Reviewed, UniProtKB/Swiss-Prot P04819 (DNLI1_YEAST)

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 (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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	Nucleus. Mitochondrion.
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. Ref.6
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
Gene Ontology (GO)
Biological process	DNA ligation Inferred from direct assay. Source: SGD DNA recombination Inferred from mutant phenotype. Source: SGD base-excision repair Inferred from mutant phenotype. Source: SGD cell division Inferred from electronic annotation. Source: UniProtKB-KW lagging strand elongation Inferred from direct assay. Source: SGD mitotic cell cycle Inferred from mutant phenotype. Source: SGD nucleotide-excision repair Inferred from mutant phenotype. Source: SGD
Cellular component	mitochondrion Ref.5 Inferred from direct assay. Source: SGD nucleus Ref.5 Inferred from direct assay. Source: SGD replication fork Non-traceable author statement. 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. Source: SGD magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ABP1	P15891	1	EBI-5991,EBI-2036
DBP5	P20449	1	EBI-1009737,EBI-5617
ECM4	P36156	1	EBI-1009737,EBI-2042717

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.

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.7 Ref.8 Ref.9
	Modified residue	75	1	Phosphoserine Ref.7 Ref.9
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.4
	Sequence conflict	724	1	R → I in CAA48158. Ref.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. 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: 3909103] [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: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"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: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"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: 8483449] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 610-755. Strain: ATCC 38626 / AH22 / NRRL Y-12843.
[5]	"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: 10531002] [Abstract] Cited for: ALTERNATIVE INITIATION.
[6]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"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: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, MASS SPECTROMETRY.
[8]	"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: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58, MASS SPECTROMETRY.
[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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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.

PIR

LQBYPX. S61049.

RefSeq

NP_010117.1.

3D structure databases

PDBPDBe

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

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:5630N.

IntAct

P04819. 22 interactions.

Proteomic databases

PeptideAtlas

P04819.

PRIDE

P04819.

Genome annotation databases

Ensembl

YDL164C. Saccharomyces cerevisiae. [Contig view]

GeneID

851391.

GenomeReviews

Gene locus YDL164C in contig Z71256_GR.

KEGG

sce:YDL164C.

NMPDR

fig|4932.3.peg.851.

Organism-specific databases

CYGD

YDL164c.

SGD

S000002323. CDC9.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P04819.

OMA

P04819. RNWLKLK.

Enzyme and pathway databases

BRENDA

6.5.1.1. 250.

Gene expression databases

ArrayExpress

P04819.

GermOnline

YDL164C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000977. DNA_ligase.
IPR012309. DNA_ligase_A_C.
IPR012310. DNA_ligase_A_M.
IPR012308. DNA_ligase_A_N.
IPR016059. DNA_ligase_CS.
IPR012340. NA-bd_OB-fold.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.

Pfam

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

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 Resources

NextBio

968546.

Entry information

Entry name

DNLI1_YEAST

Accession

Primary (citable) accession number: P04819
Secondary accession number(s): Q12736

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 107 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)