Summary: Acetohydroxy acid isomeroreductase, catalytic domain
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Acetohydroxy acid isomeroreductase, catalytic domain Provide feedback
Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.
Literature references
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Biou V, Dumas R, Cohen-Addad C, Douce R, Job D, Pebay-Peyroula E; , EMBO J 1997;16:3405-3415.: The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution. PUBMED:9218783 EPMC:9218783
External database links
SCOP: | 1yve |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000506
Ketol-acid reductoisomerase (KARI; (EC)), also known as acetohydroxy acid isomeroreductase (AHIR or AHAIR), catalyzes the conversion of acetohydroxy acids into dihydroxy valerates in the second step of the biosynthetic pathway for the essential branched-chain amino acids valine, leucine, and isoleucine. KARI catalyzes an unusual two-step reaction consisting of an alkyl migration in which the substrate, either 2-acetolactate (AL) or 2-aceto-2-hydroxybutarate (AHB), is converted to 3-hydoxy-3-methyl-2- oxobutyrate or 3-hydoxy-3-methyl-2-pentatonate, followed by a NADPH-dependent reduction to give 2,3-dihydroxy-3-isovalerate or 2,3-dihydroxy-3- methylvalerate respectively [PUBMED:9218783, PUBMED:11352718, PUBMED:12691757, PUBMED:16322583, PUBMED:25849365, PUBMED:26644020].
KARI is present only in bacteria, fungi, and plants, but not in animals. KARIs are divided into two classes on the basis of sequence length and oligomerization state. Class I KARIs are ~340 amino acid residues in length and include all fungal KARIs, whereas class II KARIs are ~490 residues long and include all plant KARIs. Bacterial KARIs can be either class I or class II. KARIs are composed of two types of domains, an N-terminal Rossmann fold domain and one or two C-terminal knotted domains. Two intertwinned knotted domains are required for function, and in the short-chain or class I KARIs, each polypeptide chain has one knotted domain. As a result, dimerization of two monomers forms two complete KARI active sites. In the long-chain or class II KARIs, a duplication of the knotted domain has occurred and, as a result, the protein does not require dimerization to complete its active site [PUBMED:9218783, PUBMED:11352718, PUBMED:12691757, PUBMED:16322583, PUBMED:25849365, PUBMED:26644020].
The alpha-helical KARI C-terminal knotted domain can be described as a six- helix core in which helices coil like cable threads around each other, thus forming a bundle [PUBMED:9218783, PUBMED:11352718, PUBMED:12691757, PUBMED:16322583, PUBMED:25849365].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | ketol-acid reductoisomerase activity (GO:0004455) |
Biological process | oxidation-reduction process (GO:0055114) |
branched-chain amino acid biosynthetic process (GO:0009082) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan 6PGD_C (CL0106), which has the following description:
This helical domain is found associated with Rossmann domains.
The clan contains the following 13 members:
3HCDH 6PGD ApbA_C DUF1932 DUF2520 HMD IlvC Mannitol_dh_C NAD_binding_11 NAD_Gly3P_dh_C Octopine_DH P5CR_dimer UDPG_MGDP_dhAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (267) |
Full (8156) |
Representative proteomes | UniProt (34753) |
NCBI (38169) |
Meta (2677) |
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RP15 (1005) |
RP35 (3820) |
RP55 (7910) |
RP75 (13670) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (267) |
Full (8156) |
Representative proteomes | UniProt (34753) |
NCBI (38169) |
Meta (2677) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1005) |
RP35 (3820) |
RP55 (7910) |
RP75 (13670) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Prodom_2380 (release 99.1) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 267 |
Number in full: | 8156 |
Average length of the domain: | 140.50 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 43.32 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 144 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the IlvC domain has been found. There are 133 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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