SubmitCancel

Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q08387

- DNLI4_YEAST

UniProt

Q08387 - DNLI4_YEAST

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein
DNA ligase 4
Gene
DNL4, LIG4, YOR005C, UND407, UNE452
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).

Cofactori

Magnesium By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei280 – 2801ATP By similarity
Active sitei282 – 2821N6-AMP-lysine intermediate By similarity
Binding sitei287 – 2871ATP By similarity
Binding sitei304 – 3041ATP By similarity
Metal bindingi340 – 3401Magnesium 1 Reviewed prediction
Metal bindingi442 – 4421Magnesium 2 Reviewed prediction
Binding sitei447 – 4471ATP By similarity
Binding sitei458 – 4581ATP By similarity
Binding sitei464 – 4641ATP By 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. DNA ligation involved in DNA repair Source: InterPro
  2. DNA recombination Source: UniProtKB-KW
  3. DNA replication Source: UniProtKB-KW
  4. cell cycle Source: UniProtKB-KW
  5. cell division Source: UniProtKB-KW
  6. double-strand break repair via nonhomologous end joining Source: SGD
  7. 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 Reviewed prediction

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 4
PRO_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.2 Publications

Protein-protein interaction databases

BioGridi34408. 49 interactions.
DIPiDIP-5801N.
IntActiQ08387. 1 interaction.
MINTiMINT-672762.
STRINGi4932.YOR005C.

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiQ08387.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini681 – 780100BRCT 1
Add
BLAST
Domaini836 – 941106BRCT 2
Add
BLAST

Sequence similaritiesi

Contains 2 BRCT domains.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00750000117695.
HOGENOMiHOG000093622.
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.
IPR012340. NA-bd_OB-fold.
[Graphical view]
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

MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY    50
YEIISNFVEM WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL 100
KLPKNSATEQ RLKDWKQRVG KGGNLSSLLV EEIAKRRAEP SSKAITIDNV 150
NHYLDSLSGD RFASGRGFKS LVKSKPFLHC VENMSFVELK YFFDIVLKNR 200
VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR LKDDDLSIKV 250
GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK 300
FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV 350
ILPFGLVKGS AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR 400
KQYLNSILSP LKNIVEIVRS SRCYGVESIK KSLEVAISLG SEGVVLKYYN 450
SSYNVASRNN NWIKVKPEYL EEFGENLDLI VIGRDSGKKD SFMLGLLVLD 500
EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI ANGISQEEFK 550
EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD 600
NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY 650
QAERSQLGLI RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE 700
DTGIRITRAE LEKTIVEHGG KLIYNVILKR HSIGDVRLIS CKTTTECKAL 750
IDRGYDILHP NWVLDCIAYK RLILIEPNYC FNVSQKMRAV AEKRVDCLGD 800
SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL FSNRIAYVPR 850
RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE 900
KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY 944
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. 49 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.
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.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
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: July 9, 2014
This is version 127 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

Similar proteinsi