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P04819 (DNLI1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 158. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase 1

EC=6.5.1.1
Alternative name(s):
DNA ligase I
Polydeoxyribonucleotide synthase [ATP] 1
Gene names
Name:CDC9
Ordered Locus Names:YDL164C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length755 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

Cofactor

Magnesium By similarity.

Subcellular location

Isoform Mitochondrial: Mitochondrion.

Isoform Nuclear: Nucleus.

Miscellaneous

Cdc9 is included within the category of so-called 'start genes', encoding proteins which are required in early G1, when the cell is faced with the option of initiating a further cell cycle.

Present with 149 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the ATP-dependent DNA ligase family.

Ontologies

Keywords
   Biological processCell cycle
Cell division
DNA damage
DNA recombination
DNA repair
DNA replication
   Cellular componentMitochondrion
Nucleus
   Coding sequence diversityAlternative initiation
   DomainTransit peptide
   LigandATP-binding
Magnesium
Metal-binding
Nucleotide-binding
   Molecular functionLigase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA ligation

Inferred from direct assay PubMed 9759502. Source: SGD

DNA ligation involved in DNA repair

Inferred from electronic annotation. Source: InterPro

DNA recombination

Inferred from mutant phenotype PubMed 9230305. Source: SGD

base-excision repair

Inferred from mutant phenotype PubMed 10052932. Source: SGD

cell division

Inferred from electronic annotation. Source: UniProtKB-KW

lagging strand elongation

Inferred from direct assay PubMed 9759502. Source: SGD

maintenance of DNA trinucleotide repeats

Inferred from mutant phenotype PubMed 16079237. Source: SGD

mitotic cell cycle

Inferred from mutant phenotype PubMed 6749599. Source: SGD

nucleotide-excision repair

Inferred from mutant phenotype PubMed 10052932. Source: SGD

   Cellular_componentmitochondrion

Inferred from direct assay Ref.6. Source: SGD

nucleus

Inferred from direct assay Ref.6. Source: SGD

replication fork

Non-traceable author statement PubMed 9759502. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA binding

Inferred from electronic annotation. Source: InterPro

DNA ligase (ATP) activity

Inferred from direct assay PubMed 1445910PubMed 6347688. Source: SGD

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]
Isoform Mitochondrial (identifier: P04819-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform Nuclear (identifier: P04819-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-23: Missing.
Note: Produced by alternative initiation at Met-24 of isoform Mitochondrial.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 4444Mitochondrion Potential
Chain45 – 755711DNA ligase 1
PRO_0000007274

Regions

Region309 – 31810Interaction with target DNA By similarity
Region493 – 4953Interaction with target DNA By similarity

Sites

Active site4191N6-AMP-lysine intermediate By similarity
Metal binding4721Magnesium 1 By similarity
Metal binding5711Magnesium 2 By similarity
Binding site4171ATP By similarity
Binding site4241ATP By similarity
Binding site4401ATP By similarity
Binding site5761ATP By similarity
Binding site5901ATP By similarity
Binding site5961ATP By similarity
Site1641Interaction with target DNA By similarity
Site4411Interaction with target DNA By similarity
Site6221Interaction with target DNA By similarity
Site6471Interaction with target DNA By similarity

Amino acid modifications

Modified residue581Phosphoserine Ref.8 Ref.9
Modified residue751Phosphoserine Ref.8 Ref.9 Ref.10
Modified residue1191Phosphoserine Ref.10
Modified residue1231Phosphoserine Ref.10

Natural variations

Alternative sequence1 – 2323Missing in isoform Nuclear.
VSP_018719

Experimental info

Sequence conflict691D → E in CAA27005. Ref.1
Sequence conflict1861L → V in CAA27005. Ref.1
Sequence conflict6711G → E in CAA48158. Ref.5
Sequence conflict7241R → I in CAA48158. Ref.5

Secondary structure

... 755
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Mitochondrial [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: B7C2ECAF5C61CAE7

FASTA75584,828
        10         20         30         40         50         60 
MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN KPTEGTPSPK 

        70         80         90        100        110        120 
KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM GSNFSSIPSS APSSGVADSP 

