CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002169
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
 CDC9 
Gene Synonyms/Alias
 YDL164C 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
266LTVGEVFKNLRAIAKacetylation[1]
535ERREYLTKVTKVVPGubiquitination[2]
Reference
 [1] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919]
 [2] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301] 
Functional Description
 DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. The mitochondrial form is required for mitochondrial DNA maintenance but is non-essential while the nuclear form is essential for cell viability. 
Sequence Annotation
 REGION 309 318 Interaction with target DNA (By
 REGION 493 495 Interaction with target DNA (By
 ACT_SITE 419 419 N6-AMP-lysine intermediate (By
 METAL 472 472 Magnesium 1 (By similarity).
 METAL 571 571 Magnesium 2 (By similarity).
 BINDING 417 417 ATP (By similarity).
 BINDING 424 424 ATP (By similarity).
 BINDING 440 440 ATP (By similarity).
 BINDING 576 576 ATP (By similarity).
 BINDING 590 590 ATP (By similarity).
 BINDING 596 596 ATP (By similarity).
 MOD_RES 58 58 Phosphoserine.
 MOD_RES 75 75 Phosphoserine.
 MOD_RES 119 119 Phosphoserine.
 MOD_RES 123 123 Phosphoserine.  
Keyword
 3D-structure; Alternative initiation; ATP-binding; Cell cycle; Cell division; Complete proteome; DNA damage; DNA recombination; DNA repair; DNA replication; Ligase; Magnesium; Metal-binding; Mitochondrion; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome; Transit peptide. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 755 AA 
Protein Sequence
MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN KPTEGTPSPK 60
KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM GSNFSSIPSS APSSGVADSP 120
QQSQRLVGEV EDALSSNNND HYSSNIPYSE VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK 180
QSSKNLIPTT YLFINRLGPD YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG 240
EIAMGARNVQ PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK 300
FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA QQKIRDAFCQ 360
VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK AINEVLDRFQ GETFTSEYKY 420
DGERAQVHLL NDGTMRIYSR NGENMTERYP EINITDFIQD LDTTKNLILD CEAVAWDKDQ 480
GKILPFQVLS TRKRKDVELN DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV 540
PGEFQYATQI TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD 600
YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT GFSDEMLQLL 660
HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD LSLSPIYKAG SATFDKGVSL 720
RFPRFLRIRE DKGVEDATSS DQIVELYENQ SHMQN 755 
Gene Ontology
 GO:0005739; C:mitochondrion; IDA:SGD.
 GO:0005634; C:nucleus; IDA:SGD.
 GO:0005657; C:replication fork; NAS:SGD.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0003910; F:DNA ligase (ATP) activity; IDA:SGD.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0006284; P:base-excision repair; IMP:SGD.
 GO:0051301; P:cell division; IEA:UniProtKB-KW.
 GO:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
 GO:0006310; P:DNA recombination; IMP:SGD.
 GO:0006273; P:lagging strand elongation; IMP:SGD.
 GO:0000278; P:mitotic cell cycle; IMP:SGD.
 GO:0006289; P:nucleotide-excision repair; IMP:SGD. 
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