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HAMAP rule MF_01032

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General rule information [?]

Accession MF_01032
Dates 10-SEP-2002 (Created)
23-AUG-2021 (Last updated, Version 31)
Name LeuD_type2
Scope
Bacteria
Archaea
Templates P04787 (LEUD1_SALTY); Q58667 (HACB_METJA): [Recover all]
Triggered by

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
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
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 RHEA:32303: (2R)-homocitrate = (2R,3S)-homoisocitrate
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 RHEA:32287: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate
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
GO:0003861; Molecular function: 3-isopropylmalate dehydratase activity.
GO:0009098; Biological process: leucine biosynthetic process.
end case

Cross-references [?]

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

Features [?]

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

Additional information [?]

Size range 161-208 amino acids
Related rules MF_01031 (LEUD)
Fusion 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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