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P04819

- DNLI1_YEAST

UniProt

P04819 - DNLI1_YEAST

Protein

DNA ligase 1

Gene

CDC9

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 159 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    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 activityi

    ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

    Cofactori

    Magnesium.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei164 – 1641Interaction with target DNABy similarity
    Binding sitei417 – 4171ATPBy similarity
    Active sitei419 – 4191N6-AMP-lysine intermediatePROSITE-ProRule annotation
    Binding sitei424 – 4241ATPBy similarity
    Binding sitei440 – 4401ATPBy similarity
    Sitei441 – 4411Interaction with target DNABy similarity
    Metal bindingi472 – 4721Magnesium 1By similarity
    Metal bindingi571 – 5711Magnesium 2By similarity
    Binding sitei576 – 5761ATPBy similarity
    Binding sitei590 – 5901ATPBy similarity
    Binding sitei596 – 5961ATPBy similarity
    Sitei622 – 6221Interaction with target DNABy similarity
    Sitei647 – 6471Interaction with target DNABy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: InterPro
    3. DNA ligase (ATP) activity Source: SGD
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. base-excision repair Source: SGD
    2. cell division Source: UniProtKB-KW
    3. DNA ligation Source: SGD
    4. DNA ligation involved in DNA repair Source: InterPro
    5. DNA recombination Source: SGD
    6. lagging strand elongation Source: SGD
    7. maintenance of DNA trinucleotide repeats Source: SGD
    8. mitotic cell cycle Source: SGD
    9. nucleotide-excision repair Source: SGD

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29556-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA ligase 1 (EC:6.5.1.1)
    Alternative name(s):
    DNA ligase I
    Polydeoxyribonucleotide synthase [ATP] 1
    Gene namesi
    Name:CDC9
    Ordered Locus Names:YDL164C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDL164c.
    SGDiS000002323. CDC9.

    Subcellular locationi

    GO - Cellular componenti

    1. mitochondrion Source: SGD
    2. nucleus Source: SGD
    3. replication fork Source: SGD

    Keywords - Cellular componenti

    Mitochondrion, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 4444MitochondrionSequence AnalysisAdd
    BLAST
    Chaini45 – 755711DNA ligase 1PRO_0000007274Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei58 – 581Phosphoserine2 Publications
    Modified residuei75 – 751Phosphoserine3 Publications
    Modified residuei119 – 1191Phosphoserine1 Publication
    Modified residuei123 – 1231Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP04819.
    PaxDbiP04819.
    PeptideAtlasiP04819.

    Expressioni

    Gene expression databases

    GenevestigatoriP04819.

    Interactioni

    Protein-protein interaction databases

    BioGridi31901. 44 interactions.
    DIPiDIP-5630N.
    IntActiP04819. 19 interactions.
    MINTiMINT-499551.
    STRINGi4932.YDL164C.

    Structurei

    Secondary structure

    1
    755
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi41 – 444

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2OD8X-ray2.80B32-53[»]
    ProteinModelPortaliP04819.
    SMRiP04819. Positions 146-751.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04819.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni309 – 31810Interaction with target DNABy similarity
    Regioni493 – 4953Interaction with target DNABy similarity

    Sequence similaritiesi

    Belongs to the ATP-dependent DNA ligase family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG1793.
    GeneTreeiENSGT00750000117745.
    HOGENOMiHOG000036006.
    KOiK10747.
    OMAiMVKMLEG.
    OrthoDBiEOG7TXKRG.

    Family and domain databases

    Gene3Di1.10.3260.10. 1 hit.
    2.40.50.140. 1 hit.
    InterProiIPR000977. 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]
    PfamiPF04679. DNA_ligase_A_C. 1 hit.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF117018. SSF117018. 1 hit.
    SSF50249. SSF50249. 1 hit.
    TIGRFAMsiTIGR00574. dnl1. 1 hit.
    PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative initiation. Align

    Isoform Mitochondrial (identifier: P04819-1) [UniParc]FASTAAdd to Basket

    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.

