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P04819

- DNLI1_YEAST

UniProt

P04819 - DNLI1_YEAST

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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

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

Mg2+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 biosynthetic process Source: InterPro
  4. DNA ligation Source: SGD
  5. DNA ligation involved in DNA repair Source: InterPro
  6. DNA recombination Source: SGD
  7. lagging strand elongation Source: SGD
  8. maintenance of DNA trinucleotide repeats Source: SGD
  9. mitotic cell cycle Source: SGD
  10. nucleotide-excision repair Source: SGD
Complete GO annotation...

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
Complete GO annotation...

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. 49 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 – 444Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP04819.
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

        10         20         30         40         50
MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN
60 70 80 90 100
KPTEGTPSPK KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM
110 120 130 140 150
GSNFSSIPSS APSSGVADSP QQSQRLVGEV EDALSSNNND HYSSNIPYSE
160 170 180 190 200
VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK QSSKNLIPTT YLFINRLGPD
210 220 230 240 250
YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG EIAMGARNVQ
260 270 280 290 300
PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK
310 320 330 340 350
FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA
360 370 380 390 400
QQKIRDAFCQ VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK
410 420 430 440 450
AINEVLDRFQ GETFTSEYKY DGERAQVHLL NDGTMRIYSR NGENMTERYP
460 470 480 490 500
EINITDFIQD LDTTKNLILD CEAVAWDKDQ GKILPFQVLS TRKRKDVELN
510 520 530 540 550
DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV PGEFQYATQI
560 570 580 590 600
TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD
610 620 630 640 650
YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT
660 670 680 690 700
GFSDEMLQLL HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD
710 720 730 740 750
LSLSPIYKAG SATFDKGVSL RFPRFLRIRE DKGVEDATSS DQIVELYENQ

SHMQN
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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. 49 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.
InParanoidi P04819.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 161 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