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Protein

DNA ligase 1

Gene

CDC9

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -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.

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

Catalytic activityi

ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei417ATPBy similarity1
Active sitei419N6-AMP-lysine intermediatePROSITE-ProRule annotation1
Binding sitei424ATPBy similarity1
Binding sitei440ATPBy similarity1
Metal bindingi472Magnesium 1By similarity1
Metal bindingi571Magnesium 2By similarity1
Binding sitei576ATPBy similarity1
Binding sitei590ATPBy similarity1
Binding sitei596ATPBy similarity1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: InterPro
  • DNA ligase (ATP) activity Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29556-MONOMER
ReactomeiR-SCE-5358565 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
R-SCE-5358606 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
R-SCE-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-69183 Processive synthesis on the lagging strand

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 1 (EC:6.5.1.1PROSITE-ProRule annotation)
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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL164C
SGDiS000002323 CDC9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 44MitochondrionSequence analysisAdd BLAST44
ChainiPRO_000000727445 – 755DNA ligase 1Add BLAST711
Isoform Nuclear (identifier: P04819-2)
Initiator methionineiRemovedCombined sources

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei58PhosphoserineCombined sources1
Modified residuei75PhosphoserineCombined sources1
Modified residuei119PhosphoserineCombined sources1
Modified residuei123PhosphoserineCombined sources1
Isoform Nuclear (identifier: P04819-2)
Modified residuei2N-acetylserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP04819
PRIDEiP04819

PTM databases

iPTMnetiP04819

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei164Interaction with target DNABy similarity1
Sitei441Interaction with target DNABy similarity1
Sitei622Interaction with target DNABy similarity1
Sitei647Interaction with target DNABy similarity1

Protein-protein interaction databases

BioGridi31901, 470 interactors
DIPiDIP-5630N
ELMiP04819
IntActiP04819, 37 interactors
MINTiP04819
STRINGi4932.YDL164C

Structurei

Secondary structure

1755
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP04819
SMRiP04819
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04819

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni309 – 318Interaction with target DNABy similarity10
Regioni493 – 495Interaction with target DNABy similarity3

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00860000133792
HOGENOMiHOG000036006
InParanoidiP04819
KOiK10747
OMAiWIKYKRD
OrthoDBiEOG092C0FHN

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
InterProiView protein in 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
IPR036599 DNA_ligase_N_sf
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF04675 DNA_ligase_A_N, 1 hit
SUPFAMiSSF117018 SSF117018, 1 hit
SSF50249 SSF50249, 1 hit
TIGRFAMsiTIGR00574 dnl1, 1 hit
PROSITEiView protein in PROSITE
PS00697 DNA_LIGASE_A1, 1 hit
PS00333 DNA_LIGASE_A2, 1 hit
PS50160 DNA_LIGASE_A3, 1 hit

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. AlignAdd to basket
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.Combined sources
Show »
Length:732
Mass (Da):82,251
Checksum:iB5267D6EE0C5C798
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti69D → E in CAA27005 (PubMed:3909103).Curated1
Sequence conflicti186L → V in CAA27005 (PubMed:3909103).Curated1
Sequence conflicti671G → E in CAA48158 (PubMed:8483449).Curated1
Sequence conflicti724R → I in CAA48158 (PubMed:8483449).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0187191 – 23Missing in isoform Nuclear. CuratedAdd BLAST23

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

Similar proteinsi

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
PIRiS61049 LQBYPX
RefSeqiNP_010117.1, NM_001180224.1 [P04819-1]

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OD8X-ray2.80B32-53[»]
ProteinModelPortaliP04819
SMRiP04819
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31901, 470 interactors
DIPiDIP-5630N
ELMiP04819
IntActiP04819, 37 interactors
MINTiP04819
STRINGi4932.YDL164C

PTM databases

iPTMnetiP04819

Proteomic databases

PaxDbiP04819
PRIDEiP04819

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YDL164C
SGDiS000002323 CDC9

Phylogenomic databases

GeneTreeiENSGT00860000133792
HOGENOMiHOG000036006
InParanoidiP04819
KOiK10747
OMAiWIKYKRD
OrthoDBiEOG092C0FHN

Enzyme and pathway databases

BioCyciYEAST:G3O-29556-MONOMER
ReactomeiR-SCE-5358565 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
R-SCE-5358606 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
R-SCE-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-69183 Processive synthesis on the lagging strand

Miscellaneous databases

EvolutionaryTraceiP04819
PROiPR:P04819

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
InterProiView protein in 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
IPR036599 DNA_ligase_N_sf
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF04675 DNA_ligase_A_N, 1 hit
SUPFAMiSSF117018 SSF117018, 1 hit
SSF50249 SSF50249, 1 hit
TIGRFAMsiTIGR00574 dnl1, 1 hit
PROSITEiView protein in PROSITE
PS00697 DNA_LIGASE_A1, 1 hit
PS00333 DNA_LIGASE_A2, 1 hit
PS50160 DNA_LIGASE_A3, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDNLI1_YEAST
AccessioniPrimary (citable) accession number: P04819
Secondary accession number(s): D6VRI7, Q12736
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: November 1, 1997
Last modified: September 12, 2018
This is version 198 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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
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