CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000659
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 D-3-phosphoglycerate dehydrogenase 
Protein Synonyms/Alias
 3-PGDH 
Gene Name
 PHGDH 
Gene Synonyms/Alias
 PGDH3 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
8MAFANLRKVLISDSLubiquitination[1]
21SLDPCCRKILQDGGLubiquitination[1, 2, 3, 4, 5, 6, 7, 8]
33GGLQVVEKQNLSKEEacetylation[9]
33GGLQVVEKQNLSKEEubiquitination[2, 3, 5, 7]
38VEKQNLSKEELIAELubiquitination[1]
58LIVRSATKVTADVINubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12]
69DVINAAEKLQVVGRAubiquitination[1, 3, 4, 5, 6, 8, 10]
129PQATASMKDGKWERKubiquitination[1, 3]
136KDGKWERKKFMGTELubiquitination[1]
137DGKWERKKFMGTELNubiquitination[1]
146MGTELNGKTLGILGLubiquitination[1, 2, 3, 5, 6, 7, 10]
289PHLGASTKEAQSRCGubiquitination[1, 2, 4, 7, 10, 12]
308VQFVDMVKGKSLTGVubiquitination[10]
351RAWAGSPKGTIQVITubiquitination[1, 2, 3, 4, 6, 7, 8, 10, 11, 12]
364ITQGTSLKNAGNCLSubiquitination[1, 3, 8, 10]
380AVIVGLLKEASKQADubiquitination[1, 3, 8, 10, 12]
384GLLKEASKQADVNLVubiquitination[1, 3, 6, 8, 10, 11, 12]
394DVNLVNAKLLVKEAGacetylation[9]
394DVNLVNAKLLVKEAGubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 10, 11]
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] 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] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [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] 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]
 [11] 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]
 [12] 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 155 156 NAD.
 NP_BIND 234 236 NAD.
 NP_BIND 283 286 NAD.
 ACT_SITE 236 236
 ACT_SITE 265 265 By similarity.
 ACT_SITE 283 283 Proton donor.
 BINDING 78 78 NAD.
 BINDING 175 175 NAD.
 BINDING 207 207 NAD; via carbonyl oxygen.
 BINDING 260 260 NAD.
 MOD_RES 2 2 N-acetylalanine.  
Keyword
 3D-structure; Acetylation; Amino-acid biosynthesis; Complete proteome; Direct protein sequencing; Disease mutation; NAD; Oxidoreductase; Reference proteome; Serine biosynthesis. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 533 AA 
Protein Sequence
MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG LIVRSATKVT 60
ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN GNSLSAAELT CGMIMCLARQ 120
IPQATASMKD GKWERKKFMG TELNGKTLGI LGLGRIGREV ATRMQSFGMK TIGYDPIISP 180
EVSASFGVQQ LPLEEIWPLC DFITVHTPLL PSTTGLLNDN TFAQCKKGVR VVNCARGGIV 240
DEGALLRALQ SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA 300
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEALG TLMRAWAGSP KGTIQVITQG 360
TSLKNAGNCL SPAVIVGLLK EASKQADVNL VNAKLLVKEA GLNVTTSHSP AAPGEQGFGE 420
CLLAVALAGA PYQAVGLVQG TTPVLQGLNG AVFRPEVPLR RDLPLLLFRT QTSDPAMLPT 480
MIGLLAEAGV RLLSYQTSLV SDGETWHVMG ISSLLPSLEA WKQHVTEAFQ FHF 533 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0009055; F:electron carrier activity; TAS:UniProtKB.
 GO:0051287; F:NAD binding; IEA:InterPro.
 GO:0004617; F:phosphoglycerate dehydrogenase activity; TAS:Reactome.
 GO:0007420; P:brain development; TAS:ProtInc.
 GO:0022402; P:cell cycle process; IEA:Compara.
 GO:0034641; P:cellular nitrogen compound metabolic process; TAS:Reactome.
 GO:0009448; P:gamma-aminobutyric acid metabolic process; IEA:Compara.
 GO:0021782; P:glial cell development; IEA:Compara.
 GO:0006541; P:glutamine metabolic process; IEA:Compara.
 GO:0006544; P:glycine metabolic process; IEA:Compara.
 GO:0006564; P:L-serine biosynthetic process; TAS:Reactome.
 GO:0021915; P:neural tube development; IEA:Compara.
 GO:0031175; P:neuron projection development; IEA:Compara.
 GO:0010468; P:regulation of gene expression; IEA:Compara.
 GO:0021510; P:spinal cord development; IEA:Compara.
 GO:0019530; P:taurine metabolic process; IEA:Compara.
 GO:0006566; P:threonine metabolic process; IEA:Compara. 
Interpro
 IPR006236; D-3-Phosphoglycerate_DH.
 IPR006139; D-isomer_2_OHA_DH_cat_dom.
 IPR006140; D-isomer_2_OHA_DH_NAD-bd.
 IPR016040; NAD(P)-bd_dom. 
Pfam
 PF00389; 2-Hacid_dh
 PF02826; 2-Hacid_dh_C 
SMART
  
PROSITE
 PS00065; D_2_HYDROXYACID_DH_1
 PS00670; D_2_HYDROXYACID_DH_2
 PS00671; D_2_HYDROXYACID_DH_3 
PRINTS