       130        140        150        160        170        180 
QQSQRLVGEV EDALSSNNND HYSSNIPYSE VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK 

       190        200        210        220        230        240 
QSSKNLIPTT YLFINRLGPD YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG 

       250        260        270        280        290        300 
EIAMGARNVQ PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK 

       310        320        330        340        350        360 
FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA QQKIRDAFCQ 

       370        380        390        400        410        420 
VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK AINEVLDRFQ GETFTSEYKY 

       430        440        450        460        470        480 
DGERAQVHLL NDGTMRIYSR NGENMTERYP EINITDFIQD LDTTKNLILD CEAVAWDKDQ 

       490        500        510        520        530        540 
GKILPFQVLS TRKRKDVELN DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV 

       550        560        570        580        590        600 
PGEFQYATQI TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD 

       610        620        630        640        650        660 
YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT GFSDEMLQLL 

       670        680        690        700        710        720 
HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD LSLSPIYKAG SATFDKGVSL 

       730        740        750 
RFPRFLRIRE DKGVEDATSS DQIVELYENQ SHMQN 

« Hide

Isoform Nuclear [UniParc].

Checksum: B5267D6EE0C5C798
Show »

FASTA73282,251

References

« Hide 'large scale' references
[1]"The nucleotide sequence of the DNA ligase gene (CDC9) from Saccharomyces cerevisiae: a gene which is cell-cycle regulated and induced in response to DNA damage."
Barker D.G., White J.H.M., Johnston L.H.
Nucleic Acids Res. 13:8323-8337(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. expand/collapse author list , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"Molecular structure and genetic regulation of SFA, a gene responsible for resistance to formaldehyde in Saccharomyces cerevisiae, and characterization of its protein product."
Wehner E.P., Rao E., Brendel M.
Mol. Gen. Genet. 237:351-358(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 610-755.
Strain: ATCC 38626 / AH22 / NRRL Y-12843.
[6]"The yeast CDC9 gene encodes both a nuclear and a mitochondrial form of DNA ligase I."
Willer M., Rainey M., Pullen T., Stirling C.J.
Curr. Biol. 9:1085-1094(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: ALTERNATIVE INITIATION.
[7]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-75; SER-119 AND SER-123, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X03246 Genomic DNA. Translation: CAA27005.1.
Z67750 Genomic DNA. Translation: CAA91582.1.
Z74212 Genomic DNA. Translation: CAA98737.1.
AY723764 Genomic DNA. Translation: AAU09681.1.
X68020 Genomic DNA. Translation: CAA48158.1.
BK006938 Genomic DNA. Translation: DAA11697.1.
PIRLQBYPX. S61049.
RefSeqNP_010117.1. NM_001180224.1. [P04819-1]

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2OD8X-ray2.80B32-53[»]
ProteinModelPortalP04819.
SMRP04819. Positions 146-751.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31901. 48 interactions.
DIPDIP-5630N.
IntActP04819. 19 interactions.
MINTMINT-499551.
STRING4932.YDL164C.

Proteomic databases

MaxQBP04819.
PaxDbP04819.
PeptideAtlasP04819.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDL164C; YDL164C; YDL164C. [P04819-1]
GeneID851391.
KEGGsce:YDL164C.

Organism-specific databases

CYGDYDL164c.
SGDS000002323. CDC9.

Phylogenomic databases

eggNOGCOG1793.
GeneTreeENSGT00750000117745.
HOGENOMHOG000036006.
KOK10747.
OMAMVKMLEG.
OrthoDBEOG7TXKRG.

Enzyme and pathway databases

BioCycYEAST:G3O-29556-MONOMER.

Gene expression databases

GenevestigatorP04819.

Family and domain databases

Gene3D1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
InterProIPR000977. 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.
[Graphical view]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP04819.
NextBio968546.
PROP04819.

Entry information

Entry nameDNLI1_YEAST
AccessionPrimary (citable) accession number: P04819
Secondary accession number(s): D6VRI7, Q12736
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: November 1, 1997
Last modified: July 9, 2014
This is version 158 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references