ID IDH_AZOVI Reviewed; 741 AA. AC P16100; DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 5. DT 13-SEP-2023, entry version 129. DE RecName: Full=Isocitrate dehydrogenase [NADP]; DE Short=IDH; DE EC=1.1.1.42; DE AltName: Full=Oxalosuccinate decarboxylase; GN Name=icd; OS Azotobacter vinelandii. OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; OC Pseudomonadaceae; Azotobacter. OX NCBI_TaxID=354; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-16. RX PubMed=12005040; DOI=10.1271/bbb.66.489; RA Sahara T., Takada Y., Takeuchi Y., Yamaoka N., Fukunaga N.; RT "Cloning, sequencing, and expression of a gene encoding the monomeric RT isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter RT vinelandii."; RL Biosci. Biotechnol. Biochem. 66:489-500(2002). RN [2] RP PRELIMINARY PROTEIN SEQUENCE OF 229-251 AND 255-260. RX PubMed=4149369; DOI=10.1021/bi00701a007; RA Edwards D.J., Heinrikson R.L., Chung A.E.; RT "Triphosphopyridine nucleotide specific isocitrate dehydrogenase from RT Azotobacter vinelandii. Alkylation of a specific methionine residue and RT amino acid sequence of the peptide containing this residue."; RL Biochemistry 13:677-683(1974). RN [3] RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEXES WITH ISOCITRATE; RP MANGANESE AND NADP, AND SUBUNIT. RX PubMed=12467571; DOI=10.1016/s0969-2126(02)00904-8; RA Yasutake Y., Watanabe S., Yao M., Takada Y., Fukunaga N., Tanaka I.; RT "Structure of the monomeric isocitrate dehydrogenase: evidence of a protein RT monomerization by a domain duplication."; RL Structure 10:1637-1648(2002). 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; CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit.; CC -!- ACTIVITY REGULATION: Inhibition of this enzyme by phosphorylation CC regulates the branch point between the Krebs cycle and the glyoxylate CC bypass, which is an alternate route that accumulates carbon for CC biosynthesis when acetate is the sole carbon source for growth. The CC phosphorylation state of this enzyme is controlled by isocitrate CC dehydrogenase kinase/phosphatase (AceK). CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC Temperature dependence: CC Optimum temperature is above 40 degrees Celsius.; CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12467571}. CC -!- SUBCELLULAR LOCATION: Cytoplasm. CC -!- DOMAIN: This molecule consists of two distinct domains, a small domain CC and a large domain. The structure of the large domain repeats a motif CC observed in the dimeric IDH. Such a fusional structure by domain CC duplication enables a single polypeptide chain to form a structure at CC the catalytic site that is homologous to the dimeric IDH, the catalytic CC site of which is located at the interface of two identical subunits. CC -!- SIMILARITY: Belongs to the monomeric-type IDH family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; D73443; BAA11169.1; -; Genomic_DNA. DR PIR; A10759; A10759. DR PIR; JC7822; JC7822. DR PDB; 1ITW; X-ray; 1.95 A; A/B/C/D=1-741. DR PDB; 1J1W; X-ray; 3.20 A; A/B/C/D=1-741. DR PDBsum; 1ITW; -. DR PDBsum; 1J1W; -. DR AlphaFoldDB; P16100; -. DR SMR; P16100; -. DR DrugBank; DB01727; Isocitric Acid. DR DrugBank; DB03461; Nicotinamide adenine dinucleotide phosphate. DR BioCyc; MetaCyc:MONOMER-13167; -. DR EvolutionaryTrace; P16100; -. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell. DR GO; GO:0004450; F:isocitrate dehydrogenase (NADP+) activity; IEA:UniProtKB-EC. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. 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; IPR004436; Isocitrate_DH_NADP_mono. DR NCBIfam; TIGR00178; monomer_idh; 1. DR PANTHER; PTHR36999; ISOCITRATE DEHYDROGENASE [NADP]; 1. DR PANTHER; PTHR36999:SF1; ISOCITRATE DEHYDROGENASE [NADP]; 1. DR Pfam; PF03971; IDH; 1. DR PIRSF; PIRSF009407; IDH_monmr; 1. DR SUPFAM; SSF53659; Isocitrate/Isopropylmalate dehydrogenase-like; 1. PE 1: Evidence at protein level; KW 3D-structure; Cytoplasm; Direct protein sequencing; Glyoxylate bypass; KW Magnesium; Manganese; Metal-binding; NADP; Oxidoreductase; Phosphoprotein; KW Tricarboxylic acid cycle. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0000269|PubMed:12005040" FT CHAIN 2..741 FT /note="Isocitrate dehydrogenase [NADP]" FT /id="PRO_0000083593" FT BINDING 82..87 FT /ligand="NADP(+)" FT /ligand_id="ChEBI:CHEBI:58349" FT BINDING 132..139 FT /ligand="substrate" FT BINDING 135 FT /ligand="NADP(+)" FT /ligand_id="ChEBI:CHEBI:58349" FT BINDING 145 FT /ligand="substrate" FT BINDING 350 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /evidence="ECO:0000269|PubMed:12467571, FT ECO:0007744|PDB:1ITW" FT BINDING 547 FT /ligand="substrate" FT BINDING 548 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /evidence="ECO:0000269|PubMed:12467571, FT ECO:0007744|PDB:1ITW" FT BINDING 584..585 FT /ligand="NADP(+)" FT /ligand_id="ChEBI:CHEBI:58349" FT BINDING 589 FT /ligand="NADP(+)" FT /ligand_id="ChEBI:CHEBI:58349" FT BINDING 600..602 FT /ligand="NADP(+)" FT /ligand_id="ChEBI:CHEBI:58349" FT BINDING 649 FT /ligand="NADP(+)" FT /ligand_id="ChEBI:CHEBI:58349" FT SITE 255 FT /note="Critical for catalysis" FT /evidence="ECO:0000250" FT SITE 420 FT /note="Critical for catalysis" FT /evidence="ECO:0000250" FT STRAND 5..10 