Reviewed, UniProtKB/Swiss-Prot Q08387 (DNLI4_YEAST)

Names and origin

Protein names

Recommended name:
    DNA ligase 4
    EC=6.5.1.1
Alternative name(s):
    DNA ligase IV
    Polydeoxyribonucleotide synthase [ATP] 4
    DNA ligase II

Gene names

Name:	DNL4
Synonyms:	LIG4
Ordered Locus Names:	YOR005C
ORF Names:	UND407, UNE452

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	944 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Has minor DNA joining activity. Can act on oligo(PDT)/poly(rA) substrate.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Subunit structure	Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex.
Subcellular location	NucleusPotential.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 2 BRCT domains.
Sequence caution	The sequence AAC49484.1 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs. The sequence AAC49485.1 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: InterPro DNA replication Inferred from electronic annotation. Source: InterPro cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW double-strand break repair via nonhomologous end joining Inferred from direct assay. Source: SGD replicative cell aging Inferred from genetic interaction. Source: SGD
Cellular component	DNA ligase IV complex Inferred from physical interaction. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 944

944

DNA ligase 4

PRO_0000059582

Regions

Domain

681 – 780

100

BRCT 1

Domain

836 – 941

106

BRCT 2

Sites

Active site

282

1

N6-AMP-lysine intermediate By similarity

Secondary structure

1

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944

Helix Strand Turn

Details...

Beta strand

694 – 698

5

Beta strand

704 – 707

4

Helix

712 – 719

8

Beta strand

737 – 740

4

Helix

745 – 750

6

Turn

751 – 754

4

Helix

764 – 767

4

Turn

784 – 787

4

Helix

788 – 791

4

Helix

792 – 794

3

Beta strand

797 – 799

3

Beta strand

801 – 804

4

Helix

808 – 813

6

Helix

861 – 867

7

Beta strand

875 – 877

3

Beta strand

879 – 882

4

Turn

888 – 890

3

Helix

891 – 894

4

Helix

897 – 900

4

Turn

901 – 907

7

Beta strand

908 – 911

4

Beta strand

917 – 919

3

Helix

922 – 928

7

Sequences

	Sequence		Length	Mass (Da)
	Q08387-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 7FB6D7927E1719B5	FASTA	944	108,515
	10 20 30 40 50 60 MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY YEIISNFVEM 70 80 90 100 110 120 WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL KLPKNSATEQ RLKDWKQRVG 130 140 150 160 170 180 KGGNLSSLLV EEIAKRRAEP SSKAITIDNV NHYLDSLSGD RFASGRGFKS LVKSKPFLHC 190 200 210 220 230 240 VENMSFVELK YFFDIVLKNR VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR 250 260 270 280 290 300 LKDDDLSIKV GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK 310 320 330 340 350 360 FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV ILPFGLVKGS 370 380 390 400 410 420 AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR KQYLNSILSP LKNIVEIVRS 430 440 450 460 470 480 SRCYGVESIK KSLEVAISLG SEGVVLKYYN SSYNVASRNN NWIKVKPEYL EEFGENLDLI 490 500 510 520 530 540 VIGRDSGKKD SFMLGLLVLD EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI 550 560 570 580 590 600 ANGISQEEFK EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD 610 620 630 640 650 660 NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY QAERSQLGLI 670 680 690 700 710 720 RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE DTGIRITRAE LEKTIVEHGG 730 740 750 760 770 780 KLIYNVILKR HSIGDVRLIS CKTTTECKAL IDRGYDILHP NWVLDCIAYK RLILIEPNYC 790 800 810 820 830 840 FNVSQKMRAV AEKRVDCLGD SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL 850 860 870 880 890 900 FSNRIAYVPR RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE 910 920 930 940 KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes." Sterky F., Holmberg A., Pettersson B., Uhlen M. Yeast 12:1091-1095(1996) [PubMed: 8896276] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"Two distinct DNA ligase activities in mitotic extracts of the yeast Saccharomyces cerevisiae." Ramos W., Tappe N., Talamantez J., Friedberg E.C., Tomkinson A.E. Nucleic Acids Res. 25:1485-1492(1997) [PubMed: 9092653] [Abstract] Cited for: CHARACTERIZATION.
[4]	"Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4." Herrmann G., Lindahl T., Schar P. EMBO J. 17:4188-4198(1998) [PubMed: 9670033] [Abstract] Cited for: INTERACTION WITH LIF1.
[5]	"A physical and functional interaction between yeast Pol4 and Dnl4-Lif1 links DNA synthesis and ligation in nonhomologous end joining." Tseng H.-M., Tomkinson A.E. J. Biol. Chem. 277:45630-45637(2002) [PubMed: 12235149] [Abstract] Cited for: INTERACTION WITH POL4.
[6]	"Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode." Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y., Jackson S.P., Pellegrini L., Blundell T.L. DNA Repair 5:362-368(2006) [PubMed: 16388993] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 681-944 IN COMPLEX WITH LIF1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U43491 Genomic DNA. Translation: AAC49485.1. Frameshift.
U43491 Genomic DNA. Translation: AAC49484.1. Frameshift.
Z74913 Genomic DNA. Translation: CAA99193.1.

PIR

S66870.

RefSeq

NP_014647.1.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Z56	X-ray	3.92	C	681-944	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:5801N.

IntAct

Q08387.

Genome annotation databases

Ensembl

YOR005C. Saccharomyces cerevisiae. [Contig view]

GeneID

854166.

GenomeReviews

Gene locus YOR005C in contig Y13140_GR.

KEGG

sce:YOR005C.

NMPDR

fig|4932.3.peg.5742.

Organism-specific databases

CYGD

YOR005c.

SGD

S000005531. DNL4.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

Q08387.

Gene expression databases

ArrayExpress

Q08387.

GermOnline

YOR005C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001357. BRCT.
IPR000977. DNA_ligase.
IPR012310. DNA_ligase_A_M.
IPR016059. DNA_ligase_CS.
IPR012340. NA-bd_OB-fold.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.

Pfam

PF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
[Graphical view]

SMART

SM00292. BRCT. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00574. dnl1. 1 hit.

PROSITE

PS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

LinkHub

Q08387.

NextBio

975950.

Entry information

Entry name

DNLI4_YEAST

Accession

Primary (citable) accession number: Q08387
Secondary accession number(s): Q02913, Q02914

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	November 25, 2008
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)