ID C8XEL3_NAKMY Unreviewed; 340 AA.
AC C8XEL3;
DT 03-NOV-2009, integrated into UniProtKB/TrEMBL.
DT 03-NOV-2009, sequence version 1.
DT 27-MAR-2024, entry version 82.
DE RecName: Full=3-isopropylmalate dehydrogenase {ECO:0000256|HAMAP-Rule:MF_01035};
DE EC=1.1.1.85 {ECO:0000256|HAMAP-Rule:MF_01035};
DE AltName: Full=3-IPM-DH {ECO:0000256|HAMAP-Rule:MF_01035};
DE AltName: Full=Beta-IPM dehydrogenase {ECO:0000256|HAMAP-Rule:MF_01035};
DE Short=IMDH {ECO:0000256|HAMAP-Rule:MF_01035};
GN Name=leuB {ECO:0000256|HAMAP-Rule:MF_01035};
GN OrderedLocusNames=Namu_1472 {ECO:0000313|EMBL:ACV77871.1};
OS Nakamurella multipartita (strain ATCC 700099 / DSM 44233 / CIP 104796 / JCM
OS 9543 / NBRC 105858 / Y-104) (Microsphaera multipartita).
OC Bacteria; Actinomycetota; Actinomycetes; Nakamurellales; Nakamurellaceae;
OC Nakamurella.
OX NCBI_TaxID=479431 {ECO:0000313|EMBL:ACV77871.1, ECO:0000313|Proteomes:UP000002218};
RN [1] {ECO:0000313|Proteomes:UP000002218}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 /
RC Y-104 {ECO:0000313|Proteomes:UP000002218};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Kyrpides N., Mavromatis K., Ivanova N.,
RA Ovchinnikova G., Sims D., Meincke L., Brettin T., Detter J.C., Han C.,
RA Larimer F., Land M., Hauser L., Markowitz V., Cheng J.-F., Hugenholtz P.,
RA Woyke T., Wu D., Klenk H.-P., Eisen J.A.;
RT "The complete genome of Nakamurella multipartita DSM 44233.";
RL Submitted (SEP-2009) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ACV77871.1, ECO:0000313|Proteomes:UP000002218}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 /
RC Y-104 {ECO:0000313|Proteomes:UP000002218};
RX PubMed=21304699;
RA Tice H., Mayilraj S., Sims D., Lapidus A., Nolan M., Lucas S.,
RA Glavina Del Rio T., Copeland A., Cheng J.F., Meincke L., Bruce D.,
RA Goodwin L., Pitluck S., Ivanova N., Mavromatis K., Ovchinnikova G.,
RA Pati A., Chen A., Palaniappan K., Land M., Hauser L., Chang Y.J.,
RA Jeffries C.D., Detter J.C., Brettin T., Rohde M., Goker M., Bristow J.,
RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.,
RA Chen F.;
RT "Complete genome sequence of Nakamurella multipartita type strain (Y-
RT 104).";
RL Stand. Genomic Sci. 2:168-175(2010).
CC -!- FUNCTION: Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-
CC methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-
CC oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.
CC {ECO:0000256|HAMAP-Rule:MF_01035}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate
CC + CO2 + NADH; Xref=Rhea:RHEA:32271, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:17865, ChEBI:CHEBI:35121, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.1.1.85;
CC Evidence={ECO:0000256|ARBA:ARBA00000624, ECO:0000256|HAMAP-
CC Rule:MF_01035};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01035};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01035};
CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_01035};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
CC -!- PATHWAY: Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine
CC from 3-methyl-2-oxobutanoate: step 3/4. {ECO:0000256|HAMAP-
CC Rule:MF_01035}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_01035}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01035}.
CC -!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
CC dehydrogenases family. LeuB type 2 subfamily. {ECO:0000256|HAMAP-
CC Rule:MF_01035}.
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DR EMBL; CP001737; ACV77871.1; -; Genomic_DNA.
DR RefSeq; WP_015746777.1; NC_013235.1.
DR AlphaFoldDB; C8XEL3; -.
DR STRING; 479431.Namu_1472; -.
DR KEGG; nml:Namu_1472; -.
DR eggNOG; COG0473; Bacteria.
DR HOGENOM; CLU_031953_0_1_11; -.
DR InParanoid; C8XEL3; -.
DR OrthoDB; 5289857at2; -.
DR UniPathway; UPA00048; UER00072.
DR Proteomes; UP000002218; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003862; F:3-isopropylmalate dehydrogenase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0009098; P:leucine biosynthetic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.718.10; Isopropylmalate Dehydrogenase; 1.
DR HAMAP; MF_01035; LeuB_type2; 1.
DR InterPro; IPR019818; IsoCit/isopropylmalate_DH_CS.
DR InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR InterPro; IPR023698; LeuB_actb.
DR PANTHER; PTHR43275; D-MALATE DEHYDROGENASE [DECARBOXYLATING]; 1.
DR PANTHER; PTHR43275:SF1; D-MALATE DEHYDROGENASE [DECARBOXYLATING]; 1.
DR Pfam; PF00180; Iso_dh; 1.
DR SMART; SM01329; Iso_dh; 1.
DR SUPFAM; SSF53659; Isocitrate/Isopropylmalate dehydrogenase-like; 1.
DR PROSITE; PS00470; IDH_IMDH; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|HAMAP-Rule:MF_01035};
KW Branched-chain amino acid biosynthesis {ECO:0000256|ARBA:ARBA00023304,
KW ECO:0000256|HAMAP-Rule:MF_01035};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01035};
KW Leucine biosynthesis {ECO:0000256|ARBA:ARBA00022430, ECO:0000256|HAMAP-
KW Rule:MF_01035}; Magnesium {ECO:0000256|HAMAP-Rule:MF_01035};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_01035};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01035};
KW NAD {ECO:0000256|HAMAP-Rule:MF_01035};
KW Oxidoreductase {ECO:0000256|HAMAP-Rule:MF_01035,
KW ECO:0000313|EMBL:ACV77871.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000002218}.
FT DOMAIN 2..334
FT /note="Isopropylmalate dehydrogenase-like"
FT /evidence="ECO:0000259|SMART:SM01329"
FT BINDING 87
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 97
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 121
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 212
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 212
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 236
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 240
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT BINDING 272..284
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT SITE 128
FT /note="Important for catalysis"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
FT SITE 179
FT /note="Important for catalysis"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01035"
SQ SEQUENCE 340 AA; 36300 MW; FF74F64C14C80C00 CRC64;
MKLAVIPGDG IGPEVVAEGL KVLRGVVPDV ETNEYDLGAA RWHRTGELLP DSVLRELREH
DAILLGAVGD PTVPSGILER GLLLRLRFEL DHHVNLRPAR LYPGVPGPLA GDKAIDLVVL
REGTEGPYVG NGGILRKDTP HEIATEVSLN TYFGVERVVR DAFERAARRP RRHLTLVHKT
NVLVHSGQLW SRVVEEVSME YQDVAVAYCH MDAAMIYLVT DPGRFDVVVT DNLFGDIFTD
LAAAVSGGIG LAASGNLDVS RTNPSMFEPV HGSAPDIAGT GTADPTATVL SVALLLDHLG
LPEAARRVEA AVAFDLATRQ SGSVGRTTAI GDRLAALASS
//