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 13..31 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 32..34 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 36..41 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 44..51 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 53..55 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 58..60 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 65..72 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 79..82 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 90..102 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 117..129 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 130..132 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 135..138 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 143..146 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 149..157 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 172..174 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 177..180 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 181..184 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 186..189 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 192..202 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 207..216 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 221..227 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 229..246 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 249..252 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 256..258 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 262..274 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 276..281 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 283..288 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 293..295 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 297..303 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 304..306 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 309..325 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 331..333 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 334..337 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 340..342 FT /evidence="ECO:0007829|PDB:1J1W" FT STRAND 346..348 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 349..358 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 359..361 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 362..364 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 368..376 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 380..396 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 401..403 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 409..411 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 414..416 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 418..421 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 423..425 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 426..428 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 430..439 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 444..450 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 455..461 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 463..480 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 484..487 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 493..506 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 516..519 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 521..533 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 539..542 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 544..559 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 562..571 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 576..580 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 587..596 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 604..620 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 624..642 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 649..653 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 656..673 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 678..693 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 695..703 FT /evidence="ECO:0007829|PDB:1ITW" FT STRAND 706..708 FT /evidence="ECO:0007829|PDB:1J1W" FT STRAND 715..717 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 720..727 FT /evidence="ECO:0007829|PDB:1ITW" FT HELIX 731..736 FT /evidence="ECO:0007829|PDB:1ITW" FT TURN 737..739 FT /evidence="ECO:0007829|PDB:1ITW" SQ SEQUENCE 741 AA; 80390 MW; 29FF35278E5AED8B CRC64; MSTPKIIYTL TDEAPALATY SLLPIIKAFT GSSGIAVETR DISLAGRLIA TFPEYLTDTQ KISDDLAELG KLATTPDANI IKLPNISASV PQLKAAIKEL QQQGYKLPDY PEEPKTDTEK DVKARYDKIK GSAVNPVLRE GNSDRRAPLS VKNYARKHPH KMGAWSADSK SHVAHMDNGD FYGSEKAALI GAPGSVKIEL IAKDGSSTVL KAKTSVQAGE IIDSSVMSKN ALRNFIAAEI EDAKKQGVLL SVHLKATMMK VSDPIMFGQI VSEFYKDALT KHAEVLKQIG FDVNNGIGDL YARIKTLPEA KQKEIEADIQ AVYAQRPQLA MVNSDKGITN LHVPSDVIVD ASMPAMIRDS GKMWGPDGKL HDTKAVIPDR CYAGVYQVVI EDCKQHGAFD PTTMGSVPNV GLMAQKAEEY GSHDKTFQIP ADGVVRVTDE SGKLLLEQSV EAGDIWRMCQ AKDAPIQDWV KLAVNRARAT NTPAVFWLDP ARAHDAQVIA KVERYLKDYD TSGLDIRILS PVEATRFSLA RIREGKDTIS VTGNVLRDYL TDLFPIMELG TSAKMLSIVP LMSGGGLFET GAGGSAPKHV QQFLEEGYLR WDSLGEFLAL AASLEHLGNA YKNPKALVLA STLDQATGKI LDNNKSPARK VGEIDNRGSH FYLALYWAQA LAAQTEDKEL QAQFTGIAKA LTDNETKIVG ELAAAQGKPV DIAGYYHPNT DLTSKAIRPS ATFNAALAPL A //