Reviewed, UniProtKB/Swiss-Prot P49916 (DNLI3_HUMAN)

Names and origin

Protein names

Recommended name:
    DNA ligase 3
    EC=6.5.1.1
Alternative name(s):
    DNA ligase III
    Polydeoxyribonucleotide synthase [ATP] 3

Gene names

Name:

LIG3

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1009 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subcellular location	Nucleus.
Tissue specificity	Testis, thymus, prostate and heart.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 1 BRCT domain. Contains 1 PARP-type zinc finger.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Zinc-finger
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding Zinc
Molecular function	Ligase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA repair Ref.2 Traceable author statement. Source: ProtInc DNA replication Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW reciprocal meiotic recombination Ref.2 Traceable author statement. Source: ProtInc spermatogenesis Ref.2 Traceable author statement. Source: ProtInc
Cellular component	nucleoplasm Inferred from Experiment. Source: Reactome
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Ref.2 Traceable author statement. Source: ProtInc DNA ligase (ATP) activity Inferred from electronic annotation. Source: EC magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ABL1	P00519	1	EBI-1753381,EBI-375543
CRK	P46108	1	EBI-1753381,EBI-886
PIK3R1	P27986	1	EBI-1753381,EBI-79464
PLCG1	P19174	1	EBI-1753381,EBI-79387
PNKP	Q96T60	1	EBI-1753381,EBI-1045072
SRC	P12931	1	EBI-1753381,EBI-621482
XRCC1	P18887	1	EBI-1753381,EBI-947466

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform Alpha (identifier: P49916-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform Beta (identifier: P49916-2)

The sequence of this isoform differs from the canonical sequence as follows:
     933-1009: VLLDIFTGVR...IRKRRLVAPC → RRPASEQRGRTVPAGRR

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1009

1009

DNA ligase 3

PRO_0000059574

Regions

Domain

933 – 1009

77

BRCT

Zinc finger

93 – 185

93

PARP-type

Sites

Active site

508

1

N6-AMP-lysine intermediate By similarity

Metal binding

560

1

Magnesium 1 By similarity

Metal binding

655

1

Magnesium 2 By similarity

Binding site

506

1

ATP By similarity

Binding site

513

1

ATP By similarity

Binding site

528

1

ATP By similarity

Binding site

660

1

ATP By similarity

Binding site

671

1

ATP By similarity

Binding site

675

1

ATP By similarity

Amino acid modifications

Modified residue

209

1

Phosphothreonine By similarity

Modified residue

210

1

Phosphoserine Ref.7 Ref.8 Ref.9 Ref.12

Modified residue

227

1

Phosphoserine Ref.10

Modified residue

242

1

Phosphoserine Ref.10

Modified residue

316

1

N6-acetyllysine Ref.13

Natural variations

Alternative sequence

933 – 1009

77

VLLDI…LVAPC → RRPASEQRGRTVPAGRR in isoform Beta.

VSP_001302

Natural variant

224

1

R → W: dbSNP rs3744356.

VAR_020196

Natural variant

717

1

D → N in a colorectal cancer sample; somatic mutation. Ref.16

VAR_036513

Natural variant

867

1

R → H: dbSNP rs3136025. Ref.3

VAR_018807

Natural variant

898

1

K → T: dbSNP rs4986974.

VAR_021938

Natural variant

986

1

P → S: dbSNP rs4986973.

VAR_020197

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

1009

Helix Strand Turn

Details...

