CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-040537
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
  
Protein Name
 DNA fragmentation factor subunit beta 
Protein Synonyms/Alias
  
Gene Name
 CAD 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
127DTRELTKKLREQGSLubiquitination[1]
137EQGSLLGKLVQNGTEubiquitination[1, 2, 3]
165LVPEVSIKTPRVFNTubiquitination[1, 2, 3, 4, 5]
186LALDCGLKYNQIRCLubiquitination[1, 3, 5, 6]
424SQAIKALKEENIQTLubiquitination[1, 2, 3, 4]
490NCGVELTKAGVLARYubiquitination[1, 3]
592TSQVLVDKSLKGWKEubiquitination[2]
598DKSLKGWKEIEYEVVubiquitination[1, 2, 5]
633RSSALASKATGYPLAubiquitination[1, 2, 3, 4, 5, 7]
676SVDYCVVKIPRWDLSubiquitination[1, 3, 5, 6]
684IPRWDLSKFLRVSTKacetylation[8, 9]
684IPRWDLSKFLRVSTKubiquitination[1, 2, 3, 4, 5, 6, 7]
691KFLRVSTKIGSCMKSubiquitination[1, 3, 5]
697TKIGSCMKSVGEVMGubiquitination[1, 3, 5]
715SFEEAFQKALRMVDEubiquitination[1, 2, 3, 4, 5, 7]
732VGFDHTVKPVSDMELubiquitination[1, 3]
745ELETPTDKRIFVVAAubiquitination[1, 3]
804PDLLQQAKCLGFSDKubiquitination[1]
811KCLGFSDKQIALAVLubiquitination[1]
826STELAVRKLRQELGIubiquitination[1]
1056SSAAAVSKEHPVVISubiquitination[1, 2, 3, 4, 5, 7]
1064EHPVVISKFIQEAKEubiquitination[1, 2, 3, 4, 5]
1148IAKDDQLKVIECNVRubiquitination[1, 5]
1165RSFPFVSKTLGVDLVubiquitination[1, 2, 3, 4, 5]
1199GSGVVGVKVPQFSFSubiquitination[1, 2, 3, 4, 5]
1238SRCEAYLKAMLSTGFubiquitination[3]
1246AMLSTGFKIPKKNILubiquitination[1, 2, 3, 4, 5]
1250TGFKIPKKNILLTIGubiquitination[1, 2, 5]
1260LLTIGSYKNKSELLPubiquitination[1, 2, 3, 4]
1262TIGSYKNKSELLPTVubiquitination[1, 2, 4, 5]
1348RLSSFVTKGYRTRRLacetylation[9]
1348RLSSFVTKGYRTRRLubiquitination[1, 2, 3, 4, 5, 6, 7]
1368VPLIIDIKCTKLFVEubiquitination[1, 2, 3, 5]
1371IIDIKCTKLFVEALGubiquitination[3, 5]
1387IGPAPPLKVHVDCMTubiquitination[3]
1397VDCMTSQKLVRLPGLubiquitination[1, 5]
1555HICHVARKEEILLIKubiquitination[1, 2, 5]
1562KEEILLIKAAKARGLubiquitination[1, 2, 3, 5]
1594LERLGPGKGEVRPELubiquitination[1, 2, 4, 5, 7]
1715WTPFEGQKVKGTVRRubiquitination[1, 3, 4]
1806GLPAEEPKEKSSRKVubiquitination[1]
1812PKEKSSRKVAEPELMubiquitination[1]
1898ERSLDILKGKVMASMubiquitination[2]
1900SLDILKGKVMASMFYubiquitination[1, 4]
1973GAVELAAKHCRRPVIubiquitination[1, 3, 5]
2062FVASRGTKQEEFESIubiquitination[1, 2, 3, 4]
2115IMTRAKKKMVVMHPMubiquitination[1]
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] 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] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [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] 
Functional Description
  
Sequence Annotation
  
Keyword
 Complete proteome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 2162 AA 
Protein Sequence
MAALVLEDGS VLRGQPFGAA VSTAGEVVFQ TGMVGYPEAL TDPSYKAQIL VLTYPLIGNY 60
GIPPDEMDEF GLCKWFESSG IHVAALVVGE CCPTPSHWSA TRTLHEWLQQ HGIPGLQGVD 120
TRELTKKLRE QGSLLGKLVQ NGTEPSSLPF LDPNARPLVP EVSIKTPRVF NTGGAPRILA 180
LDCGLKYNQI RCLCQRGAEV TVVPWDHALD SQEYEGLFLS NGPGDPASYP SVVSTLSRVL 240
SEPNPRPVFG ICLGHQLLAL AIGAKTYKMR YGNRGHNQPC LLVGSGRCFL TSQNHGFAVE 300
TDSLPADWAP LFTNANDGSN EGIVHNSLPF FSVQFHPEHQ AGPSDMELLF DIFLETVKEA 360
TAGNPGGQTV RERLTERLCP PGIPTPGSGL PPPRKVLILG SGGLSIGQAG EFDYSGSQAI 420
KALKEENIQT LLINPNIATV QTSQGLADKV YFLPITPHYV TQVIRNERPD GVLLTFGGQT 480
ALNCGVELTK AGVLARYGVR VLGTPVETIE LTEDRRAFAA RMAEIGEHVA PSEAANSLEQ 540
AQAAAERLGY PVLVRAAFAL GGLGSGFASN REELSALVAP AFAHTSQVLV DKSLKGWKEI 600
EYEVVRDAYG NCVTYYIIEV NARLSRSSAL ASKATGYPLA YVAAKLALGI PLPELRNSVT 660
GGTAAFEPSV DYCVVKIPRW DLSKFLRVST KIGSCMKSVG EVMGIGRSFE EAFQKALRMV 720
DENCVGFDHT VKPVSDMELE TPTDKRIFVV AAALWAGYSV DRLYELTRID RWFLHRMKRI 780
IAHAQLLEQH RGQPLPPDLL QQAKCLGFSD KQIALAVLST ELAVRKLRQE LGICPAVKQI 840
DTVAAEWPAQ TNYLYLTYWG TTHDLTFRTP HVLVLGSGVY RIGSSVEFDW CAVGCIQQLR 900
KMGYKTIMVN YNPETVSTDY DMCDRLYFDE ISFEVVMDIY ELENPEGVIL SMGGQLPNNM 960
AMALHRQQCR VLGTSPEAID SAENRFKFSR LLDTIGISQP QWRELSDLES ARQFCQTVGY 1020
PCVVRPSYVL SGAAMNVAYT DGDLERFLSS AAAVSKEHPV VISKFIQEAK EIDVDAVASD 1080
GVVAAIAISE HVENAGVHSG DATLVTPPQD ITAKTLERIK AIVHAVGQEL QVTGPFNLQL 1140
IAKDDQLKVI ECNVRVSRSF PFVSKTLGVD LVALATRVIM GEEVEPVGLM TGSGVVGVKV 1200
PQFSFSRLAG ADVVLGVEMT STGEVAGFGE SRCEAYLKAM LSTGFKIPKK NILLTIGSYK 1260
NKSELLPTVR LLESLGYSLY ASLGTADFYT EHGVKVTAVD WHFEEAVDGE CPPQRSILEQ 1320
LAEKNFELVI NLSMRGAGGR RLSSFVTKGY RTRRLAADFS VPLIIDIKCT KLFVEALGQI 1380
GPAPPLKVHV DCMTSQKLVR LPGLIDVHVH LREPGGTHKE DFASGTAAAL AGGITMVCAM 1440
PNTRPPIIDA PALALAQKLA EAGARCDFAL FLGASSENAG TLGTVAGSAA GLKLYLNETF 1500
SELRLDSVVQ WMEHFETWPS HLPIVAHAEQ QTVAAVLMVA QLTQRSVHIC HVARKEEILL 1560
IKAAKARGLP VTCEVAPHHL FLSHDDLERL GPGKGEVRPE LGSRQDVEAL WENMAVIDCF 1620
