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HAMAP rule MF_01032

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General rule information [?]

Accession MF_01032
Dates 10-SEP-2002 (Created)
1-JUN-2023 (Last updated, Version 32)
Name LeuD_type2
Scope(s) Bacteria
Template(s) P04787 (LEUD1_SALTY); Q58667 (HACB_METJA); [ Recover all ]
Triggered by HAMAP; MF_01032 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

case <FTTag:HACNmotif>
Identifier HACB
Protein name RecName: Full=Methanogen homoaconitase small subunit;
AltName: Full=Homoaconitate hydratase;
Gene name Name=hacB;
Identifier LEUD
Protein name RecName: Full=3-isopropylmalate dehydratase small subunit;
AltName: Full=Alpha-IPM isomerase;
AltName: Full=Isopropylmalate isomerase;
Gene name Name=leuD;
end case

Comments [?]

case <FTTag:HACNmotif>
FUNCTIONHydro-lyase with broad substrate specificity for cis- unsaturated tricarboxylic acids. Catalyzes both the reversible dehydration of (R)-homocitrate ((R)-2-hydroxybutane-1,2,4- tricarboxylate) to produce cis-homoaconitate ((Z)-but-1-ene-1,2,4- tricarboxylate), and its hydration to homoisocitrate ((1R,2S)-1- hydroxybutane-1,2,4-tricarboxylate). Is also able to hydrate the analogous longer chain substrates cis-homo(2)-aconitate, cis-homo(3)- aconitate. All these reactions are part of the biosynthesis pathway of coenzyme B.
CATALYTIC ACTIVITY Reaction=(2R)-homocitrate = (2R,3S)-homoisocitrate; Xref=Rhea:RHEA:32303, ChEBI:CHEBI:15404, ChEBI:CHEBI:58884; EC=;
PATHWAYOrganic acid metabolism; 2-oxosuberate biosynthesis.
SUBUNITHeterotetramer of 2 HacA and 2 HacB proteins.
FUNCTIONCatalyzes the isomerization between 2-isopropylmalate and 3- isopropylmalate, via the formation of 2-isopropylmaleate.
CATALYTIC ACTIVITY Reaction=(2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate; Xref=Rhea:RHEA:32287, ChEBI:CHEBI:1178, ChEBI:CHEBI:35121; EC=;
PATHWAYAmino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4.
SUBUNITHeterodimer of LeuC and LeuD.
end case
SIMILARITYBelongs to the LeuD family. LeuD type 2 subfamily.

Keywords [?]

Gene Ontology [?]

case <FTTag:HACNmotif>
GO:0004409; Molecular function:homoaconitate hydratase activity
GO:0019298; Biological process:coenzyme B biosynthetic process
else; https://www.ebi.ac.uk/QuickGO/term/else
GO:0003861; Molecular function:3-isopropylmalate dehydratase activity
GO:0009098; Biological process:leucine biosynthetic process
end case

Cross-references [?]

Pfam PF00694; Aconitase_C; 1;
NCBIfam TIGR02084; leud; 1;
NCBIfam TIGR02087; LEUD_arch; 1;

Features [?]

From: HACB_METJA (Q58667)
Key From To Description Tag Condition FTGroup
case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanomicrobia> or <OC:Methanopyri>
MOTIF 24 27 /note="YLRT" HACNmotif Y-L-R-T
SITE 26 26 /note="Critical for substrate specificity" R
end case

Additional information [?]

Size range 161-208 amino acids
Related rules MF_01031
Fusion Nter: None Cter: None
Comments The family member in THET2 is shown to function as a homoaconitase (for lysine biosynthesis), as well as one of the 2 copies found in METJA that catalyzes both the dehydration of (R)-homocitrate and the hydration of cis-homoaconitate for coenzyme B biosynthesis. The other copy in METJA functions both in leucine and isoleucine biosynthesis, since it catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate and between 2-methylmalate and 3-methylmalate. In Archaea, a motif that indicates the protein specificity has been determined (see PubMed=20170198): the presence of the YLRT motif likely indicates HACN activity, while proteins with the YLV(Y/I/M) sequence are IPMIs enzymes.

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