Q6C8A3 (DNLI4_YARLI) Reviewed, UniProtKB/Swiss-Prot

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

Gene names

Name:	LIG4
Ordered Locus Names:	YALI0D21384g

Organism

Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica) [Reference proteome]

Taxonomic identifier

284591 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Dipodascaceae › Yarrowia › Yarrowia lipolytica

Protein attributes

Sequence length	956 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Involved in ds DNA break repair. Has a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining By similarity.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 2 BRCT domains.

Ontologies

Keywords
Biological process	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	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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 electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 956	956	DNA ligase 4		PRO_0000278386
Regions
	Domain	700 – 793	94	BRCT 1
	Domain	857 – 956	100	BRCT 2
Sites
	Active site	309	1	N6-AMP-lysine intermediate By similarity
	Metal binding	371	1	Magnesium 1 Potential
	Metal binding	476	1	Magnesium 2 Potential
	Binding site	307	1	ATP By similarity
	Binding site	314	1	ATP By similarity
	Binding site	331	1	ATP By similarity
	Binding site	481	1	ATP By similarity
	Binding site	492	1	ATP By similarity
	Binding site	498	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q6C8A3 [UniParc]. Last modified August 16, 2004. Version 1. Checksum: 5169CFB807F4183B	FASTA	956	108,061
	10 20 30 40 50 60 MSSERRPELE ETAVDPATGS AASRKFSIVQ DAVETTIVAP TNHGPSPRFS TLVRNLFEPL 70 80 90 100 110 120 VNLSAVVAAL RKKPTEAKAH IASQFIKGWV EEVGKDIYPA FRLILPDKDR ERAVYGLKEK 130 140 150 160 170 180 ALGRLWVKVL NLAKDSPDAK ALSEWKQGGN ESAGNFSKRC YEVLSKRTSL TDYGHMTVDE 190 200 210 220 230 240 VNERLDLLAD GETDQAKQIE ILTYFYKHMN ATELKWLVNI ILRQMKMNAT EKVFFEPWHP 250 260 270 280 290 300 DAESLFNVTA SLKRVCWELT DPTKRLTSAE AQVSLFACFM PQIAAFPKYS GQDIAGKHFK 310 320 330 340 350 360 GRPFYIEEKI DGERMQMHMS EYGNKFHWWS RRSKDFTETY GNSLDDASGS LTKRLRGIIN 370 380 390 400 410 420 PKVRNCVLDG EMVAYDPATK KIIPFGTLRT ANRNEQNDLN LTKPMFMVFD ILLLNDKPLV 430 440 450 460 470 480 DYTLAERKRT LRTIFARTDN ETVGQEGVLE VLPYTEATTA AEIETCMRKI IAESSEGLVI 490 500 510 520 530 540 KDPTSVYRVN TRDDSWLKMK PEYMSEFGEK LDVVIIGGYY GSGKRGSILS SYLCGLRADG 550 560 570 580 590 600 SDQFWSFFKV GGGLTAGDYQ AIRTKTEGKW KRWDKNDKPK NVLLAGPNGD LERPDVWIEP 610 620 630 640 650 660 SDSVVVEVKA ASVVASDQYK VGLCLRFPRF RALRLDKTWE DGLTISQFAE LRQTVEMEAE 670 680 690 700 710 720 NKELELEDRK RRNAGPGRGA KRLKLANVSS DEDELGTDER PTSVFKATSF AVLSDMSSPR 730 740 750 760 770 780 YMSKAAVENL IKKHGGTVFQ TVEGPHTIPV ADTRTIKVQA LTKRVHGVDV IRPNWLLDCI 790 800 810 820 830 840 NEEKLVALEP RNLLESSAET LALAKTNVDE FGDSYTRPLT YKEMQEVLRF MDQFDLDQTN 850 860 870 880 890 900 PPDLMMEVLE TNDGAVPKGM LFYGKKVYMS TSNMDTVALE TQFRAYDALR CLQFGGANLV 910 920 930 940 950 TDMKDLVVAV AKTEEEAKEL RRVSSEQVFP FRVVSIKWVE ESWKNGTVEI EDDYPL

References

[1]

"Genome evolution in yeasts." Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I., de Montigny J., Marck C., Neuveglise C., Talla E., Goffard N., Frangeul L., Aigle M., Anthouard V., Babour A., Barbe V., Barnay S., Blanchin S. , Beckerich J.-M., Beyne E., Bleykasten C., Boisrame A., Boyer J., Cattolico L., Confanioleri F., de Daruvar A., Despons L., Fabre E., Fairhead C., Ferry-Dumazet H., Groppi A., Hantraye F., Hennequin C., Jauniaux N., Joyet P., Kachouri R., Kerrest A., Koszul R., Lemaire M., Lesur I., Ma L., Muller H., Nicaud J.-M., Nikolski M., Oztas S., Ozier-Kalogeropoulos O., Pellenz S., Potier S., Richard G.-F., Straub M.-L., Suleau A., Swennen D., Tekaia F., Wesolowski-Louvel M., Westhof E., Wirth B., Zeniou-Meyer M., Zivanovic Y., Bolotin-Fukuhara M., Thierry A., Bouchier C., Caudron B., Scarpelli C., Gaillardin C., Weissenbach J., Wincker P., Souciet J.-L. Nature 430:35-44(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CLIB 122 / E 150.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CR382130 Genomic DNA. Translation: CAG81303.1.
RefSeq	XP_503109.1. XM_503109.1.
3D structure databases
ProteinModelPortal	Q6C8A3.
ModBase	Search...
Protein-protein interaction databases
STRING	4952.Q6C8A3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	2911076.
KEGG	yli:YALI0D21384g.
Phylogenomic databases
eggNOG	COG1793.
HOGENOM	HOG000176213.
KO	K10777.
OMA	CSIANGI.
OrthoDB	EOG41K2MD.
Family and domain databases
Gene3D	2.40.50.140. 1 hit.
InterPro	IPR001357. BRCT_dom. IPR000977. DNA_ligase_ATP-dep. IPR012309. DNA_ligase_ATP-dep_C. IPR012310. DNA_ligase_ATP-dep_cent. IPR012308. DNA_ligase_ATP-dep_N. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF00533. BRCT. 1 hit. PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SMART	SM00292. BRCT. 2 hits. [Graphical view]
SUPFAM	SSF52113. BRCT. 1 hit. SSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS50172. BRCT. 2 hits. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI4_YARLI

Accession

Primary (citable) accession number: Q6C8A3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 20, 2007
Last sequence update:	August 16, 2004
Last modified:	May 1, 2013
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program