CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001276
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Isocitrate dehydrogenase [NADP] cytoplasmic 
Protein Synonyms/Alias
 IDH; Cytosolic NADP-isocitrate dehydrogenase; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase 
Gene Name
 IDH1 
Gene Synonyms/Alias
 PICD 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
29IWELIKEKLIFPYVEubiquitination[1]
58ATNDQVTKDAAEAIKubiquitination[2]
65KDAAEAIKKHNVGVKubiquitination[3]
81ATITPDEKRVEEFKLacetylation[4]
81ATITPDEKRVEEFKLubiquitination[1]
87EKRVEEFKLKQMWKSubiquitination[1, 3]
89RVEEFKLKQMWKSPNubiquitination[1]
93FKLKQMWKSPNGTIRacetylation[4]
126RLVSGWVKPIIIGRHubiquitination[1, 3, 5, 6]
151FVVPGPGKVEITYTPubiquitination[2, 3]
224KKYDGRFKDIFQEIYacetylation[4, 7, 8, 9, 10]
224KKYDGRFKDIFQEIYubiquitination[5, 6]
233IFQEIYDKQYKSQFEubiquitination[3, 5, 6]
243KSQFEAQKIWYEHRLubiquitination[1]
321RHYRMYQKGQETSTNacetylation[4, 8]
321RHYRMYQKGQETSTNubiquitination[5, 6]
381KDLAACIKGLPNVQRubiquitination[1]
400NTFEFMDKLGENLKIubiquitination[3]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [4] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [5] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [6] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [7] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [8] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [9] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [10] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
  
Sequence Annotation
 NP_BIND 75 77 NADP.
 NP_BIND 310 315 NADP.
 REGION 94 100 Substrate binding.
 METAL 252 252 Magnesium or manganese.
 METAL 275 275 Magnesium or manganese.
 BINDING 77 77 Substrate.
 BINDING 82 82 NADP.
 BINDING 109 109 Substrate.
 BINDING 132 132 Substrate.
 BINDING 260 260 NADP.
 BINDING 328 328 NADP; via amide nitrogen and carbonyl
 MOD_RES 321 321 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Cytoplasm; Direct protein sequencing; Glyoxylate bypass; Magnesium; Manganese; Metal-binding; NADP; Oxidoreductase; Peroxisome; Polymorphism; Reference proteome; Tricarboxylic acid cycle. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 414 AA 
Protein Sequence
MSKKISGGSV VEMQGDEMTR IIWELIKEKL IFPYVELDLH SYDLGIENRD ATNDQVTKDA 60
AEAIKKHNVG VKCATITPDE KRVEEFKLKQ MWKSPNGTIR NILGGTVFRE AIICKNIPRL 120
VSGWVKPIII GRHAYGDQYR ATDFVVPGPG KVEITYTPSD GTQKVTYLVH NFEEGGGVAM 180
GMYNQDKSIE DFAHSSFQMA LSKGWPLYLS TKNTILKKYD GRFKDIFQEI YDKQYKSQFE 240
AQKIWYEHRL IDDMVAQAMK SEGGFIWACK NYDGDVQSDS VAQGYGSLGM MTSVLVCPDG 300
KTVEAEAAHG TVTRHYRMYQ KGQETSTNPI ASIFAWTRGL AHRAKLDNNK ELAFFANALE 360
EVSIETIEAG FMTKDLAACI KGLPNVQRSD YLNTFEFMDK LGENLKIKLA QAKL 414 
Gene Ontology
 GO:0005829; C:cytosol; IDA:UniProtKB.
 GO:0005739; C:mitochondrion; IEA:Compara.
 GO:0005782; C:peroxisomal matrix; TAS:Reactome.
 GO:0004450; F:isocitrate dehydrogenase (NADP+) activity; IDA:UniProtKB.
 GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
 GO:0051287; F:NAD binding; IEA:InterPro.
 GO:0050661; F:NADP binding; IEA:Compara.
 GO:0006103; P:2-oxoglutarate metabolic process; IDA:UniProtKB.
 GO:0044255; P:cellular lipid metabolic process; TAS:Reactome.
 GO:0008585; P:female gonad development; IEA:Compara.
 GO:0006749; P:glutathione metabolic process; IEA:Compara.
 GO:0006097; P:glyoxylate cycle; IEA:UniProtKB-KW.
 GO:0006102; P:isocitrate metabolic process; IDA:UniProtKB.
 GO:0006740; P:NADPH regeneration; TAS:Reactome.
 GO:0006979; P:response to oxidative stress; IEA:Compara.
 GO:0048545; P:response to steroid hormone stimulus; IEA:Compara.
 GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW. 
Interpro
 IPR019818; IsoCit/isopropylmalate_DH_CS.
 IPR004790; Isocitrate_DH_NADP.
 IPR024084; IsoPropMal-DH-like_dom. 
Pfam
 PF00180; Iso_dh 
SMART
  
PROSITE
 PS00470; IDH_IMDH 
PRINTS