HAMAP rule MF_01032

General rule information [?]

Accession	MF_01032
Dates	10-SEP-2002 (Created) 1-JUN-2023 (Last updated, Version 32)
Name	LeuD_type2
Scope(s)	Bacteria Archaea
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; Short=HACN; EC=4.2.1.114; AltName: Full=Homoaconitate hydratase;
Gene name	Name=hacB;
else
Identifier	LEUD
Protein name	RecName: Full=3-isopropylmalate dehydratase small subunit; EC=4.2.1.33; AltName: Full=Alpha-IPM isomerase; Short=IPMI; AltName: Full=Isopropylmalate isomerase;
Gene name	Name=leuD;
end case

Comments [?]

case <FTTag:HACNmotif>
FUNCTION	Hydro-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=4.2.1.114;
PATHWAY	Organic acid metabolism; 2-oxosuberate biosynthesis.
SUBUNIT	Heterotetramer of 2 HacA and 2 HacB proteins.
else
FUNCTION	Catalyzes 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=4.2.1.33;
PATHWAY	Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4.
SUBUNIT	Heterodimer of LeuC and LeuD.
end case
SIMILARITY	Belongs to the LeuD family. LeuD type 2 subfamily.

Keywords [?]

case not <FTTag:HACNmotif>
Amino-acid biosynthesis
Branched-chain amino acid biosynthesis
Leucine biosynthesis
end case
Lyase

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 [?]

Features [?]

From: HACB_METJA (Q58667)

Key

From

Description

Tag

Condition

FTGroup

case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanomicrobia> or <OC:Methanopyri>

MOTIF

/note="YLRT"

HACNmotif

Y-L-R-T

SITE

/note="Critical for substrate specificity"

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.