Q9FMT1 · LEU31_ARATH
- Protein3-isopropylmalate dehydrogenase 1, chloroplastic
- GeneIMDH1
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids409 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Involved in both glucosinolate and leucine biosynthesis; catalyzes the oxidative decarboxylation step in both leucine biosynthesis (primary metabolism) and methionine chain elongation of glucosinolates (specialized metabolism) (PubMed:19493961, PubMed:19674406, PubMed:21697089).
Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate, 3-IPM) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate (PubMed:15849421, PubMed:20840499).
Required during pollen development and involved in embryo sac development (PubMed:20840499).
More active on 3-isopropylmalate and NAD+ than towards D-malate (PubMed:19674406).
Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate, 3-IPM) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate (PubMed:15849421, PubMed:20840499).
Required during pollen development and involved in embryo sac development (PubMed:20840499).
More active on 3-isopropylmalate and NAD+ than towards D-malate (PubMed:19674406).
Catalytic activity
- (2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH
Cofactor
Mn2+ (UniProtKB | Rhea| CHEBI:29035 )
Note: Binds 1 Mg2+ or Mn2+ ion per subunit.
Activity regulation
Regulated by a thiol-based redox modification; oxidation by CuCl2 leads to a decreased activity.
Kinetics
KM | SUBSTRATE | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|---|
45.3 μM | 3-(2'-methylthio)ethylmalate | |||||
25.2 μM | 3-isopropylmalate | 7.5 | in reduced form | |||
187.1 μM | NAD+ | 7.5 | in reduced form | |||
1100 μM | D-malate | 7.5 | in reduced form | |||
68.62 μM | 3-isopropylmalate | 7.5 | in oxidized form | |||
242.1 μM | NAD+ | 7.5 | in oxidized form | |||
1400 μM | D-malate | 7.5 | in oxidized form |
Vmax | pH | TEMPERATURE[C] | NOTES | EVIDENCE | |
---|---|---|---|---|---|
0.93 μmol/min/mg | 7.5 | with 3-isopropylmalate as substrate, in reduced form | |||
1.01 μmol/min/mg | 7.5 | with NAD+ as substrate, in reduced form | |||
0.16 μmol/min/mg | 7.5 | with D-malate as substrate, in reduced form | |||
0.45 μmol/min/mg | 7.5 | with 3-isopropylmalate as substrate, in oxidized form | |||
0.82 μmol/min/mg | 7.5 | with NAD+ as substrate, in oxidized form | |||
0.11 μmol/min/mg | 7.5 | with D-malate as substrate, in oxidized form |
kcat is 37 min-1 with 3-isopropylmalate as substrate (PubMed:20840499, PubMed:21697089).
kcat is 51 min-1 with 3-(2'-methylthio)ethylmalate as substrate (PubMed:21697089).
kcat is 51 min-1 with 3-(2'-methylthio)ethylmalate as substrate (PubMed:21697089).
pH Dependence
Optimum pH is 7.6.
Temperature Dependence
Optimum temperature is 60 degrees Celsius.
Pathway
Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4.
Secondary metabolite biosynthesis.
Features
Showing features for binding site, site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 118-133 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: IGGYKWDKNEKHLRPE | ||||||
Site | 137 | Confers substrate specificity | ||||
Sequence: F | ||||||
Binding site | 140 | substrate | ||||
Sequence: R | ||||||
Binding site | 150 | substrate | ||||
Sequence: R | ||||||
Binding site | 178 | substrate | ||||
Sequence: R | ||||||
Site | 185 | Important for catalysis | ||||
Sequence: Y | ||||||
Site | 232 | Essential for redox regulation | ||||
Sequence: C | ||||||
Site | 236 | Important for catalysis | ||||
Sequence: K | ||||||
Binding site | 238 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 268 | Mg2+ (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 268 | substrate | ||||
Sequence: D | ||||||
Binding site | 269 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 292 | Mg2+ (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 296 | Mg2+ (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 322-338 | NAD+ (UniProtKB | ChEBI) | ||||
Sequence: EPIHGSAPDIAGQDKAN | ||||||
Site | 390 | Essential for redox regulation | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chloroplast | |
Cellular Component | chloroplast stroma | |
Cellular Component | cytosol | |
Cellular Component | plastid | |
Molecular Function | 3-isopropylmalate dehydrogenase activity | |
Molecular Function | magnesium ion binding | |
Molecular Function | NAD binding | |
Biological Process | embryo sac development | |
Biological Process | glucosinolate biosynthetic process | |
Biological Process | L-leucine biosynthetic process | |
Biological Process | pollen development | |
Biological Process | response to jasmonic acid | |
Biological Process | response to wounding |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended name3-isopropylmalate dehydrogenase 1, chloroplastic
- EC number
- Short names3-IPM-DH 1 ; AtIMDH1 ; IMDH 1
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis
Accessions
- Primary accessionQ9FMT1
- Secondary accessions
Proteomes
Organism-specific databases
Genome annotation databases
Subcellular Location
Phenotypes & Variants
Disruption phenotype
No discernible vegetative or reproductive phenotypes except a slight reduction of both male and female transmission efficiency, but decreased leucine biosynthetic enzyme activities and lower free leucine concentrations (PubMed:19674406, PubMed:20840499).
