2))A in a coupled reaction |
| GO:0008483 transaminase activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA transaminase activity. Reason: Consistent with the direct biochemistry. Supporting Evidence: PMID:19348502 WbpB and WbpE are a dehydrogenase/aminotransferase pair that converts UDP-GlcNAcA to UDP-GlcNAc(3NH(2))A in a coupled reaction |
| GO:0008483 transaminase activity | IDA PMID:19348502 Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: e... | ACCEPT | Summary: UniProt IDA transaminase activity from the coupled WbpB/WbpE assay with purified enzymes. Reason: Direct biochemistry. Supporting Evidence: PMID:19348502 WbpB and WbpE are a dehydrogenase/aminotransferase pair that converts UDP-GlcNAcA to UDP-GlcNAc(3NH(2))A in a coupled reaction |
| GO:0009103 lipopolysaccharide biosynthetic process | IDA PMID:18621892 Biosynthesis of a rare di-N-acetylated sugar in the lipopoly... | TOO GENERAL | Summary: UniProt IDA LPS biosynthesis; wbpE knockout lacks B-band O antigen, restored by wbpE or wlbC. Reason: True, but the LPS component affected is the B-band O antigen; GO:0009243 O antigen biosynthetic process, accepted here, is an is_a descendant of GO:0009103. Supporting Evidence: PMID:18621892 The evidence presented here demonstrates that B-band O antigen is not produced when wbpB or wbpE is knocked out in P. aeruginosa |
| GO:0009243 O antigen biosynthetic process | EXP PMID:18621892 Biosynthesis of a rare di-N-acetylated sugar in the lipopoly... | ACCEPT | Summary: PseudoCAP EXP O antigen biosynthesis from the wbpE knockout and complementation. Reason: Full text read. The knockout lacks B-band O antigen and core-plus-one, and is complemented by His6-WbpE or by B. pertussis wlbC. With the enzymology (PMID:19348502), WbpE makes a dedicated O-antigen sugar precursor, so the process is direct. (IMP would be the more usual code.) Supporting Evidence: PMID:18621892 The evidence presented here demonstrates that B-band O antigen is not produced when wbpB or wbpE is knocked out in P. aeruginosa |
| GO:0009243 O antigen biosynthetic process | IDA PMID:19348502 Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: e... | ACCEPT | Summary: UniProt IDA O antigen biosynthesis; in vitro synthesis of the UDP-ManNAc3NAcA O-antigen donor. Reason: Direct enzymology of a dedicated O-antigen precursor pathway. Supporting Evidence: PMID:19348502 WbpA, WbpB, WbpE, WbpD, and WbpI can be combined in vitro to generate UDP-ManNAc(3NAc)A in a single reaction vessel |
| GO:0009243 O antigen biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping to LPS O-antigen biosynthesis. Reason: Consistent with the experimental rows. Supporting Evidence: PMID:18621892 The evidence presented here demonstrates that B-band O antigen is not produced when wbpB or wbpE is knocked out in P. aeruginosa |
| GO:0030170 pyridoxal phosphate binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA PLP binding from PTN001250039. Reason: PLP is the cofactor of the whole DegT family; WbpE was crystallised with PLP, PMP and the PLP-product external aldimine. Supporting Evidence: PMID:20604544 we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA PLP binding. Reason: Consistent with the crystal structure. Supporting Evidence: PMID:20604544 we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) |
| GO:0030170 pyridoxal phosphate binding | IDA PMID:20604544 Structural analysis of WbpE from Pseudomonas aeruginosa PAO1... | ACCEPT | Summary: UniProt IDA PLP binding from the crystal structure. Reason: Direct structural evidence. Supporting Evidence: PMID:20604544 we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) |
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