DNA ligase 4 - Saccharomyces cerevisiae (Baker's 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

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Protein attributes

Sequence length	944 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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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).
Cofactor	Magnesium By similarity.
Subunit structure	Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex. Ref.4 Ref.5
Subcellular location	Nucleus Potential.
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.

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Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW 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: 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...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
LIF1	P53150	2	EBI-5983,EBI-23865

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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

Metal binding

340

1

Magnesium 1 Potential

Metal binding

442

1

Magnesium 2 Potential

Binding site

280

1

ATP By similarity

Binding site

287

1

ATP By similarity

Binding site

304

1

ATP By similarity

Binding site

447

1

ATP By similarity

Binding site

458

1

ATP By similarity

Binding site

464

1

ATP By similarity

Secondary structure

1

.

944

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q08387-1 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 7FB6D7927E1719B5
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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

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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. 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.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

PDBe
RCSB PDB
PDBj

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. 16 interactions.

STRING

Q08387.

Genome annotation databases

Ensembl

YOR005C; YOR005C; YOR005C; Saccharomyces cerevisiae. [Genome view]

GeneID

854166.

KEGG

sce:YOR005C.

NMPDR

fig|4932.3.peg.5742.

Organism-specific databases

CYGD

YOR005c.

SGD

S000005531. DNL4.

Phylogenomic databases

eggNOG

HOGENOM

OMA

OrthoDB

PhylomeDB

Q08387.

Enzyme and pathway databases

BRENDA

6.5.1.1. 250.

Gene expression databases

ArrayExpress

Q08387.

Genevestigator

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

NextBio

975950.

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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:	February 9, 2010
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents