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Q08387

- DNLI4_YEAST

UniProt

Q08387 - DNLI4_YEAST

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Protein

DNA ligase 4

Gene

DNL4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Has minor DNA joining activity. Can act on oligo(PDT)/poly(rA) substrate.

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

Cofactori

Magnesium.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei280 – 2801ATPBy similarity
Active sitei282 – 2821N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei287 – 2871ATPBy similarity
Binding sitei304 – 3041ATPBy similarity
Metal bindingi340 – 3401Magnesium 1Sequence Analysis
Metal bindingi442 – 4421Magnesium 2Sequence Analysis
Binding sitei447 – 4471ATPBy similarity
Binding sitei458 – 4581ATPBy similarity
Binding sitei464 – 4641ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: InterPro
  3. DNA ligase (ATP) activity Source: SGD
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. DNA biosynthetic process Source: InterPro
  4. DNA ligation involved in DNA repair Source: InterPro
  5. DNA recombination Source: UniProtKB-KW
  6. DNA replication Source: UniProtKB-KW
  7. double-strand break repair via nonhomologous end joining Source: SGD
  8. replicative cell aging Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33555-MONOMER.
BRENDAi6.5.1.1. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 4 (EC:6.5.1.1)
Alternative name(s):
DNA ligase II
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene namesi
Name:DNL4
Synonyms:LIG4
Ordered Locus Names:YOR005C
ORF Names:UND407, UNE452
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

CYGDiYOR005c.
SGDiS000005531. DNL4.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. DNA ligase IV complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 944944DNA ligase 4PRO_0000059582Add
BLAST

Proteomic databases

PaxDbiQ08387.

Expressioni

Gene expression databases

GenevestigatoriQ08387.

Interactioni

Subunit structurei

Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex.3 Publications

Protein-protein interaction databases

BioGridi34408. 50 interactions.
DIPiDIP-5801N.
IntActiQ08387. 1 interaction.
MINTiMINT-672762.
STRINGi4932.YOR005C.

Structurei

Secondary structure

1
944
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi694 – 6985
Beta strandi704 – 7074
Helixi712 – 7198
Beta strandi737 – 7404
Helixi745 – 7506
Turni751 – 7544
Helixi764 – 7674
Turni784 – 7874
Helixi788 – 7914
Helixi792 – 7943
Beta strandi797 – 7993
Beta strandi801 – 8044
Helixi808 – 8136
Helixi861 – 8677
Beta strandi875 – 8773
Beta strandi879 – 8824
Turni888 – 8903
Helixi891 – 8944
Helixi897 – 9004
Turni901 – 9077
Beta strandi908 – 9114
Beta strandi917 – 9193
Helixi922 – 9287

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Z56X-ray3.92C681-943[»]
ProteinModelPortaliQ08387.
SMRiQ08387. Positions 43-599, 683-939.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08387.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini681 – 780100BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini836 – 941106BRCT 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 2 BRCT domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00750000117695.
HOGENOMiHOG000093622.
InParanoidiQ08387.
KOiK10777.
OMAiISHFLCA.
OrthoDBiEOG7QC84G.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR001357. 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.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 2 hits.
SSF52113. SSF52113. 3 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08387-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY
60 70 80 90 100
YEIISNFVEM WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL
110 120 130 140 150
KLPKNSATEQ RLKDWKQRVG KGGNLSSLLV EEIAKRRAEP SSKAITIDNV
160 170 180 190 200
NHYLDSLSGD RFASGRGFKS LVKSKPFLHC VENMSFVELK YFFDIVLKNR
210 220 230 240 250
VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR LKDDDLSIKV
260 270 280 290 300
GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK
310 320 330 340 350
FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV
360 370 380 390 400
ILPFGLVKGS AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR
410 420 430 440 450
KQYLNSILSP LKNIVEIVRS SRCYGVESIK KSLEVAISLG SEGVVLKYYN
460 470 480 490 500
SSYNVASRNN NWIKVKPEYL EEFGENLDLI VIGRDSGKKD SFMLGLLVLD
510 520 530 540 550
EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI ANGISQEEFK
560 570 580 590 600
EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD
610 620 630 640 650
NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY
660 670 680 690 700
QAERSQLGLI RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE
710 720 730 740 750
DTGIRITRAE LEKTIVEHGG KLIYNVILKR HSIGDVRLIS CKTTTECKAL
760 770 780 790 800
IDRGYDILHP NWVLDCIAYK RLILIEPNYC FNVSQKMRAV AEKRVDCLGD
810 820 830 840 850
SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL FSNRIAYVPR
860 870 880 890 900
RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE
910 920 930 940
KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY
Length:944
Mass (Da):108,515
Last modified:November 1, 1996 - v1
Checksum:i7FB6D7927E1719B5
GO

Sequence cautioni

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.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiS66870.
RefSeqiNP_014647.1. NM_001183424.1.

Genome annotation databases

EnsemblFungiiYOR005C; YOR005C; YOR005C.
GeneIDi854166.
KEGGisce:YOR005C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi S66870.
RefSeqi NP_014647.1. NM_001183424.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1Z56 X-ray 3.92 C 681-943 [» ]
ProteinModelPortali Q08387.
SMRi Q08387. Positions 43-599, 683-939.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34408. 50 interactions.
DIPi DIP-5801N.
IntActi Q08387. 1 interaction.
MINTi MINT-672762.
STRINGi 4932.YOR005C.

Proteomic databases

PaxDbi Q08387.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOR005C ; YOR005C ; YOR005C .
GeneIDi 854166.
KEGGi sce:YOR005C.

Organism-specific databases

CYGDi YOR005c.
SGDi S000005531. DNL4.

Phylogenomic databases

eggNOGi COG1793.
GeneTreei ENSGT00750000117695.
HOGENOMi HOG000093622.
InParanoidi Q08387.
KOi K10777.
OMAi ISHFLCA.
OrthoDBi EOG7QC84G.

Enzyme and pathway databases

BioCyci YEAST:G3O-33555-MONOMER.
BRENDAi 6.5.1.1. 984.

Miscellaneous databases

EvolutionaryTracei Q08387.
NextBioi 975950.
PROi Q08387.

Gene expression databases

Genevestigatori Q08387.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
InterProi 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.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
PANTHERi PTHR10459:SF7. PTHR10459:SF7. 1 hit.
Pfami PF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view ]
SMARTi SM00292. BRCT. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 2 hits.
SSF52113. SSF52113. 3 hits.
TIGRFAMsi TIGR00574. dnl1. 1 hit.
PROSITEi PS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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.

Entry informationi

Entry nameiDNLI4_YEAST
AccessioniPrimary (citable) accession number: Q08387
Secondary accession number(s): D6W271, Q02913, Q02914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: October 29, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

External Data

Dasty 3