IMDH1 (IPMDH1, AtIMD1, MAM-D1; At5g14200) is a chloroplast-stromal, NAD+- and Mg2+/Mn2+-dependent 3-isopropylmalate dehydrogenase of the isocitrate/isopropylmalate dehydrogenase family. It catalyzes the oxidative decarboxylation of 3-alkylmalates to 2-oxo acids, the third step of each chain-elongation cycle. Among the three Arabidopsis IPMDHs, IMDH1 is specialized for the methionine chain-elongation pathway of aliphatic glucosinolate biosynthesis: it acts on 3-(2'-methylthio)ethylmalate and longer homologues with far higher efficiency than its paralogs, a specificity conferred by an active-site phenylalanine (Phe-137) in place of the leucine found in leucine-pathway IPMDHs. Loss of IMDH1 reduces aliphatic glucosinolates with four or more side-chain carbons and also lowers free leucine, reflecting a secondary contribution to leucine biosynthesis, which is dominated by IPMDH2 and IPMDH3. IMDH1 is co-expressed with and regulated like other aliphatic glucosinolate genes (MYB28 target; induced by wounding and jasmonate), its activity is modulated by thiol-based redox regulation, and it has been reported to associate with the IPMI large subunit IIL1.
Definition: Catalysis of the NAD+-dependent oxidative decarboxylation of a 3-(omega-methylthio)alkylmalate to the corresponding omega-methylthio-2-oxoalkanoate, producing carbon dioxide and NADH. This reaction is the oxidative decarboxylation step of methionine chain elongation.
Justification: GO:0003862 explicitly specifies 3-isopropylmalate and its leucine-pathway product, not the chemically distinct methylthioalkylmalate substrates. GO:0103093 is obsolete; its replacement instruction does not broaden the reaction definition of GO:0003862. A substrate-appropriate active term is needed.
Parent term: oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Magnesium ion binding from the isocitrate/isopropylmalate dehydrogenase family signature. Reason: IPMDHs require a divalent metal (Mg2+ or Mn2+) bound by conserved Asp residues; these are conserved in the plant enzymes (He et al. 2011 structure of the AtIPMDH2 paralog). Cofactor binding is a supporting, not core, MF. Supporting Evidence: PMID:21697089 Asp-288, and Asp-292 are positioned to interact with a catalytically essential divalent metal |
| GO:0003862 3-isopropylmalate dehydrogenase activity | EXP PMID:19674406 A redox-active isopropylmalate dehydrogenase functions in th... | ACCEPT | Summary: Recombinant AtIPMDH1 oxidatively decarboxylates 3-isopropylmalate with NAD+ (He et al. 2009; kinetic constants in UniProt). Reason: Retain the experimentally established 3-isopropylmalate reaction in leucine biosynthesis. The exact GO definition does not cover methylthioalkylmalate substrates, despite replacement of obsolete GO:0103093 by this identifier; the specialized reaction is represented separately as a proposed molecular function. Supporting Evidence: PMID:19674406 This work characterized an enzyme in plants that catalyzes the oxidative decarboxylation step in both leucine biosynthesis (primary metabolism) and methionine chain elongation of glucosinolates (specialized metabolism). PMID:19674406 Complementation of the mutant phenotype by ectopic expression of AtIPMDH1, together with the enzyme's substrate specificity, implicates AtIPMDH1 in both glucosinolate and leucine biosynthesis. |
| GO:0003862 3-isopropylmalate dehydrogenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of IPMDH activity for the LeuB family. Reason: IMDH1 retains IPMDH activity experimentally (with reduced efficiency toward 3-IPM compared with IMDH2/3); its own experimental annotation is among the node's sources, which is expected rather than circular. Supporting Evidence: PMID:15849421 AtIMD1, AtIMD2, and AtIMD3 were able to complement a leu2 mutant of yeast, suggesting that these genes encode functional IPMDH. PMID:21697089 AtIPMDH1 accepts both substrates with comparable k cat / K m values, but was ∼500-fold more efficient with the glucosinolate substrate than the other two isoforms. |
| GO:0003862 3-isopropylmalate dehydrogenase activity | IDA PMID:15849421 Cloning of cDNAs encoding isopropylmalate dehydrogenase from... | ACCEPT | Summary: AtIMD1 (IMDH1) complemented a yeast leu2 (IPMDH-deficient) mutant. Reason: Functional complementation demonstrates IPMDH activity in vivo (abstract-only cache). Supporting Evidence: PMID:15849421 AtIMD1, AtIMD2, and AtIMD3 were able to complement a leu2 mutant of yeast, suggesting that these genes encode functional IPMDH. |
| GO:0003862 3-isopropylmalate dehydrogenase activity | IDA PMID:20840499 Functional characterization of Arabidopsis thaliana isopropy... | ACCEPT | Summary: Recombinant IPMDH1 has IPMDH activity toward 3-IPM, lower than that of IPMDH2 and IPMDH3. Reason: Consistent with other biochemical data (abstract-only cache). Supporting Evidence: PMID:20840499 IPMDH2 and IPMDH3 proteins exhibited significantly higher activity toward 3-IPM than IPMDH1, which is indicative of a pivotal role in leucine biosynthesis. |
| GO:0003862 3-isopropylmalate dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic EC 1.1.1.85 / RHEA:32271 assignment. Reason: Consistent with experimental data. Supporting Evidence: PMID:15849421 AtIMD1, AtIMD2, and AtIMD3 were able to complement a leu2 mutant of yeast, suggesting that these genes encode functional IPMDH. |
| GO:0003862 3-isopropylmalate dehydrogenase activity | IMP PMID:20840499 Functional characterization of Arabidopsis thaliana isopropy... | ACCEPT | Summary: Mutant combinations including ipmdh1 have reduced leucine biosynthetic (IPMDH) enzyme activities. Reason: Mutant analysis showing loss of IPMDH activity; consistent with direct biochemistry. Full text not cached. Supporting Evidence: PMID:20840499 This mutant and a triple mutant containing one allele of IPMDH2 or IPMDH3 had decreased leucine biosynthetic enzyme activities and lower free leucine concentrations. |
| GO:0003862 3-isopropylmalate dehydrogenase activity | IMP PMID:21697089 Structural and functional evolution of isopropylmalate dehyd... | ACCEPT | Summary: He et al. 2011 kinetics and in planta complementation: IMDH1 accepts both 3-IPM and 3-(2'-methylthio)ethylmalate and is ~500-fold more efficient with the glucosinolate substrate than IMDH2/3; F137L substitution abolishes glucosinolate-substrate preference and fails to complement ipmdh1. Reason: Retain the experimentally established 3-isopropylmalate reaction in leucine biosynthesis. The exact GO definition does not cover methylthioalkylmalate substrates, despite replacement of obsolete GO:0103093 by this identifier; the specialized reaction is represented separately as a proposed molecular function. Supporting Evidence: PMID:21697089 AtIPMDH1 accepts both substrates with comparable k cat / K m values, but was ∼500-fold more efficient with the glucosinolate substrate than the other two isoforms. PMID:21697089 Site-directed mutagenesis of Phe-137 to a leucine in AtIPMDH1 (AtIPMDH1-F137L) reduced activity toward 3-(2′-methylthio)ethylmalate by 200-fold PMID:21697089 the altered glucosinolate profile of the atipmdh1 mutant could only be rescued by expression of AtIPMDH1 |
| GO:0005829 cytosol | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | UNDECIDED | Summary: Detected by SEC-MS in the crude cytosolic (soluble) fraction of leaf extracts (Aryal et al. 2014). Reason: The source reports a cytosolic protein-complex fraction, whereas independent experiments establish chloroplast-stromal localization. The available main text does not resolve a genuine additional cytosolic pool versus organelle carry-over for this target; do not infer contamination or reject an experimental location without the target-specific evidence. Supporting Evidence: PMID:25293756 Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves using size exclusion chromatography PMID:19674406 This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma |
| GO:0009098 L-leucine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of L-leucine biosynthesis for the LeuB/IPMDH family. Reason: IMDH1 does contribute to Leu biosynthesis in planta (ipmdh1 mutants have reduced free leucine), though IMDH2/IMDH3 play the dominant roles. Unlike the IPMI small subunits, the evidence does not show loss of the ancestral function, so the IBA stands. Supporting Evidence: PMID:19674406 Mutation of AtIPMDH1 leads to a significant reduction in the levels of free leucine and of glucosinolates with side chains of four or more carbons. PMID:21697089 all three AtIPMDHs are involved in leucine biosynthesis, with AtIPMDH2 and AtIPMDH3 exhibiting dominant roles |
| GO:0009098 L-leucine biosynthetic process | IDA PMID:15849421 Cloning of cDNAs encoding isopropylmalate dehydrogenase from... | ACCEPT | Summary: Complementation of yeast leu2 by AtIMD1. Reason: Shows the enzyme can support Leu biosynthesis; supported in planta by reduced leucine in ipmdh1 mutants. Supporting Evidence: PMID:15849421 AtIMD1, AtIMD2, and AtIMD3 were able to complement a leu2 mutant of yeast, suggesting that these genes encode functional IPMDH. |
| GO:0009098 L-leucine biosynthetic process | IDA PMID:20840499 Functional characterization of Arabidopsis thaliana isopropy... | ACCEPT | Summary: Enzyme activity toward 3-IPM supports a role in leucine biosynthesis (He et al. 2011). Reason: IMDH1 has lower 3-IPM activity than IMDH2/3 but is still involved in Leu biosynthesis. Supporting Evidence: PMID:20840499 IPMDH2 and IPMDH3 proteins exhibited significantly higher activity toward 3-IPM than IPMDH1, which is indicative of a pivotal role in leucine biosynthesis. PMID:21697089 all three AtIPMDHs are involved in leucine biosynthesis, with AtIPMDH2 and AtIPMDH3 exhibiting dominant roles |
| GO:0009098 L-leucine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic Leu biosynthesis annotation from UniPathway/ARBA/InterPro. Reason: Consistent with experimental data. Supporting Evidence: PMID:21697089 all three AtIPMDHs are involved in leucine biosynthesis, with AtIPMDH2 and AtIPMDH3 exhibiting dominant roles |
| GO:0009098 L-leucine biosynthetic process | IMP PMID:19674406 A redox-active isopropylmalate dehydrogenase functions in th... | ACCEPT | Summary: ipmdh1 mutants have significantly reduced free leucine, restored by complementation. Reason: Direct genetic evidence that IMDH1 catalyzes a step in Leu biosynthesis in planta. Supporting Evidence: PMID:19674406 Mutation of AtIPMDH1 leads to a significant reduction in the levels of free leucine and of glucosinolates with side chains of four or more carbons. PMID:19674406 Complementation of the mutant phenotype by ectopic expression of AtIPMDH1, together with the enzyme's substrate specificity, implicates AtIPMDH1 in both glucosinolate and leucine biosynthesis. |
| GO:0009098 L-leucine biosynthetic process | IMP PMID:20840499 Functional characterization of Arabidopsis thaliana isopropy... | ACCEPT | Summary: Higher-order ipmdh mutants have decreased leucine biosynthetic enzyme activities and lower free leucine. Reason: Consistent with a (minor) catalytic contribution of IMDH1 to Leu biosynthesis. Supporting Evidence: PMID:20840499 This mutant and a triple mutant containing one allele of IPMDH2 or IPMDH3 had decreased leucine biosynthetic enzyme activities and lower free leucine concentrations. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MODIFY | Summary: Detected by MS in purified chloroplasts. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:19597944 which also reported BCAT3, MAM1 and all three potential isopropylmalate dehydrogenases in protein fractions from plastids PMID:19674406 This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | MODIFY | Summary: AtSubP chloroplast prediction. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:15849421 Deduced amino acid sequences of the three genes contain a putative transit-peptide for plastidic localization. |
| GO:0009536 plastid | ISS PMID:15849421 Cloning of cDNAs encoding isopropylmalate dehydrogenase from... | MODIFY | Summary: Plastid localization inferred from a putative plastid transit peptide. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:15849421 Deduced amino acid sequences of the three genes contain a putative transit-peptide for plastidic localization. |
| GO:0009553 embryo sac development | IMP PMID:20840499 Functional characterization of Arabidopsis thaliana isopropy... | KEEP AS NON CORE | Summary: Mutant combinations of IPMDH genes affect embryo sac development; ipmdh1 contributes only in higher-order combinations / slight transmission effects. Reason: Retain the curated target-specific developmental phenotype as non-core relative to IMDH1 metabolic catalysis. The UniProt experimental note explicitly includes IMDH1, while the abstract emphasizes the stronger IPMDH2/3 effects; that emphasis is not evidence of misattribution. Supporting Evidence: file:ARATH/IMDH1/IMDH1-uniprot.txt Required during pollen development and involved in embryo sac development (PubMed:20840499). |
| GO:0009555 pollen development | IMP PMID:20840499 Functional characterization of Arabidopsis thaliana isopropy... | KEEP AS NON CORE | Summary: Pollen development defects in ipmdh mutant combinations. Reason: Retain the curated target-specific developmental phenotype as non-core relative to IMDH1 metabolic catalysis. The UniProt experimental note explicitly includes IMDH1, while the abstract emphasizes the stronger IPMDH2/3 effects; that emphasis is not evidence of misattribution. Supporting Evidence: file:ARATH/IMDH1/IMDH1-uniprot.txt Required during pollen development and involved in embryo sac development (PubMed:20840499). |
| GO:0009570 chloroplast stroma | HDA PMID:16207701 The oligomeric stromal proteome of Arabidopsis thaliana chlo... | ACCEPT | Summary: Identified in the oligomeric stromal proteome. Reason: Consistent with IDA stromal localization. Supporting Evidence: PMID:16207701 This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. |
| GO:0009570 chloroplast stroma | HDA PMID:18633119 Quantitative proteomics of a chloroplast SRP54 sorting mutan... | ACCEPT | Summary: Detected in chloroplast proteome (Rutschow et al. 2008). Reason: Consistent with IDA stromal localization. Supporting Evidence: PMID:18633119 a quantitative comparison of ffc2-1 was carried out for total leaf proteomes of young seedlings and for chloroplast proteomes of fully developed leaves PMID:19674406 This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: AT_CHLORO subplastidial assignment to stroma. Reason: Consistent with IDA stromal localization. Supporting Evidence: PMID:20061580 We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). PMID:19674406 This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma |
| GO:0009570 chloroplast stroma | IDA PMID:19674406 A redox-active isopropylmalate dehydrogenase functions in th... | ACCEPT | Summary: AtIPMDH1 localized to the chloroplast stroma. Reason: Direct experimental localization; the stroma is where the Met chain-elongation and Leu pathways operate. Supporting Evidence: PMID:19674406 This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma |
| GO:0009570 chloroplast stroma | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (chloroplast stroma). Reason: Based on experimental data. Supporting Evidence: PMID:19674406 This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma |
| GO:0009611 response to wounding | IEP PMID:19674406 A redox-active isopropylmalate dehydrogenase functions in th... | KEEP AS NON CORE | Summary: IMDH1 expression is induced by wounding (per UniProt, from He et al. 2009). Reason: Retain the expression response as non-core. The curated UniProt induction statement is explicitly tied to PMID:19674406; the local abstract alone does not contain the induction experiment. Coexpression is not being substituted for induction evidence. Supporting Evidence: file:ARATH/IMDH1/IMDH1-uniprot.txt INDUCTION: By wounding and jasmonic acid (MeJA). {ECO:0000269|PubMed:19674406}. |
| GO:0009753 response to jasmonic acid | IEP PMID:19674406 A redox-active isopropylmalate dehydrogenase functions in th... | KEEP AS NON CORE | Summary: IMDH1 expression is induced by methyl jasmonate (per UniProt, from He et al. 2009). Reason: Retain the expression response as non-core. The curated UniProt induction statement is explicitly tied to PMID:19674406; the local abstract alone does not contain the induction experiment. Coexpression is not being substituted for induction evidence. Supporting Evidence: file:ARATH/IMDH1/IMDH1-uniprot.txt INDUCTION: By wounding and jasmonic acid (MeJA). {ECO:0000269|PubMed:19674406}. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: Generic NAD(P)-dependent CH-OH oxidoreductase activity from InterPro. Reason: Refine the correct NAD(P)-dependent CH-OH oxidoreductase parent to the demonstrated 3-isopropylmalate reaction and the distinct specialized methylthioalkylmalate reaction; the latter requires an active substrate-appropriate term. Proposed replacements: 3-isopropylmalate dehydrogenase activity methylthioalkylmalate dehydrogenase (NAD+) activity Supporting Evidence: PMID:21697089 involves oxidation of the alcohol by deprotonation and hydride transfer to NAD |
| GO:0019761 glucosinolate biosynthetic process | IMP PMID:19493961 Omics-based approaches to methionine side chain elongation i... | ACCEPT | Summary: atimd1 knockouts have reduced Met-derived (especially long-chain) glucosinolates; gene named MAM-D1. Reason: IMDH1 catalyzes the oxidative decarboxylation step of each Met chain-elongation cycle; core process. Supporting Evidence: PMID:19493961 In this study we found that knocking out either of the candidate genes, AtleuC1 or AtIMD1 , reduced the level of Met-GSLs, indicating that both genes are actually involved in Met-GSL biosynthesis. PMID:19493961 the levels of Met-GSLs with long chains (C7–C8) were significantly lower in the knockout lines |
| GO:0019761 glucosinolate biosynthetic process | IMP PMID:19674406 A redox-active isopropylmalate dehydrogenase functions in th... | ACCEPT | Summary: ipmdh1 mutation reduces glucosinolates with side chains of four or more carbons; complementation restores them. Reason: Core process, directly supported by mutant and complementation data. Supporting Evidence: PMID:19674406 Mutation of AtIPMDH1 leads to a significant reduction in the levels of free leucine and of glucosinolates with side chains of four or more carbons. PMID:19674406 Complementation of the mutant phenotype by ectopic expression of AtIPMDH1, together with the enzyme's substrate specificity, implicates AtIPMDH1 in both glucosinolate and leucine biosynthesis. |
| GO:0019761 glucosinolate biosynthetic process | IMP PMID:21697089 Structural and functional evolution of isopropylmalate dehyd... | ACCEPT | Summary: ipmdh1 glucosinolate phenotype is rescued by IMDH1 (or L->F variants of IMDH2/3) but not by IMDH1-F137L. Reason: Core process; ties the substrate-specificity determinant Phe-137 to in planta glucosinolate synthesis. Supporting Evidence: PMID:21697089 the altered glucosinolate profile of the atipmdh1 mutant could only be rescued by expression of AtIPMDH1 PMID:21697089 AtIPMDH1 is primarily involved in methionine chain-elongation of aliphatic glucosinolate biosynthesis. |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: NAD binding from the IPMDH family signature. Reason: IPMDH uses NAD+ as the hydride acceptor; NAD+ Km determined for IMDH1 (UniProt, He et al. 2009). Cofactor-binding, non-core supporting term. Supporting Evidence: PMID:21697089 involves oxidation of the alcohol by deprotonation and hydride transfer to NAD |
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Download this section (compressed HTML)Q: GO obsoleted the methylthioalkylmalate dehydrogenase activity terms into GO:0003862; should a specific 3-(omega-methylthio)alkylmalate dehydrogenase term (analogous to GO:0120528 for the isomerase) be reinstated to distinguish IMDH1 from the Leu-pathway paralogs?
Q: How does thiol-based redox regulation of IMDH1 couple Met chain elongation to chloroplast redox/light status in vivo?
Q: Does the reported IIL1 (LeuC)-IMDH1 interaction form a channeling metabolon in the chloroplast stroma, and does it influence glucosinolate chain-length distribution?
Experiment: Determine kcat/Km of IMDH1 with the full series of 3-(omega-methylthio)alkylmalates (C1-C6 side chains) to test whether IMDH1 contributes to chain-length specificity.
Type: in vitro enzyme kinetics
Experiment: Identify the redox-sensitive cysteines of IMDH1 by mutagenesis and test thioredoxin-dependent activation in chloroplast extracts and in planta glucosinolate profiles.
Type: biochemistry/reverse genetics
Experiment: Solve a crystal structure of IMDH1 with a methylthioalkylmalate ligand to define how Phe-137 accommodates the methylthioalkyl side chain.
Type: structural biology
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