DNA ligase 4 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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Q08387 (DNLI4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 115. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA ligase 4
EC=6.5.1.1

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

Gene names

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

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	944 AA.
Sequence status	Complete.
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).
Cofactor	Magnesium By similarity.
Subunit structure	Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex. Ref.5 Ref.6
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.

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 Reference proteome
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro 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 PubMed 15342630. Source: SGD replicative cell aging Inferred from genetic interaction PubMed 18627461. Source: SGD
Cellular_component	DNA ligase IV complex Inferred from physical interaction PubMed 17567543. 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 9242411. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
LIF1	P53150	3	EBI-5983,EBI-23865

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

N6-AMP-lysine intermediate By similarity

Metal binding

340

Magnesium 1 Potential

Metal binding

442

Magnesium 2 Potential

Binding site

280

ATP By similarity

Binding site

287

ATP By similarity

Binding site

304

ATP By similarity

Binding site

447

ATP By similarity

Binding site

458

ATP By similarity

Binding site

464

ATP By similarity

Secondary structure

944

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q08387 [UniParc].

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

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[5]	"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] [Europe PMC] [Abstract] Cited for: INTERACTION WITH LIF1.
[6]	"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] [Europe PMC] [Abstract] Cited for: INTERACTION WITH POL4.
[7]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 681-944 IN COMPLEX WITH LIF1.
+	Additional computationally mapped references.

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.
BK006948 Genomic DNA. Translation: DAA10787.1.

PIR

S66870.

RefSeq

NP_014647.1. NM_001183424.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

Q08387.

SMR

Q08387. Positions 13-599, 683-939.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5801N.

IntAct

Q08387. 16 interactions.

MINT

MINT-672762.

STRING

4932.YOR005C.

Proteomic databases

PaxDb

Q08387.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOR005C; YOR005C; YOR005C.

GeneID

854166.

KEGG

sce:YOR005C.

Organism-specific databases

CYGD

YOR005c.

SGD

S000005531. DNL4.

Phylogenomic databases

eggNOG

COG1793.

GeneTree

ENSGT00700000104500.

HOGENOM

HOG000093622.

K10777.

OMA

CSIANGI.

OrthoDB

EOG41K2MD.

Enzyme and pathway databases

BRENDA

6.5.1.1. 984.

Gene expression databases

Genevestigator

Q08387.

GermOnline

YOR005C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

InterPro

IPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
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

PF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]

SMART

SM00292. BRCT. 1 hit.
[Graphical view]

SUPFAM

SSF52113. BRCT. 2 hits.
SSF50249. Nucleic_acid_OB. 1 hit.

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

EvolutionaryTrace

Q08387.

NextBio

975950.

Entry information

Entry name

DNLI4_YEAST

Accession

Primary (citable) accession number: Q08387
Secondary accession number(s): D6W271, Q02913, Q02914

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 115 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

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

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents