CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002448
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 L-lactate dehydrogenase B chain 
Protein Synonyms/Alias
 LDH-B; LDH heart subunit; LDH-H; Renal carcinoma antigen NY-REN-46 
Gene Name
 LDHB 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
5***MATLKEKLIAPVubiquitination[1, 2]
7*MATLKEKLIAPVAEacetylation[3]
7*MATLKEKLIAPVAEubiquitination[2, 4]
58LVDVLEDKLKGEMMDacetylation[3]
58LVDVLEDKLKGEMMDubiquitination[2, 4, 5]
60DVLEDKLKGEMMDLQubiquitination[2, 4, 5, 6, 7, 8]
77SLFLQTPKIVADKDYubiquitination[2, 4, 5, 6, 8]
82TPKIVADKDYSVTANubiquitination[2, 4, 5, 6, 8]
91YSVTANSKIVVVTAGubiquitination[2, 4]
119QRNVNVFKFIIPQIVacetylation[3]
119QRNVNVFKFIIPQIVubiquitination[2, 4, 5, 6, 7, 8]
156WKLSGLPKHRVIGSGubiquitination[2]
233ENWKEVHKMVVESAYubiquitination[6, 8, 9]
244ESAYEVIKLKGYTNWacetylation[10, 11]
244ESAYEVIKLKGYTNWubiquitination[2, 4, 5, 6, 8, 9, 11, 12, 13]
308LTSVINQKLKDDEVAacetylation[10]
308LTSVINQKLKDDEVAubiquitination[1, 2, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15]
310SVINQKLKDDEVAQLacetylation[10, 11]
310SVINQKLKDDEVAQLubiquitination[1, 2, 4, 5, 11, 12, 13, 15]
318DDEVAQLKKSADTLWacetylation[11]
318DDEVAQLKKSADTLWubiquitination[2, 4, 5, 11, 13, 15]
319DEVAQLKKSADTLWDacetylation[3, 11]
319DEVAQLKKSADTLWDubiquitination[2, 4, 5, 6, 7, 8, 11, 13]
329DTLWDIQKDLKDL**acetylation[3, 10, 11, 16]
329DTLWDIQKDLKDL**ubiquitination[1, 2, 4, 5, 6, 7, 8, 11, 13]
332WDIQKDLKDL*****ubiquitination[1, 2, 4, 5, 11, 13, 15]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [10] 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]
 [11] 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]
 [12] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [13] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [14] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [15] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [16] 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
Functional Description
  
Sequence Annotation
 NP_BIND 31 53 NAD (By similarity).
 ACT_SITE 194 194 Proton acceptor.
 BINDING 100 100 NAD.
 BINDING 107 107 Substrate.
 BINDING 139 139 NAD or substrate.
 BINDING 170 170 Substrate.
 BINDING 249 249 Substrate.
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 7 7 N6-acetyllysine.
 MOD_RES 44 44 Phosphoserine.
 MOD_RES 58 58 N6-acetyllysine.
 MOD_RES 119 119 N6-acetyllysine.
 MOD_RES 240 240 Phosphotyrosine.
 MOD_RES 329 329 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Cytoplasm; Direct protein sequencing; Disease mutation; Glycolysis; NAD; Oxidoreductase; Phosphoprotein; Polymorphism; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 334 AA 
Protein Sequence
MATLKEKLIA PVAEEEATVP NNKITVVGVG QVGMACAISI LGKSLADELA LVDVLEDKLK 60
GEMMDLQHGS LFLQTPKIVA DKDYSVTANS KIVVVTAGVR QQEGESRLNL VQRNVNVFKF 120
IIPQIVKYSP DCIIIVVSNP VDILTYVTWK LSGLPKHRVI GSGCNLDSAR FRYLMAEKLG 180
IHPSSCHGWI LGEHGDSSVA VWSGVNVAGV SLQELNPEMG TDNDSENWKE VHKMVVESAY 240
EVIKLKGYTN WAIGLSVADL IESMLKNLSR IHPVSTMVKG MYGIENEVFL SLPCILNARG 300
LTSVINQKLK DDEVAQLKKS ADTLWDIQKD LKDL 334 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005739; C:mitochondrion; IEA:Compara.
 GO:0004459; F:L-lactate dehydrogenase activity; TAS:ProtInc.
 GO:0051287; F:NAD binding; IEA:Compara.
 GO:0044262; P:cellular carbohydrate metabolic process; IEA:InterPro.
 GO:0006096; P:glycolysis; IEA:UniProtKB-KW.
 GO:0006089; P:lactate metabolic process; IEA:Compara.
 GO:0019674; P:NAD metabolic process; IEA:Compara.
 GO:0006090; P:pyruvate metabolic process; TAS:Reactome. 
Interpro
 IPR001557; L-lactate/malate_DH.
 IPR011304; L-lactate_DH.
 IPR018177; L-lactate_DH_AS.
 IPR022383; Lactate/malate_DH_C.
 IPR001236; Lactate/malate_DH_N.
 IPR015955; Lactate_DH/Glyco_Ohase_4_C.
 IPR016040; NAD(P)-bd_dom. 
Pfam
 PF02866; Ldh_1_C
 PF00056; Ldh_1_N 
SMART
  
PROSITE
 PS00064; L_LDH 
PRINTS
 PR00086; LLDHDRGNASE.