ID H6LA32_SAPGL Unreviewed; 399 AA.
AC H6LA32;
DT 18-APR-2012, integrated into UniProtKB/TrEMBL.
DT 18-APR-2012, sequence version 1.
DT 27-MAR-2024, entry version 55.
DE RecName: Full=Isocitrate dehydrogenase [NADP] {ECO:0000256|RuleBase:RU004446};
DE EC=1.1.1.42 {ECO:0000256|RuleBase:RU004446};
GN Name=icd {ECO:0000313|EMBL:AFC25500.1};
GN OrderedLocusNames=SGRA_2772 {ECO:0000313|EMBL:AFC25500.1};
OS Saprospira grandis (strain Lewin).
OC Bacteria; Bacteroidota; Saprospiria; Saprospirales; Saprospiraceae;
OC Saprospira.
OX NCBI_TaxID=984262 {ECO:0000313|EMBL:AFC25500.1, ECO:0000313|Proteomes:UP000007519};
RN [1] {ECO:0000313|EMBL:AFC25500.1, ECO:0000313|Proteomes:UP000007519}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Lewin {ECO:0000313|EMBL:AFC25500.1,
RC ECO:0000313|Proteomes:UP000007519};
RX PubMed=22675601; DOI=10.4056/sigs.2445005;
RA Saw J.H., Yuryev A., Kanbe M., Hou S., Young A.G., Aizawa S., Alam M.;
RT "Complete genome sequencing and analysis of Saprospira grandis str. Lewin,
RT a predatory marine bacterium.";
RL Stand. Genomic Sci. 6:84-93(2012).
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 Evidence={ECO:0000256|ARBA:ARBA00023554};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|PIRSR:PIRSR604439-3};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|PIRSR:PIRSR604439-3};
CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit.
CC {ECO:0000256|PIRSR:PIRSR604439-3};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
CC -!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
CC dehydrogenases family. {ECO:0000256|ARBA:ARBA00007769}.
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DR EMBL; CP002831; AFC25500.1; -; Genomic_DNA.
DR AlphaFoldDB; H6LA32; -.
DR STRING; 984262.SGRA_2772; -.
DR KEGG; sgn:SGRA_2772; -.
DR eggNOG; COG0538; Bacteria.
DR HOGENOM; CLU_031953_7_1_10; -.
DR Proteomes; UP000007519; 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 Gene3D; 3.40.718.10; Isopropylmalate Dehydrogenase; 1.
DR InterPro; IPR019818; IsoCit/isopropylmalate_DH_CS.
DR InterPro; IPR004439; Isocitrate_DH_NADP_dimer_prok.
DR InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR NCBIfam; TIGR00183; prok_nadp_idh; 1.
DR PANTHER; PTHR43504; ISOCITRATE DEHYDROGENASE [NADP]; 1.
DR PANTHER; PTHR43504:SF1; ISOCITRATE DEHYDROGENASE [NADP]; 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 Glyoxylate bypass {ECO:0000256|ARBA:ARBA00022435,
KW ECO:0000256|RuleBase:RU004446};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|PIRSR:PIRSR604439-3};
KW Manganese {ECO:0000256|PIRSR:PIRSR604439-3, ECO:0000256|RuleBase:RU004446};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|RuleBase:RU004446};
KW NADP {ECO:0000256|ARBA:ARBA00022857, ECO:0000256|PIRSR:PIRSR604439-2};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002,
KW ECO:0000313|EMBL:AFC25500.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000007519};
KW Tricarboxylic acid cycle {ECO:0000256|ARBA:ARBA00022532,
KW ECO:0000256|RuleBase:RU004446}.
FT DOMAIN 13..395
FT /note="Isopropylmalate dehydrogenase-like"
FT /evidence="ECO:0000259|SMART:SM01329"
FT BINDING 87
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-2"
FT BINDING 96
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-1"
FT BINDING 98
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-1"
FT BINDING 102
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-1"
FT BINDING 112
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-1"
FT BINDING 136
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-1"
FT BINDING 288
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-3"
FT BINDING 322..328
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-2"
FT BINDING 335
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-2"
FT BINDING 374
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-2"
FT BINDING 378
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-2"
FT SITE 143
FT /note="Critical for catalysis"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-4"
FT SITE 213
FT /note="Critical for catalysis"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-4"
FT MOD_RES 83
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-5"
FT MOD_RES 96
FT /note="Phosphoserine"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-5"
FT MOD_RES 125
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-5"
FT MOD_RES 225
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000256|PIRSR:PIRSR604439-5"
SQ SEQUENCE 399 AA; 43945 MW; 47D01E79740B344D CRC64;
MKEGQLQVPN QPIIPFIEGD GIGPDIWAAS VRVFDAAVEK AYAGERKIEW KEVLAGQKAF
DTTQEWLPQA TLDAIEEYLV AIKGPLTTPV GGGIRSLNVA LRQKLDLFAC VRPVRWFQGV
PSPVKQPELV DMTIFRENTE DIYAGIEYLT GTPENDKVKK FLIEEMGVSQ IRFPETASLG
VKPVSIEGTE RLVKAALDYA IANNRKSVTL VHKGNIMKFT EGKFKEWGYA LAKRDYNAKD
LDGGPWQVID NNGQEIIVKD VIADAFLQQI LLRPAEYDVI ATLNLNGDYV SDALAAIVGG
IGIAPGANIN YTNGKAIFEA THGTAPKYAG QDKVNPSSVI LSGEMMFRYM GWNEAADLIV
KGIEGAIQKK TVTYDFHRLM DDAKLLKCSE FGDAIIENM
//