The double mutant ipmdh2 ipmdh3 is lethal in male gametophytes (small aborted pollen grains abnormal in cellular structure, and arrested in germination) and had reduced transmission through female gametophytes (slow embryo sacs development) (PubMed:20840499).
In atimd1-1 and atipmdh1 mutants, reduced levels of methionine-derived glucosinolates (Met-GSLs) with long chains (C7-C8) and, to some extent, with short chains (C4-C6) (PubMed:19493961, PubMed:19674406, PubMed:21697089).
Altered glucosinolate profile is restored by constructs expressing IPMDH2-L134F or IPMDH3-L133F mutants (PubMed:21697089).
The double mutant ipmdh2 ipmdh3 is lethal in male gametophytes (small aborted pollen grains abnormal in cellular structure, and arrested in germination) and had reduced transmission through female gametophytes (slow embryo sacs development) (PubMed:20840499).
In atimd1-1 and atipmdh1 mutants, reduced levels of methionine-derived glucosinolates (Met-GSLs) with long chains (C7-C8) and, to some extent, with short chains (C4-C6) (PubMed:19493961, PubMed:19674406, PubMed:21697089).
Altered glucosinolate profile is restored by constructs expressing IPMDH2-L134F or IPMDH3-L133F mutants (PubMed:21697089).
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 137 | Reduced activity toward 3-(2'-methylthio)-ethylmalate, but enhanced catalytic efficiency with 3-isopropylmalate. | ||||
Sequence: F → L | ||||||
Mutagenesis | 232 | Reduced sensitivity to oxidation on enzyme activity regulation. | ||||
Sequence: C → S | ||||||
Mutagenesis | 390 | Reduced sensitivity to oxidation on enzyme activity regulation. | ||||
Sequence: C → S |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 26 variants from UniProt as well as other sources including ClinVar and dbSNP.
PTM/Processing
Features
Showing features for transit peptide, chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Transit peptide | 1-37 | Chloroplast | ||||
Sequence: MAAFLQTNISLNAIKIVPGKYSSLTDHQFRAPYRIRC | ||||||
Chain | PRO_0000014455 | 38-409 | 3-isopropylmalate dehydrogenase 1, chloroplastic | |||
Sequence: AAASPGKKRYNIALLPGDGIGPEVISVAKNVLQKAGSLEGLEFDFKEMPVGGAALDLVGVPLPEETFTAAKLSDAILLGAIGGYKWDKNEKHLRPEMALFYLRRDLKVFANLRPATVLPQLVDASTLKKEVAEGVDMMIVRELTGGIYFGEPRGITINENGEEVGVSTEIYAAHEIDRIARVAFETARKRRGKLCSVDKANVLDASILWRKRVTALASEYPDVELSHMYVDNAAMQLIRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVVDALNKGFRTGDIYSPGNKLVGCKEMGEEVLKSVESKVPATV | ||||||
Modified residue | 74 | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Tissue specificity
Highly expressed in seedlings, leaves, stems and roots and, to a lower extent, in flowers, pollen and siliques.
Induction
By wounding and jasmonic acid (MeJA).
Developmental stage
In young seedlings, expressed in all tissues except in the root tip. Later accumulates in cotyledons, newly emerging leaves and the lower region of roots. In rosettes, predominantly observed in the main veins of leaves. In flowers, present in petals, pistils and in the ends of young siliques.
Gene expression databases
Structure
Sequence
- Sequence statusComplete
- Sequence processingThe displayed sequence is further processed into a mature form.
This entry describes 1 isoforms produced by Alternative splicing. A number of isoforms are produced. According to EST sequences.
Q9FMT1-1
This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
- Name1
- Length409
- Mass (Da)44,162
- Last updated2001-03-01 v1
- Checksum471293D4C3FB55DD
Computationally mapped potential isoform sequences
There are 2 potential isoforms mapped to this entry
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 251 | in Ref. 4; AAL67125 | ||||
Sequence: T → A |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AB007650 EMBL· GenBank· DDBJ | BAB08299.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002688 EMBL· GenBank· DDBJ | AED91997.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AY074587 EMBL· GenBank· DDBJ | AAL67125.1 EMBL· GenBank· DDBJ | mRNA |