IDH_AZOVI
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 03-AUG-2022, entry version 124.
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; Proteobacteria; 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 PRIDE; P16100; -.
DR BioCyc; MetaCyc:MON-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 InterPro; IPR004436; Isocitrate_DH_NADP_mono.
DR PANTHER; PTHR36999; PTHR36999; 1.
DR Pfam; PF03971; IDH; 1.
DR PIRSF; PIRSF009407; IDH_monmr; 1.
DR TIGRFAMs; TIGR00178; monomer_idh; 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
