CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-013252
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Putative oxidoreductase GLYR1 
Protein Synonyms/Alias
 3-hydroxyisobutyrate dehydrogenase-like protein; Cytokine-like nuclear factor N-PAC; Glyoxylate reductase 1 homolog; Nuclear protein NP60; Nuclear protein of 60 kDa 
Gene Name
 GLYR1 
Gene Synonyms/Alias
 HIBDL; NP60 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
25RYPPWPGKIVNPPKDacetylation[1]
190IPESSTVKGMMAGPMubiquitination[2]
201AGPMAAFKWQPTASEubiquitination[2]
211PTASEPVKDADPHFHubiquitination[3, 4]
269SITPTDKKIGFLGLGsumoylation[5]
302VWNRTAEKCDLFIQEubiquitination[6]
335FACVSDPKAAKDLVLubiquitination[6]
338VSDPKAAKDLVLGPSubiquitination[3, 4, 6]
495NILQGNFKPDFYLKYubiquitination[3, 4, 6, 7]
505FYLKYIQKDLRLAIAubiquitination[6]
532AAANEVYKRAKALDQubiquitination[6]
535NEVYKRAKALDQSDNubiquitination[2, 3, 4, 6, 8]
Reference
 [1] 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]
 [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] 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]
 [5] Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif.
 Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC.
 Mol Cell. 2010 Aug 27;39(4):641-52. [PMID: 20797634]
 [6] 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]
 [7] 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]
 [8] 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
 May have oxidoreductase activity. Regulates p38 MAP kinase activity by mediating stress activation of p38alpha/MAPK14 and specifically regulating MAPK14 signaling. Indirectly promotes phosphorylation of MAPK14 and activation of ATF2. The phosphorylation of MAPK14 requires upstream activity of MAP2K4 and MAP2K6. Recruited on chromatin, recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). 
Sequence Annotation
 DOMAIN 8 66 PWWP.
 DNA_BIND 168 180 A.T hook.
 NP_BIND 271 285 NAD (By similarity).
 BINDING 362 362 NAD (By similarity).
 BINDING 505 505 NAD (By similarity).
 MOD_RES 130 130 Phosphoserine.
 MOD_RES 167 167 Phosphoserine.
 MOD_RES 540 540 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; Complete proteome; DNA-binding; NAD; Nucleus; Oxidoreductase; Phosphoprotein; Polymorphism; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 553 AA 
Protein Sequence
MAAVSLRLGD LVWGKLGRYP PWPGKIVNPP KDLKKPRGKK CFFVKFFGTE DHAWIKVEQL 60
KPYHAHKEEM IKINKGKRFQ QAVDAVEEFL RRAKGKDQTS SHNSSDDKNR RNSSEERSRP 120
NSGDEKRKLS LSEGKVKKNM GEGKKRVSSG SSERGSKSPL KRAQEQSPRK RGRPPKDEKD 180
LTIPESSTVK GMMAGPMAAF KWQPTASEPV KDADPHFHHF LLSQTEKPAV CYQAITKKLK 240
ICEEETGSTS IQAADSTAVN GSITPTDKKI GFLGLGLMGS GIVSNLLKMG HTVTVWNRTA 300
EKCDLFIQEG ARLGRTPAEV VSTCDITFAC VSDPKAAKDL VLGPSGVLQG IRPGKCYVDM 360
STVDADTVTE LAQVIVSRGG RFLEAPVSGN QQLSNDGMLV ILAAGDRGLY EDCSSCFQAM 420
GKTSFFLGEV GNAAKMMLIV NMVQGSFMAT IAEGLTLAHV TGQSQQTLLD ILNQGQLASI 480
FLDQKCQNIL QGNFKPDFYL KYIQKDLRLA IALGDAVNHP TPMAAAANEV YKRAKALDQS 540
DNDMSAVYRA YIH 553 
Gene Ontology
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0050662; F:coenzyme binding; IEA:InterPro.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0035064; F:methylated histone residue binding; IDA:UniProtKB.
 GO:0004616; F:phosphogluconate dehydrogenase (decarboxylating) activity; IEA:InterPro.
 GO:0006098; P:pentose-phosphate shunt; IEA:InterPro. 
Interpro
 IPR008927; 6-PGluconate_DH_C-like.
 IPR006115; 6PGDH_NADP-bd.
 IPR017956; AT_hook_DNA-bd_motif.
 IPR013328; DH_multihelical.
 IPR015815; HIBADH-type.
 IPR016040; NAD(P)-bd_dom.
 IPR000313; PWWP. 
Pfam
 PF03446; NAD_binding_2
 PF00855; PWWP 
SMART
 SM00384; AT_hook 
PROSITE
 PS00895; 3_HYDROXYISOBUT_DH
 PS50812; PWWP 
PRINTS