ASDHAPHTLE EKCGSRPPPG FPGLETMLPL LLTAVSEGRL SLDDLLQRLH HNPRRIFHLP 1680
PQEDTYVEVD LEHEWTIPSH MPFSKAHWTP FEGQKVKGTV RRVVLRGEVA YIDGQVLVPP 1740
GYGQDVRKWP QGAVPQLPPS APATSEMTTT PERPRRGIPG LPDGRFHLPP RIHRASDPGL 1800
PAEEPKEKSS RKVAEPELMG TPDGTCYPPP PVPRQASPQN LGTPGLLHPQ TSPLLHSLVG 1860
QHILSVQQFT KDQMSHLFNV AHTLRMMVQK ERSLDILKGK VMASMFYEVS TRTSSSFAAA 1920
MARLGGAVLS FSEATSSVQK GESLADSVQT MSCYADVVVL RHPQPGAVEL AAKHCRRPVI 1980
NAGDGVGEHP TQALLDIFTI REELGTVNGM TITMVGDLKH GRTVHSLACL LTQYRVSLRY 2040
VAPPSLRMPP TVRAFVASRG TKQEEFESIE EALPDTDVLY MTRIQKERFG STQEYEACFG 2100
QFILTPHIMT RAKKKMVVMH PMPRVNEISV EVDSDPRAAY FRQAENGMYI RMALLATVLG 2160
RF 2162 
Gene Ontology
 GO:0016597; F:amino acid binding; IEA:InterPro.
 GO:0004070; F:aspartate carbamoyltransferase activity; IEA:InterPro.
 GO:0005524; F:ATP binding; IEA:InterPro.
 GO:0016812; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides; IEA:InterPro.
 GO:0046872; F:metal ion binding; IEA:InterPro.
 GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IEA:InterPro.
 GO:0070409; P:carbamoyl phosphate biosynthetic process; IEA:InterPro.
 GO:0006543; P:glutamine catabolic process; IEA:InterPro. 
Interpro
 IPR006132; Asp/Orn_carbamoyltranf_P-bd.
 IPR006130; Asp/Orn_carbamoylTrfase.
 IPR002082; Asp_carbamoyltransf.
 IPR006131; Asp_carbamoyltransf_Asp/Orn-bd.
 IPR011761; ATP-grasp.
 IPR013816; ATP_grasp_subdomain_2.
 IPR006275; CarbamoylP_synth_lsu.
 IPR005481; CarbamoylP_synth_lsu_N.
 IPR005480; CarbamoylP_synth_lsu_oligo.
 IPR006274; CarbamoylP_synth_ssu.
 IPR002474; CarbamoylP_synth_ssu_N.
 IPR005479; CbamoylP_synth_lsu-like_ATP-bd.
 IPR005483; CbamoylP_synth_lsu_CPSase_dom.
 IPR002195; Dihydroorotase_CS.
 IPR017926; GATASE.
 IPR011059; Metal-dep_hydrolase_composite.
 IPR011607; MGS-like_dom.
 IPR016185; PreATP-grasp_dom. 
Pfam
 PF00289; CPSase_L_chain
 PF02786; CPSase_L_D2
 PF02787; CPSase_L_D3
 PF00988; CPSase_sm_chain
 PF00117; GATase
 PF02142; MGS
 PF00185; OTCace
 PF02729; OTCace_N 
SMART
 SM01096; CPSase_L_D3
 SM01097; CPSase_sm_chain
 SM00851; MGS 
PROSITE
 PS50975; ATP_GRASP
 PS00097; CARBAMOYLTRANSFERASE
 PS00866; CPSASE_1
 PS00867; CPSASE_2
 PS00482; DIHYDROOROTASE_1
 PS00483; DIHYDROOROTASE_2
 PS51273; GATASE_TYPE_1 
PRINTS
 PR00100; AOTCASE.
 PR00101; ATCASE.
 PR00098; CPSASE.