CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002810
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Dihydrolipoyl dehydrogenase, mitochondrial 
Protein Synonyms/Alias
 Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein 
Gene Name
 DLD 
Gene Synonyms/Alias
 GCSL; LAD; PHE3 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
59GGYVAAIKAAQLGFKubiquitination[1]
104YYHMAHGKDFASRGIubiquitination[2, 3]
127LDKMMEQKSTAVKALubiquitination[4]
132EQKSTAVKALTGGIAubiquitination[2, 3, 4]
143GGIAHLFKQNKVVHVacetylation[5, 6]
143GGIAHLFKQNKVVHVubiquitination[2, 3, 4]
159GYGKITGKNQVTATKubiquitination[1, 4]
166KNQVTATKADGGTQVubiquitination[1, 7]
267NFQRILQKQGFKFKLacetylation[5]
320IGRRPFTKNLGLEELacetylation[5]
320IGRRPFTKNLGLEELubiquitination[1, 2, 3, 4]
346VNTRFQTKIPNIYAIubiquitination[1, 2, 3, 7]
410GKSEEQLKEEGIEYKacetylation[5]
410GKSEEQLKEEGIEYKubiquitination[1, 7]
417KEEGIEYKVGKFPFAacetylation[5]
417KEEGIEYKVGKFPFAubiquitination[1]
420GIEYKVGKFPFAANSacetylation[5]
420GIEYKVGKFPFAANSubiquitination[1, 4]
430FAANSRAKTNADTDGubiquitination[4]
440ADTDGMVKILGQKSTubiquitination[1, 2, 3]
445MVKILGQKSTDRVLGubiquitination[1, 4]
505NLAASFGKSINF***ubiquitination[1]
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] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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] 
Functional Description
 Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction. 
Sequence Annotation
 NP_BIND 71 80 FAD.
 NP_BIND 183 185 FAD.
 NP_BIND 220 227 NAD.
 NP_BIND 361 364 FAD.
 ACT_SITE 487 487 Proton acceptor (By similarity).
 BINDING 89 89 FAD.
 BINDING 154 154 FAD; via amide nitrogen and carbonyl
 BINDING 243 243 NAD.
 BINDING 278 278 NAD; via amide nitrogen and carbonyl
 BINDING 314 314 NAD; via amide nitrogen.
 BINDING 355 355 FAD.
 MOD_RES 127 127 N6-acetyllysine (By similarity).
 MOD_RES 143 143 N6-acetyllysine.
 MOD_RES 410 410 N6-acetyllysine.
 MOD_RES 417 417 N6-acetyllysine.
 DISULFID 80 85 Redox-active.  
Keyword
 3D-structure; Acetylation; Complete proteome; Disease mutation; Disulfide bond; FAD; Flavoprotein; Mitochondrion; NAD; Oxidoreductase; Phosphoprotein; Polymorphism; Redox-active center; Reference proteome; Transit peptide. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 509 AA 
Protein Sequence
MQSWSRVYCS LAKRGHFNRI SHGLQGLSAV PLRTYADQPI DADVTVIGSG PGGYVAAIKA 60
AQLGFKTVCI EKNETLGGTC LNVGCIPSKA LLNNSHYYHM AHGKDFASRG IEMSEVRLNL 120
DKMMEQKSTA VKALTGGIAH LFKQNKVVHV NGYGKITGKN QVTATKADGG TQVIDTKNIL 180
IATGSEVTPF PGITIDEDTI VSSTGALSLK KVPEKMVVIG AGVIGVELGS VWQRLGADVT 240
AVEFLGHVGG VGIDMEISKN FQRILQKQGF KFKLNTKVTG ATKKSDGKID VSIEAASGGK 300
AEVITCDVLL VCIGRRPFTK NLGLEELGIE LDPRGRIPVN TRFQTKIPNI YAIGDVVAGP 360
MLAHKAEDEG IICVEGMAGG AVHIDYNCVP SVIYTHPEVA WVGKSEEQLK EEGIEYKVGK 420
FPFAANSRAK TNADTDGMVK ILGQKSTDRV LGAHILGPGA GEMVNEAALA LEYGASCEDI 480
ARVCHAHPTL SEAFREANLA ASFGKSINF 509 
Gene Ontology
 GO:0043159; C:acrosomal matrix; IEA:Compara.
 GO:0005759; C:mitochondrial matrix; TAS:Reactome.
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0004148; F:dihydrolipoyl dehydrogenase activity; TAS:ProtInc.
 GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
 GO:0009083; P:branched-chain amino acid catabolic process; TAS:Reactome.
 GO:0045454; P:cell redox homeostasis; IEA:InterPro.
 GO:0034641; P:cellular nitrogen compound metabolic process; TAS:Reactome.
 GO:0007369; P:gastrulation; IEA:Compara.
 GO:0006554; P:lysine catabolic process; TAS:Reactome.
 GO:0006120; P:mitochondrial electron transport, NADH to ubiquinone; IEA:Compara.
 GO:0006508; P:proteolysis; IEA:Compara.
 GO:0006090; P:pyruvate metabolic process; TAS:Reactome.
 GO:0010510; P:regulation of acetyl-CoA biosynthetic process from pyruvate; TAS:Reactome.
 GO:0042391; P:regulation of membrane potential; IEA:Compara.
 GO:0048240; P:sperm capacitation; IEA:Compara.
 GO:0006099; P:tricarboxylic acid cycle; TAS:Reactome. 
Interpro
 IPR016156; FAD/NAD-linked_Rdtase_dimer.
 IPR013027; FAD_pyr_nucl-diS_OxRdtase.
 IPR006258; Lipoamide_DH.
 IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
 IPR023753; Pyr_nucl-diS_OxRdtase_FAD/NAD.
 IPR012999; Pyr_OxRdtase_I_AS.
 IPR001327; Pyr_OxRdtase_NAD-bd_dom. 
Pfam
 PF00070; Pyr_redox
 PF07992; Pyr_redox_2
 PF02852; Pyr_redox_dim 
SMART
  
PROSITE
 PS00076; PYRIDINE_REDOX_1 
PRINTS
 PR00368; FADPNR.