IDH_BACSU
ID IDH_BACSU Reviewed; 423 AA.
AC P39126;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Isocitrate dehydrogenase [NADP];
DE Short=IDH;
DE EC=1.1.1.42;
DE AltName: Full=IDP;
DE AltName: Full=NADP(+)-specific ICDH;
DE AltName: Full=Oxalosuccinate decarboxylase;
GN Name=icd; Synonyms=citC; OrderedLocusNames=BSU29130;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / SMY;
RX PubMed=8045898; DOI=10.1128/jb.176.15.4669-4679.1994;
RA Jin S., Sonenshein A.L.;
RT "Identification of two distinct Bacillus subtilis citrate synthase genes.";
RL J. Bacteriol. 176:4669-4679(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9387221; DOI=10.1099/00221287-143-11-3431;
RA Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.;
RT "Sequencing and functional annotation of the Bacillus subtilis genes in the
RT 200 kb rrnB-dnaB region.";
RL Microbiology 143:3431-3441(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP PHOSPHORYLATION.
RX PubMed=11751849; DOI=10.1074/jbc.m107908200;
RA Singh S.K., Miller S.P., Dean A., Banaszak L.J., LaPorte D.C.;
RT "Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for
RT Escherichia coli isocitrate dehydrogenase kinase/phosphatase.";
RL J. Biol. Chem. 277:7567-7573(2002).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH CITRATE, AND
RP SUBUNIT.
RX PubMed=11290745; DOI=10.1074/jbc.m101191200;
RA Singh S.K., Matsuno K., LaPorte D.C., Banaszak L.J.;
RT "Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A.
RT Insights into the nature of substrate specificity exhibited by Escherichia
RT coli isocitrate dehydrogenase kinase/phosphatase.";
RL J. Biol. Chem. 276:26154-26163(2001).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH;
CC Xref=Rhea:RHEA:19629, ChEBI:CHEBI:15562, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.1.1.42;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000250};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11290745}.
CC -!- INTERACTION:
CC P39126; P49814: mdh; NbExp=3; IntAct=EBI-7829570, EBI-7827708;
CC -!- MISCELLANEOUS: The enzyme can be phosphorylated in vitro by the E.coli
CC isocitrate dehydrogenase kinase/phosphatase, but B.subtilis lacks such
CC an enzyme.
CC -!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
CC dehydrogenases family. {ECO:0000305}.
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DR EMBL; U05257; AAA96342.1; -; Genomic_DNA.
DR EMBL; AF008220; AAC00346.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14873.1; -; Genomic_DNA.
DR PIR; I40382; I40382.
DR RefSeq; NP_390791.1; NC_000964.3.
DR RefSeq; WP_003229433.1; NZ_JNCM01000036.1.
DR PDB; 1HQS; X-ray; 1.55 A; A/B=1-423.
DR PDBsum; 1HQS; -.
DR AlphaFoldDB; P39126; -.
DR SMR; P39126; -.
DR IntAct; P39126; 2.
DR MINT; P39126; -.
DR STRING; 224308.BSU29130; -.
DR DrugBank; DB02159; (R)-Propylene glycol.
DR DrugBank; DB04349; (S)-propane-1,2-diol.
DR DrugBank; DB04272; Citric acid.
DR DrugBank; DB04530; S,S-(2-Hydroxyethyl)Thiocysteine.
DR jPOST; P39126; -.
DR PaxDb; P39126; -.
DR PRIDE; P39126; -.
DR EnsemblBacteria; CAB14873; CAB14873; BSU_29130.
DR GeneID; 938183; -.
DR KEGG; bsu:BSU29130; -.
DR PATRIC; fig|224308.179.peg.3163; -.
DR eggNOG; COG0538; Bacteria.
DR InParanoid; P39126; -.
DR OMA; CVRPCRY; -.
DR PhylomeDB; P39126; -.
DR BioCyc; BSUB:BSU29130-MON; -.
DR SABIO-RK; P39126; -.
DR EvolutionaryTrace; P39126; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0004450; F:isocitrate dehydrogenase (NADP+) activity; IEA:UniProtKB-EC.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0006097; P:glyoxylate cycle; IEA:UniProtKB-KW.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
DR InterPro; IPR019818; IsoCit/isopropylmalate_DH_CS.
DR InterPro; IPR004439; Isocitrate_DH_NADP_dimer_prok.
DR InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR PANTHER; PTHR43504; PTHR43504; 1.
DR Pfam; PF00180; Iso_dh; 1.
DR SMART; SM01329; Iso_dh; 1.
DR TIGRFAMs; TIGR00183; prok_nadp_idh; 1.
DR PROSITE; PS00470; IDH_IMDH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glyoxylate bypass; Magnesium; Manganese; Metal-binding; NADP;
KW Oxidoreductase; Reference proteome; Tricarboxylic acid cycle.
FT CHAIN 1..423
FT /note="Isocitrate dehydrogenase [NADP]"
FT /id="PRO_0000083549"
FT BINDING 95
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 96
FT /ligand="substrate"
FT BINDING 104
FT /ligand="substrate"
FT BINDING 106
FT /ligand="substrate"
FT BINDING 110
FT /ligand="substrate"
FT BINDING 120
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 144
FT /ligand="substrate"
FT BINDING 311
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 345..351
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 358
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 397
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 401
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT SITE 151
FT /note="Critical for catalysis"
FT /evidence="ECO:0000250"
FT SITE 221
FT /note="Critical for catalysis"
FT /evidence="ECO:0000250"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 18..25
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 31..50
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 65..71
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 77..86
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 88..91
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 105..112
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 139..145
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 149..152
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 161..173
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 182..184
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 185..193
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 194..211
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 214..220
FT /evidence="ECO:0007829|PDB:1HQS"
FT TURN 222..224
FT /evidence="ECO:0007829|PDB:1HQS"
FT TURN 226..228
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 229..244
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 251..275
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 279..285
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 286..295
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 301..305
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 307..320
FT /evidence="ECO:0007829|PDB:1HQS"
FT TURN 324..326
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 328..332
FT /evidence="ECO:0007829|PDB:1HQS"
FT TURN 334..336
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 339..344
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 349..351
FT /evidence="ECO:0007829|PDB:1HQS"
FT TURN 352..355
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 360..373
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 376..391
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 397..400
FT /evidence="ECO:0007829|PDB:1HQS"
FT STRAND 403..405
FT /evidence="ECO:0007829|PDB:1HQS"
FT HELIX 411..420
FT /evidence="ECO:0007829|PDB:1HQS"
SQ SEQUENCE 423 AA; 46418 MW; CC69E694EB66D0D8 CRC64;
MAQGEKITVS NGVLNVPNNP IIPFIEGDGT GPDIWNAASK VLEAAVEKAY KGEKKITWKE
VYAGEKAYNK TGEWLPAETL DVIREYFIAI KGPLTTPVGG GIRSLNVALR QELDLFVCLR
PVRYFTGVPS PVKRPEDTDM VIFRENTEDI YAGIEYAKGS EEVQKLISFL QNELNVNKIR
FPETSGIGIK PVSEEGTSRL VRAAIDYAIE HGRKSVTLVH KGNIMKFTEG AFKNWGYELA
EKEYGDKVFT WAQYDRIAEE QGKDAANKAQ SEAEAAGKII IKDSIADIFL QQILTRPNEF
DVVATMNLNG DYISDALAAQ VGGIGIAPGA NINYETGHAI FEATHGTAPK YAGLDKVNPS
SVILSGVLLL EHLGWNEAAD LVIKSMEKTI ASKVVTYDFA RLMDGATEVK CSEFGEELIK
NMD
