P04819 (DNLI1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	755 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Mitochondrion Nucleus
Coding sequence diversity	Alternative initiation
Domain	Transit peptide
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	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 mutant phenotype PubMed 9759502. 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_component	mitochondrion 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_function	ATP 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 44

44

Mitochondrion Potential

Chain

45 – 755

711

DNA ligase 1

PRO_0000007274

Regions

Region

309 – 318

10

Interaction with target DNA By similarity

Region

493 – 495

3

Interaction with target DNA By similarity

Sites

Active site

419

1

N6-AMP-lysine intermediate By similarity

Metal binding

472

1

Magnesium 1 By similarity

Metal binding

571

1

Magnesium 2 By similarity

Binding site

417

1

ATP By similarity

Binding site

424

1

ATP By similarity

Binding site

440

1

ATP By similarity

Binding site

576

1

ATP By similarity

Binding site

590

1

ATP By similarity

Binding site

596

1

ATP By similarity

Site

164

1

Interaction with target DNA By similarity

Site

441

1

Interaction with target DNA By similarity

Site

622

1

Interaction with target DNA By similarity

Site

647

1

Interaction with target DNA By similarity

Amino acid modifications

Modified residue

58

1

Phosphoserine Ref.8 Ref.9 Ref.10

Modified residue

75

1

Phosphoserine Ref.8 Ref.10

Natural variations

Alternative sequence

1 – 23

23

Missing in isoform Nuclear.

VSP_018719

Experimental info

Sequence conflict

69

1

D → E in CAA27005. Ref.1

Sequence conflict

186

1

L → V in CAA27005. Ref.1

Sequence conflict

671

1

G → E in CAA48158. Ref.5

Sequence conflict

724

1

R → I in CAA48158. Ref.5

Secondary structure

1

.

.

.

755

Helix Strand Turn

Details...

Helix

41 – 44

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform Mitochondrial [UniParc]. Last modified November 1, 1997. Version 2. Checksum: B7C2ECAF5C61CAE7	FASTA	755	84,828
	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
	Isoform Nuclear [UniParc]. Checksum: B5267D6EE0C5C798	FASTA	732	82,251
	10 20 30 40 50 60 MSSSLPSSAG KKPKQATLAR FFTSMKNKPT EGTPSPKKSS KHMLEDRMDN VSGEEEYATK 70 80 90 100 110 120 KLKQTAVTHT VAAPSSMGSN FSSIPSSAPS SGVADSPQQS QRLVGEVEDA LSSNNNDHYS 130 140 150 160 170 180 SNIPYSEVCE VFNKIEAISS RLEIIRICSD FFIKIMKQSS KNLIPTTYLF INRLGPDYEA 190 200 210 220 230 240 GLELGLGENL LMKTISETCG KSMSQIKLKY KDIGDLGEIA MGARNVQPTM FKPKPLTVGE 250 260 270 280 290 300 VFKNLRAIAK TQGKDSQLKK MKLIKRMLTA CKGIEAKFLI RSLESKLRIG LAEKTVLISL 310 320 330 340 350 360 SKALLLHDEN REDSPDKDVP MDVLESAQQK IRDAFCQVPN YEIVINSCLE HGIMNLDKYC 370 380 390 400 410 420 TLRPGIPLKP MLAKPTKAIN EVLDRFQGET FTSEYKYDGE RAQVHLLNDG TMRIYSRNGE 430 440 450 460 470 480 NMTERYPEIN ITDFIQDLDT TKNLILDCEA VAWDKDQGKI LPFQVLSTRK RKDVELNDVK 490 500 510 520 530 540 VKVCLFAFDI LCYNDERLIN KSLKERREYL TKVTKVVPGE FQYATQITTN NLDELQKFLD 550 560 570 580 590 600 ESVNHSCEGL MVKMLEGPES HYEPSKRSRN WLKLKKDYLE GVGDSLDLCV LGAYYGRGKR 610 620 630 640 650 660 TGTYGGFLLG CYNQDTGEFE TCCKIGTGFS DEMLQLLHDR LTPTIIDGPK ATFVFDSSAE 670 680 690 700 710 720 PDVWFEPTTL FEVLTADLSL SPIYKAGSAT FDKGVSLRFP RFLRIREDKG VEDATSSDQI 730 VELYENQSHM QN

References

	« Hide 'large scale' referencesShow '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. , 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]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. , 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, MASS SPECTROMETRY.
[9]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58, MASS SPECTROMETRY.
[10]	"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, MASS SPECTROMETRY.
+	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.

PIR

LQBYPX. S61049.

RefSeq

NP_010117.1. NM_001180224.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2OD8	X-ray	2.80	B	32-53	[»]

ProteinModelPortal

P04819.

SMR

P04819. Positions 146-751.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5630N.

IntAct

P04819. 23 interactions.

MINT

MINT-499551.

STRING

4932.YDL164C.

Proteomic databases

PaxDb

P04819.

PeptideAtlas

P04819.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL164C; YDL164C; YDL164C.

GeneID

851391.

KEGG

sce:YDL164C.

Organism-specific databases

CYGD

YDL164c.

SGD

S000002323. CDC9.

Phylogenomic databases

eggNOG

COG1793.

GeneTree

ENSGT00700000104556.

HOGENOM

HOG000036006.

KO

K10747.

OMA

AQVACLY.

OrthoDB

EOG4RV60K.

Gene expression databases

Genevestigator

P04819.

GermOnline

YDL164C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.

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.
[Graphical view]

Pfam

PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.
SSF117018. SSF117018. 1 hit.

TIGRFAMs

TIGR00574. dnl1. 1 hit.

PROSITE

PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P04819.

NextBio

968546.

Entry information

Entry name

DNLI1_YEAST

Accession

Primary (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:	May 1, 2013
This is version 148 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program