CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-007426
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Malate dehydrogenase, mitochondrial 
Protein Synonyms/Alias
  
Gene Name
 MDH2 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
26TSAQNNAKVAVLGASubiquitination[1]
45QPLSLLLKNSPLVSRubiquitination[1]
74DLSHIETKAAVKGYLubiquitination[1, 2]
78IETKAAVKGYLGPEQubiquitination[3, 4, 5, 6]
91EQLPDCLKGCDVVVIubiquitination[5]
165HGVYNPNKIFGVTTLacetylation[7]
165HGVYNPNKIFGVTTLubiquitination[1]
185NTFVAELKGLDPARVacetylation[7, 8]
185NTFVAELKGLDPARVubiquitination[1, 2, 5]
203VIGGHAGKTIIPLISubiquitination[5]
239EAGTEVVKAKAGAGSubiquitination[1, 2, 5, 9]
241GTEVVKAKAGAGSATubiquitination[1, 2, 5]
296STPLLLGKKGIEKNLubiquitination[1]
301LGKKGIEKNLGIGKVacetylation[7, 8]
301LGKKGIEKNLGIGKVubiquitination[3, 6]
307EKNLGIGKVSSFEEKacetylation[8]
307EKNLGIGKVSSFEEKubiquitination[1, 2, 5]
314KVSSFEEKMISDAIPacetylation[7, 8]
314KVSSFEEKMISDAIPubiquitination[1, 2, 5]
324SDAIPELKASIKKGEubiquitination[1, 5]
329ELKASIKKGEDFVKTacetylation[7]
335KKGEDFVKTLK****acetylation[7]
335KKGEDFVKTLK****ubiquitination[5]
Reference
 [1] 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]
 [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] 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]
 [4] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [5] 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]
 [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] 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]
 [8] 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]
 [9] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724] 
Functional Description
  
Sequence Annotation
 NP_BIND 31 37 NAD.
 NP_BIND 140 142 NAD.
 ACT_SITE 200 200 Proton acceptor (By similarity).
 BINDING 57 57 NAD.
 BINDING 104 104 Substrate.
 BINDING 110 110 Substrate.
 BINDING 117 117 NAD.
 BINDING 142 142 Substrate.
 BINDING 176 176 Substrate.
 BINDING 251 251 NAD.
 MOD_RES 157 157 N6-acetyllysine (By similarity).
 MOD_RES 165 165 N6-acetyllysine.
 MOD_RES 185 185 N6-acetyllysine.
 MOD_RES 239 239 N6-malonyllysine; alternate (By
 MOD_RES 239 239 N6-succinyllysine; alternate (By
 MOD_RES 301 301 N6-acetyllysine; alternate.
 MOD_RES 301 301 N6-succinyllysine; alternate (By
 MOD_RES 307 307 N6-acetyllysine; alternate.
 MOD_RES 307 307 N6-malonyllysine; alternate.
 MOD_RES 314 314 N6-acetyllysine.
 MOD_RES 328 328 N6-acetyllysine; alternate (By
 MOD_RES 328 328 N6-succinyllysine; alternate (By
 MOD_RES 329 329 N6-acetyllysine; alternate.
 MOD_RES 329 329 N6-malonyllysine; alternate (By
 MOD_RES 335 335 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Mitochondrion; NAD; Oxidoreductase; Polymorphism; Reference proteome; Transit peptide; Tricarboxylic acid cycle. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 338 AA 
Protein Sequence
MLSALARPAS AALRRSFSTS AQNNAKVAVL GASGGIGQPL SLLLKNSPLV SRLTLYDIAH 60
TPGVAADLSH IETKAAVKGY LGPEQLPDCL KGCDVVVIPA GVPRKPGMTR DDLFNTNATI 120
VATLTAACAQ HCPEAMICVI ANPVNSTIPI TAEVFKKHGV YNPNKIFGVT TLDIVRANTF 180
VAELKGLDPA RVNVPVIGGH AGKTIIPLIS QCTPKVDFPQ DQLTALTGRI QEAGTEVVKA 240
KAGAGSATLS MAYAGARFVF SLVDAMNGKE GVVECSFVKS QETECTYFST PLLLGKKGIE 300
KNLGIGKVSS FEEKMISDAI PELKASIKKG EDFVKTLK 338 
Gene Ontology
 GO:0005743; C:mitochondrial inner membrane; IEA:Compara.
 GO:0005759; C:mitochondrial matrix; TAS:Reactome.
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0005886; C:plasma membrane; IDA:HPA.
 GO:0030060; F:L-malate dehydrogenase activity; IDA:UniProtKB.
 GO:0046554; F:malate dehydrogenase (NADP+) activity; IEA:Compara.
 GO:0044262; P:cellular carbohydrate metabolic process; IEA:InterPro.
 GO:0006094; P:gluconeogenesis; TAS:Reactome.
 GO:0006475; P:internal protein amino acid acetylation; IDA:UniProtKB.
 GO:0006108; P:malate metabolic process; IDA:UniProtKB.
 GO:0006734; P:NADH metabolic process; IEA:Compara.
 GO:0006107; P:oxaloacetate metabolic process; IEA:Compara.
 GO:0006099; P:tricarboxylic acid cycle; TAS:Reactome. 
Interpro
 IPR001557; L-lactate/malate_DH.
 IPR022383; Lactate/malate_DH_C.
 IPR001236; Lactate/malate_DH_N.
 IPR015955; Lactate_DH/Glyco_Ohase_4_C.
 IPR001252; Malate_DH_AS.
 IPR010097; Malate_DH_type1.
 IPR016040; NAD(P)-bd_dom. 
Pfam
 PF02866; Ldh_1_C
 PF00056; Ldh_1_N 
SMART
  
PROSITE
 PS00068; MDH 
PRINTS