CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-004713
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA ligase 1 
Protein Synonyms/Alias
 DNA ligase I; Polydeoxyribonucleotide synthase [ATP] 1 
Gene Name
 LIG1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
40PPPKAALKEWNGVVSubiquitination[1]
226KPPRRAPKTLSSFFTubiquitination[1, 2, 3]
286ACWKPGQKVPYLAVAubiquitination[4]
298AVARTFEKIEEVSARubiquitination[4]
376VRAEAAEKGDVGLVAubiquitination[5]
407TASGVFSKFRDIARLubiquitination[1, 2, 3, 4]
422TGSASTAKKIDIIKGubiquitination[3, 6]
428AKKIDIIKGLFVACRubiquitination[4]
541LSPGIPLKPMLAHPTubiquitination[4]
556RGISEVLKRFEEAAFubiquitination[4]
630VAWDREKKQIQPFQVubiquitination[4]
737DATYEIAKRSHNWLKubiquitination[4]
744KRSHNWLKLKKDYLDubiquitination[4]
866RGLVDSDKGISLRFPubiquitination[4]
Reference
 [1] 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]
 [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] 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]
 [6] Proteomic analysis of ubiquitinated proteins in normal hepatocyte cell line Chang liver cells.
 Tan F, Lu L, Cai Y, Wang J, Xie Y, Wang L, Gong Y, Xu BE, Wu J, Luo Y, Qiang B, Yuan J, Sun X, Peng X.
 Proteomics. 2008 Jul;8(14):2885-96. [PMID: 18655026] 
Functional Description
 DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. 
Sequence Annotation
 REGION 449 458 Interaction with target DNA.
 REGION 642 644 Interaction with target DNA.
 ACT_SITE 568 568 N6-AMP-lysine intermediate (By
 METAL 621 621 Magnesium 1 (Probable).
 METAL 720 720 Magnesium 2 (Probable).
 BINDING 566 566 ATP.
 BINDING 573 573 ATP.
 BINDING 589 589 ATP.
 BINDING 725 725 ATP.
 BINDING 738 738 ATP (By similarity).
 BINDING 744 744 ATP.
 MOD_RES 47 47 Phosphoserine.
 MOD_RES 49 49 Phosphoserine.
 MOD_RES 51 51 Phosphoserine.
 MOD_RES 66 66 Phosphoserine.
 MOD_RES 76 76 Phosphoserine.
 MOD_RES 141 141 Phosphoserine.
 MOD_RES 195 195 Phosphothreonine.
 MOD_RES 201 201 Phosphoserine.
 MOD_RES 233 233 Phosphothreonine.
 MOD_RES 911 911 Phosphoserine.
 MOD_RES 913 913 Phosphoserine.
 CROSSLNK 422 422 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; ATP-binding; Cell cycle; Cell division; Complete proteome; DNA damage; DNA recombination; DNA repair; DNA replication; Isopeptide bond; Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 919 AA 
Protein Sequence
MQRSIMSFFH PKKEGKAKKP EKEASNSSRE TEPPPKAALK EWNGVVSESD SPVKRPGRKA 60
ARVLGSEGEE EDEALSPAKG QKPALDCSQV SPPRPATSPE NNASLSDTSP MDSSPSGIPK 120
RRTARKQLPK RTIQEVLEEQ SEDEDREAKR KKEEEEEETP KESLTEAEVA TEKEGEDGDQ 180
PTTPPKPLKT SKAETPTESV SEPEVATKQE LQEEEEQTKP PRRAPKTLSS FFTPRKPAVK 240
KEVKEEEPGA PGKEGAAEGP LDPSGYNPAK NNYHPVEDAC WKPGQKVPYL AVARTFEKIE 300
EVSARLRMVE TLSNLLRSVV ALSPPDLLPV LYLSLNHLGP PQQGLELGVG DGVLLKAVAQ 360
ATGRQLESVR AEAAEKGDVG LVAENSRSTQ RLMLPPPPLT ASGVFSKFRD IARLTGSAST 420
AKKIDIIKGL FVACRHSEAR FIARSLSGRL RLGLAEQSVL AALSQAVSLT PPGQEFPPAM 480
VDAGKGKTAE ARKTWLEEQG MILKQTFCEV PDLDRIIPVL LEHGLERLPE HCKLSPGIPL 540
KPMLAHPTRG ISEVLKRFEE AAFTCEYKYD GQRAQIHALE GGEVKIFSRN QEDNTGKYPD 600
IISRIPKIKL PSVTSFILDT EAVAWDREKK QIQPFQVLTT RKRKEVDASE IQVQVCLYAF 660
DLIYLNGESL VREPLSRRRQ LLRENFVETE GEFVFATSLD TKDIEQIAEF LEQSVKDSCE 720
GLMVKTLDVD ATYEIAKRSH NWLKLKKDYL DGVGDTLDLV VIGAYLGRGK RAGRYGGFLL 780
ASYDEDSEEL QAICKLGTGF SDEELEEHHQ SLKALVLPSP RPYVRIDGAV IPDHWLDPSA 840
VWEVKCADLS LSPIYPAARG LVDSDKGISL RFPRFIRVRE DKQPEQATTS AQVACLYRKQ 900
SQIQNQQGED SGSDPEDTY 919 
Gene Ontology
 GO:0005694; C:chromosome; IBA:RefGenome.
 GO:0005739; C:mitochondrion; IBA:RefGenome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; TAS:ProtInc.
 GO:0003910; F:DNA ligase (ATP) activity; IBA:RefGenome.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0009653; P:anatomical structure morphogenesis; TAS:ProtInc.
 GO:0006284; P:base-excision repair; TAS:Reactome.
 GO:0051301; P:cell division; IEA:UniProtKB-KW.
 GO:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
 GO:0000724; P:double-strand break repair via homologous recombination; TAS:Reactome.
 GO:0006303; P:double-strand break repair via nonhomologous end joining; IEA:Compara.
 GO:0006273; P:lagging strand elongation; IBA:RefGenome.
 GO:0000278; P:mitotic cell cycle; TAS:Reactome.
 GO:0006297; P:nucleotide-excision repair, DNA gap filling; TAS:Reactome.
 GO:0042542; P:response to hydrogen peroxide; IEA:Compara.
 GO:0000722; P:telomere maintenance via recombination; TAS:Reactome.
 GO:0032201; P:telomere maintenance via semi-conservative replication; TAS:Reactome.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; TAS:Reactome. 
Interpro
 IPR000977; DNA_ligase_ATP-dep.
 IPR012309; DNA_ligase_ATP-dep_C.
 IPR012310; DNA_ligase_ATP-dep_cent.
 IPR016059; DNA_ligase_ATP-dep_CS.
 IPR012308; DNA_ligase_ATP-dep_N.
 IPR012340; NA-bd_OB-fold. 
Pfam
 PF04679; DNA_ligase_A_C
 PF01068; DNA_ligase_A_M
 PF04675; DNA_ligase_A_N 
SMART
  
PROSITE
 PS00697; DNA_LIGASE_A1
 PS00333; DNA_LIGASE_A2
 PS50160; DNA_LIGASE_A3 
PRINTS