ilvC

UniProt ID: Q88DZ0
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

ilvC encodes NADP-dependent ketol-acid reductoisomerase, a Mg-dependent enzyme in branched-chain amino acid biosynthesis.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000287 magnesium ion binding
IEA
GO_REF:0000104 		KEEP AS NON CORE
Summary: Magnesium binding is a required cofactor feature but not the specific gene function.
Reason: UniProt indicates two Mg(2+) ions per subunit for IlvC; this supports retention as non-core cofactor information.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
Binds 2 magnesium ions per subunit
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0000287 magnesium ion binding
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
IlvC requires **NADPH** for the reduction half-reaction and a **divalent metal ion (most commonly Mg²⁺)** to support the alkyl-migration/isomerization chemistry, which is mechanistically integrated in a single catalytic cycle for most KARIs.
GO:0004455 ketol-acid reductoisomerase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Ketol-acid reductoisomerase activity is the specific catalytic function of IlvC.
Reason: The reviewed UniProt entry assigns EC 1.1.1.86 and describes the alkyl-migration/reduction reaction in BCAA biosynthesis.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
Catalyzes an alkyl-migration followed by a ketol-acid reduction
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0004455 ketol-acid reductoisomerase activity
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
Ketol-acid reductoisomerase (KARI; IlvC/AHAIR)** is a conserved bacterial enzyme family within the 6-phosphogluconate dehydrogenase (6PGDH)-type superfamily that performs a chemically coupled **alkyl-migration (isomerization)** and **NADP(H)-dependent reduction** step in BCAA biosynthesis.
file:PSEPK/ilvC/ilvC-deep-research-openscientist.md
The gene **_ilvC_** (ordered locus **PP_4678**; UniProt **Q88DZ0**) of *Pseudomonas putida* strain KT2440 (ATCC 47054 / DSM 6125 / NCIMB 11950) encodes **ketol-acid reductoisomerase (KARI)**
GO:0005829 cytosol
IEA
GO_REF:0000118 		KEEP AS NON CORE
Summary: Cytosol is plausible cellular context but not the defining function.
Reason: The TreeGrafter cytosol annotation is consistent with a soluble bacterial biosynthetic enzyme but should remain non-core. Falcon deep research supports cytosolic localization by homology, noting no KT2440-specific localization experiment was retrieved.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0005829 cytosol
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
a Gram-negative bacterial IlvC homolog was reported as a **soluble protein** that could be purified without detergents, consistent with a **cytosolic enzyme** (as expected for a central-metabolism biosynthetic enzyme operating on cytosolic intermediates).
GO:0009082 branched-chain amino acid biosynthetic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Branched-chain amino acid biosynthetic process is true but less specific than the valine/isoleucine branch terms.
Reason: IlvC acts at a shared BCAA pathway step; the specific L-valine annotation and missing isoleucine annotation are more informative.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
Involved in the biosynthesis of branched-chain amino acids
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0009082 branched-chain amino acid biosynthetic process
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
IlvC is the second step in the pyruvate-to-2-ketoisovalerate segment of **branched-chain amino-acid biosynthesis**. It supports synthesis of valine and isoleucine directly and leucine indirectly via 2-oxoisovalerate-derived metabolism.
GO:0009099 L-valine biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: IlvC participates directly in L-valine biosynthesis.
Reason: UniProt maps IlvC to the L-valine biosynthesis route from pyruvate, step 2 of 4. Falcon deep research provides KT2440-specific genetic evidence (conditional essentiality on minimal medium and BCAA auxotrophy of ilvC mutants).
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
L-valine from pyruvate: step 2/4
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0009099 L-valine biosynthetic process
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
A genome-wide knockout screen on glucose minimal medium identified **ilvC (PP4678)** among genes whose disruption prevents growth on M9 minimal medium, i.e., conditionally essential in that environment.
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Oxidoreductase activity is a broad parent of the specific ketol-acid reductoisomerase function.
Reason: The specific EC-linked ketol-acid reductoisomerase annotation should be preferred over the broad oxidoreductase parent.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
EC=1.1.1.86
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0016491 oxidoreductase activity
GO:0050661 NADP binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: NADP binding is a cofactor feature of IlvC.
Reason: The reaction uses NADP/NADPH, but binding alone is less informative than the enzyme activity.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
NADP(+)
file:PSEPK/ilvC/ilvC-goa.tsv
GO:0050661 NADP binding
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
IlvC requires **NADPH** for the reduction half-reaction and a **divalent metal ion (most commonly Mg²⁺)** to support the alkyl-migration/isomerization chemistry, which is mechanistically integrated in a single catalytic cycle for most KARIs.
GO:1901705 L-isoleucine biosynthetic process
IEA
GO_REF:0000120 		NEW
Summary: IlvC also participates directly in isoleucine biosynthesis.
Reason: The reviewed UniProt entry has an L-isoleucine biosynthesis pathway statement, but the fetched GOA table lacks this specific process annotation. Falcon deep research independently reports isoleucine auxotrophy of KT2440 ilvC mutants, supporting a direct role in isoleucine biosynthesis.
Supporting Evidence:
file:PSEPK/ilvC/ilvC-uniprot.txt
L-isoleucine from 2-oxobutanoate: step 2/4
file:PSEPK/ilvC/ilvC-deep-research-falcon.md
*ilvC* mutants showed branched-chain amino-acid auxotrophy, with reported requirements involving isoleucine and valine/leucine supplementation depending on the assay context.

Core Functions

Mg-dependent NADP ketol-acid reductoisomerase catalyzing a shared valine/isoleucine biosynthetic step.

Molecular Function:
ketol-acid reductoisomerase activity
Directly Involved In:
L-valine biosynthetic process L-isoleucine biosynthetic process
Supporting Evidence:
  • file:PSEPK/ilvC/ilvC-uniprot.txt
    Catalyzes an alkyl-migration followed by a ketol-acid reduction
  • file:PSEPK/ilvC/ilvC-uniprot.txt
    L-valine from pyruvate: step 2/4
  • file:PSEPK/ilvC/ilvC-uniprot.txt
    L-isoleucine from 2-oxobutanoate: step 2/4
  • file:PSEPK/ilvC/ilvC-deep-research-falcon.md
    IlvC/AHAIR is the **second** enzyme in the pyruvate-to-2-ketoisovalerate segment (AHAS → AHAIR/IlvC → DHAD/IlvD).
  • file:PSEPK/ilvC/ilvC-deep-research-openscientist.md
    The gene **_ilvC_** (ordered locus **PP_4678**; UniProt **Q88DZ0**) of *Pseudomonas putida* strain KT2440 (ATCC 47054 / DSM 6125 / NCIMB 11950) encodes **ketol-acid reductoisomerase (KARI)**

References

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Suggested Questions for Experts

Q: Does KT2440 IlvC show physiologically meaningful differences in activity toward acetolactate versus acetohydroxybutyrate substrates?

Suggested Experiments

Experiment: Measure purified IlvC kinetics with valine- and isoleucine-branch ketol-acid substrates and test ilvC knockout rescue by branched-chain amino acid supplementation.

Type: enzyme kinetics and genetic complementation

Deep Research

Falcon

(ilvC-deep-research-falcon.md)

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OpenScientist

(ilvC-deep-research-openscientist.md)

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