    « Hide

    MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN    50
    KPTEGTPSPK KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM 100
    GSNFSSIPSS APSSGVADSP QQSQRLVGEV EDALSSNNND HYSSNIPYSE 150
    VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK QSSKNLIPTT YLFINRLGPD 200
    YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG EIAMGARNVQ 250
    PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK 300
    FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA 350
    QQKIRDAFCQ VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK 400
    AINEVLDRFQ GETFTSEYKY DGERAQVHLL NDGTMRIYSR NGENMTERYP 450
    EINITDFIQD LDTTKNLILD CEAVAWDKDQ GKILPFQVLS TRKRKDVELN 500
    DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV PGEFQYATQI 550
    TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD 600
    YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT 650
    GFSDEMLQLL HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD 700
    LSLSPIYKAG SATFDKGVSL RFPRFLRIRE DKGVEDATSS DQIVELYENQ 750
    SHMQN 755
    Length:755
    Mass (Da):84,828
    Last modified:November 1, 1997 - v2
    Checksum:iB7C2ECAF5C61CAE7
    GO
    Isoform Nuclear (identifier: P04819-2) [UniParc]FASTAAdd to Basket

    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.

    Show »
    Length:732
    Mass (Da):82,251
    Checksum:iB5267D6EE0C5C798
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti69 – 691D → E in CAA27005. (PubMed:3909103)Curated
    Sequence conflicti186 – 1861L → V in CAA27005. (PubMed:3909103)Curated
    Sequence conflicti671 – 6711G → E in CAA48158. (PubMed:8483449)Curated
    Sequence conflicti724 – 7241R → I in CAA48158. (PubMed:8483449)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 2323Missing in isoform Nuclear. CuratedVSP_018719Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    PIRiS61049. LQBYPX.
    RefSeqiNP_010117.1. NM_001180224.1. [P04819-1]

    Genome annotation databases

    EnsemblFungiiYDL164C; YDL164C; YDL164C. [P04819-1]
    GeneIDi851391.
    KEGGisce:YDL164C.

    Keywords - Coding sequence diversityi

    Alternative initiation

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    PIRi S61049. LQBYPX.
    RefSeqi NP_010117.1. NM_001180224.1. [P04819-1 ]

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2OD8 X-ray 2.80 B 32-53 [» ]
    ProteinModelPortali P04819.
    SMRi P04819. Positions 146-751.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31901. 44 interactions.
    DIPi DIP-5630N.
    IntActi P04819. 19 interactions.
    MINTi MINT-499551.
    STRINGi 4932.YDL164C.

    Proteomic databases

    MaxQBi P04819.
    PaxDbi P04819.
    PeptideAtlasi P04819.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDL164C ; YDL164C ; YDL164C . [P04819-1 ]
    GeneIDi 851391.
    KEGGi sce:YDL164C.

    Organism-specific databases

    CYGDi YDL164c.
    SGDi S000002323. CDC9.

    Phylogenomic databases

    eggNOGi COG1793.
    GeneTreei ENSGT00750000117745.
    HOGENOMi HOG000036006.
    KOi K10747.
    OMAi MVKMLEG.
    OrthoDBi EOG7TXKRG.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29556-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P04819.
    NextBioi 968546.
    PROi P04819.

    Gene expression databases

    Genevestigatori P04819.

    Family and domain databases

    Gene3Di 1.10.3260.10. 1 hit.
    2.40.50.140. 1 hit.
    InterProi 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.
    [Graphical view ]
    Pfami PF04679. DNA_ligase_A_C. 1 hit.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF117018. SSF117018. 1 hit.
    SSF50249. SSF50249. 1 hit.
    TIGRFAMsi TIGR00574. dnl1. 1 hit.
    PROSITEi PS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.
      , 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. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. 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. 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. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiDNLI1_YEAST
    AccessioniPrimary (citable) accession number: P04819
    Secondary accession number(s): D6VRI7, Q12736
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 159 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    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.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3