LiuE (PA2011) is the bifunctional hydroxyacyl-CoA lyase of the liuRABCDE cluster of Pseudomonas aeruginosa. It is a 300-residue, divalent cation-dependent homodimeric enzyme of the HMG-CoA lyase family. It cleaves (3S)-3-hydroxy-3-methylglutaryl-CoA to acetyl-CoA plus acetoacetate (EC 4.1.3.4), the terminal step of L-leucine and isovalerate catabolism, and it also cleaves 3-hydroxy-3-isohexenylglutaryl-CoA to 7-methyl-3-oxooct-6-enoyl-CoA plus acetate (EC 4.1.3.26), the corresponding step of the geranyl-CoA pathway that degrades acyclic monoterpenes of the citronellol family. Because the atu cluster that handles the terpene pathway has no lyase of its own, LiuE serves both routes, and cells lacking it cannot grow on leucine, isovalerate or acyclic terpenes. The acetoacetate it produces is a catabolic intermediate feeding central metabolism, not a circulating fuel as in vertebrate ketogenesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004419 hydroxymethylglutaryl-CoA lyase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the seven-seed GO:0004419 IBD at PTN000031222, the HMG-CoA lyase node, seeded by the directly characterised human, rat and mouse HMGCL enzymes, human HMGCLL1, Arabidopsis AT2G26800 and this gene itself. LiuE's own EXP rows are what put Q9I2A0 in the WITH/FROM list, which is expected rather than circular, and the inherited claim is the activity measured on purified LiuE. Reason: Well-seeded family-level activity, independently demonstrated for this protein with kinetics. Supporting Evidence: PMID:19459965 LiuE showed HMG-CoA lyase optimal activity at a pH of 7.0 and 37 degrees C, an apparent K(m) of 100 microM for HMG-CoA and a V(max) of 21 micromol min(-1) mg(-1). |
| GO:0006552 L-leucine catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the three-seed GO:0006552 IBD at the same node (mouse Hmgcl, Aspergillus Q5B2F7 and this gene). HMG-CoA cleavage is the terminal step of leucine catabolism, and LiuE catalyses it, so the gene product performs part of the process rather than merely being required for it. Reason: Participation by catalysis of a pathway step, confirmed in this organism by both the growth phenotype and the purified enzyme. Supporting Evidence: PMID:19459965 These results demonstrate that the liuE gene of P. aeruginosa encodes for the HMG-CoA lyase, an essential enzyme for growth in both leucine and acyclic terpenes. |
| GO:0046951 ketone body biosynthetic process | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: A third IBD at PTN000031222, seeded only by animal HMGCL and HMGCLL1 proteins. In vertebrate liver, HMG-CoA cleavage is the last step of ketogenesis and the term names that physiological programme. LiuE runs the same chemistry as the terminal step of leucine, isovalerate and acyclic terpene catabolism - the acetoacetate is an intermediate entering central metabolism, and P. aeruginosa has no ketone-body biosynthesis to be part of. Reason: The chemistry is shared, so the row is not a simple error, but the process is lineage-specific to animals and does not exist in this organism. The node spans bacteria, fungi, plants and animals, so the animal-seeded IBD should not reach the bacterial members; recorded as a GO_CENTRAL defect below. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH ROLE CONFLATION Sources checked: PANTHER:PTN000031222 · PTN000031222 SUPPORTS SOURCE BUT NOT TARGET All five seeds of the GO:0046951 IBD are animal HMGCL/HMGCLL1 proteins (human, rat, mouse, Drosophila). The node also holds bacterial, fungal and plant lyases, where the same reaction is catabolic rather than ketogenic. UniProtKB:P35914 · human HMGCL SUPPORTS SOURCE BUT NOT TARGET Mitochondrial HMGCL genuinely performs the last step of hepatic ketogenesis; the process term is right for it and wrong for the bacterial leaf. Supporting Evidence: PMID:19459965 A mutant in the liuE gene (ORF PA2011) of P. aeruginosa was unable to utilize both leucine/isovalerate and acyclic terpenes as the carbon source. |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO root-level catalytic activity from the HMG-CoA lyase signature. Reason: Root-of-branch term, entailed by the specific lyase activities accepted in this review. |
| GO:0004419 hydroxymethylglutaryl-CoA lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assertion from the InterPro HMG-CoA lyase signature plus the RHEA/EC mapping, agreeing with the EXP row on the same term. Reason: Consistent with the measured activity on purified LiuE; the reaction (RHEA:24404) is the one UniProt records with experimental evidence. |
| GO:0016833 oxo-acid-lyase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO parent-level lyase activity. Both GO:0004419 and GO:0047445, accepted here, are descendants of it. Reason: Uninformative given the two specific lyase activities asserted in this review. |
| GO:0047445 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: RHEA/EC mapping of the second activity, which agrees with the two EXP rows on the same term. Reason: The mapped reaction is the one demonstrated on purified protein. |
| GO:0004419 hydroxymethylglutaryl-CoA lyase activity | EXP PMID:19597963 The bifunctional role of LiuE from Pseudomonas aeruginosa, d... | ACCEPT | Summary: UniProt EXP row. Purified His-tagged LiuE cleaves HMG-CoA to acetyl-CoA and acetoacetate; kinetics and the divalent-cation requirement were measured in the companion paper. This is a core activity of the protein. Reason: Direct enzymological evidence for the annotated reaction. Supporting Evidence: PMID:19597963 The LiuE protein was purified as a His-tagged recombinant protein and in addition to show HMG-CoA lyase activity PMID:19459965 LiuE showed HMG-CoA lyase optimal activity at a pH of 7.0 and 37 degrees C, an apparent K(m) of 100 microM for HMG-CoA and a V(max) of 21 micromol min(-1) mg(-1). |
| GO:0047445 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity | EXP PMID:19459965 The Pseudomonas aeruginosa liuE gene encodes the 3-hydroxy-3... | ACCEPT | Summary: UniProt EXP row for the second, terpene-pathway activity, supported by the mutant's inability to grow on acyclic terpenes and by the purified-enzyme work reported across the two papers from this group. Reason: Core activity; the atu cluster encodes no lyase of its own, so this reaction in the geranyl-CoA pathway is LiuE's. Supporting Evidence: PMID:16517656 it was named the atu cluster (acyclic terpene utilization), consisting of the atuCDEF genes and lacking the hydroxymethyl-glutaryl-coenzyme A (CoA) lyase (HMG-CoA lyase) homolog. |
| GO:0047445 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity | EXP PMID:19597963 The bifunctional role of LiuE from Pseudomonas aeruginosa, d... | ACCEPT | Summary: Second UniProt EXP row for the same activity, from the paper that demonstrated the HIHG-CoA lyase activity on purified protein. It reinforces the row above rather than duplicating it. Reason: Direct enzymological evidence for the annotated reaction. Supporting Evidence: PMID:19597963 The LiuE protein was purified as a His-tagged recombinant protein and in addition to show HMG-CoA lyase activity |
| GO:0004419 hydroxymethylglutaryl-CoA lyase activity | IMP PMID:16517656 The atu and liu clusters are involved in the catabolic pathw... | ACCEPT | Summary: PseudoCAP row and one of the seven seeds of the GO:0004419 IBD at PTN000031222. The cited paper mutagenised the atu and liu clusters and inferred the enzyme assignment from sequence, calling it a "probable" HMG-CoA lyase; the activity itself was measured three years later (PMID:19459965, PMID:19597963), which is where the EXP rows come from. The term is right and the gene is right, so the row stays; the reservation is the IMP coding of a molecular function on a sequence-based "probable" assignment. Reason: Correct claim, now independently confirmed by purified-enzyme assays, so the seed is sound for the node. Only the evidence coding is questioned, recorded as a source defect rather than by changing the action. Supporting Evidence: PMID:16517656 The liuE gene encodes a probable hydroxy-acyl-CoA lyase (probably HMG-CoA lyase), an enzyme with bifunctional activity that is essential for both AMTC and leucine degradation. |
| GO:0006552 L-leucine catabolic process | IMP PMID:19459965 The Pseudomonas aeruginosa liuE gene encodes the 3-hydroxy-3... | ACCEPT | Summary: PseudoCAP row and the seed of the GO:0006552 IBD at PTN000031222. The mutant cannot grow on leucine or isovalerate, and the same study shows that the purified protein performs the pathway's terminal cleavage, so this is participation by catalysis rather than necessity alone. Reason: Core process, with the gene product catalysing one of its steps; a sound seed for the node term. Supporting Evidence: PMID:19459965 A mutant in the liuE gene (ORF PA2011) of P. aeruginosa was unable to utilize both leucine/isovalerate and acyclic terpenes as the carbon source. |
| GO:0008300 isoprenoid catabolic process | IMP PMID:16517656 The atu and liu clusters are involved in the catabolic pathw... | TOO GENERAL | Summary: PseudoCAP row for the terpene side of the pathway. True, but GO:0046247 terpene catabolic process, accepted below from the same body of work, is a descendant of it and names the actual substrates - acyclic monoterpenes of the citronellol family. Reason: Entailed by the accepted GO:0046247 row; the specific term is the informative one for this gene. Supporting Evidence: PMID:16517656 The liuE gene encodes a probable hydroxy-acyl-CoA lyase (probably HMG-CoA lyase), an enzyme with bifunctional activity that is essential for both AMTC and leucine degradation. |
| GO:0046247 terpene catabolic process | IMP PMID:19459965 The Pseudomonas aeruginosa liuE gene encodes the 3-hydroxy-3... | ACCEPT | Summary: PseudoCAP row. The mutant cannot grow on acyclic terpenes and accumulates intermediates of that pathway, and the purified enzyme carries out the HIHG-CoA cleavage step of the geranyl-CoA route, so LiuE performs part of the process. Reason: Core process for this bifunctional enzyme, supported by both the phenotype and the enzymology. Supporting Evidence: PMID:19459965 A mutant in the liuE gene (ORF PA2011) of P. aeruginosa was unable to utilize both leucine/isovalerate and acyclic terpenes as the carbon source. PMID:19597963 The LiuE protein was purified as a His-tagged recombinant protein and in addition to show HMG-CoA lyase activity |
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Download this section (compressed HTML)Q: How does one active site accommodate both HMG-CoA and the much bulkier HIHG-CoA, and what are the relative catalytic efficiencies? Only HMG-CoA kinetics have been published.
Q: Should the animal-seeded ketone body biosynthesis IBD at PANTHER PTN000031222 be restricted to the animal clade, so that bacterial, fungal and plant HMG-CoA lyases are not annotated to ketogenesis?
Experiment: Measure steady-state kinetics of purified LiuE side by side on HMG-CoA and on enzymatically prepared HIHG-CoA, and test whether active-site variants can separate the two activities, which would show whether the bifunctionality is incidental or selected for.
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