Beta strand

92 – 97

6

Beta strand

117 – 124

8

Helix

140 – 149

10

Beta strand

152 – 154

3

Beta strand

161 – 165

5

Turn

166 – 168

3

Helix

171 – 185

15

Beta strand

188 – 190

3

Helix

924 – 927

4

Beta strand

936 – 938

3

Helix

952 – 962

11

Beta strand

978 – 980

3

Helix

993 – 1002

10

Sequences

	Sequence		Length	Mass (Da)
	Isoform Alpha [UniParc]. Last modified July 7, 2009. Version 2. Checksum: 0E4057E33C3F19A6	FASTA	1,009	112,907
	10 20 30 40 50 60 MSLAFKIFFP QTLRALSRKE LCLFRKHHWR DVRQFSQWSE TDLLHGHPLF LRRKPVLSFQ 70 80 90 100 110 120 GSHLRSRATY LVFLPGLHVG LCSGPCEMAE QRFCVDYAKR GTAGCKKCKE KIVKGVCRIG 130 140 150 160 170 180 KVVPNPFSES GGDMKEWYHI KCMFEKLERA RATTKKIEDL TELEGWEELE DNEKEQITQH 190 200 210 220 230 240 IADLSSKAAG TPKKKAVVQA KLTTTGQVTS PVKGASFVTS TNPRKFSGFS AKPNNSGEAP 250 260 270 280 290 300 SSPTPKRSLS SSKCDPRHKD CLLREFRKLC AMVADNPSYN TKTQIIQDFL RKGSAGDGFH 310 320 330 340 350 360 GDVYLTVKLL LPGVIKTVYN LNDKQIVKLF SRIFNCNPDD MARDLEQGDV SETIRVFFEQ 370 380 390 400 410 420 SKSFPPAAKS LLTIQEVDEF LLRLSKLTKE DEQQQALQDI ASRCTANDLK CIIRLIKHDL 430 440 450 460 470 480 KMNSGAKHVL DALDPNAYEA FKASRNLQDV VERVLHNAQE VEKEPGQRRA LSVQASLMTP 490 500 510 520 530 540 VQPMLAEACK SVEYAMKKCP NGMFSEIKYD GERVQVHKNG DHFSYFSRSL KPVLPHKVAH 550 560 570 580 590 600 FKDYIPQAFP GGHSMILDSE VLLIDNKTGK PLPFGTLGVH KKAAFQDANV CLFVFDCIYF 610 620 630 640 650 660 NDVSLMDRPL CERRKFLHDN MVEIPNRIMF SEMKRVTKAL DLADMITRVI QEGLEGLVLK 670 680 690 700 710 720 DVKGTYEPGK RHWLKVKKDY LNEGAMADTA DLVVLGAFYG QGSKGGMMSI FLMGCYDPGS 730 740 750 760 770 780 QKWCTVTKCA GGHDDATLAR LQNELDMVKI SKDPSKIPSW LKVNKIYYPD FIVPDPKKAA 790 800 810 820 830 840 VWEITGAEFS KSEAHTADGI SIRFPRCTRI RDDKDWKSAT NLPQLKELYQ LSKEKADFTV 850 860 870 880 890 900 VAGDEGSSTT GGSSEENKGP SGSAVSRKAP SKPSASTKKA EGKLSNSNSK DGNMQTAKPS 910 920 930 940 950 960 AMKVGEKLAT KSSPVKVGEK RKAADETLCQ TKVLLDIFTG VRLYLPPSTP DFSRLRRYFV 970 980 990 1000 AFDGDLVQEF DMTSATHVLG SRDKNPAAQQ VSPEWIWACI RKRRLVAPC
	Isoform Beta. Checksum: 0C10E40E0686DB77	FASTA	949	106,018
	10 20 30 40 50 60 MSLAFKIFFP QTLRALSRKE LCLFRKHHWR DVRQFSQWSE TDLLHGHPLF LRRKPVLSFQ 70 80 90 100 110 120 GSHLRSRATY LVFLPGLHVG LCSGPCEMAE QRFCVDYAKR GTAGCKKCKE KIVKGVCRIG 130 140 150 160 170 180 KVVPNPFSES GGDMKEWYHI KCMFEKLERA RATTKKIEDL TELEGWEELE DNEKEQITQH 190 200 210 220 230 240 IADLSSKAAG TPKKKAVVQA KLTTTGQVTS PVKGASFVTS TNPRKFSGFS AKPNNSGEAP 250 260 270 280 290 300 SSPTPKRSLS SSKCDPRHKD CLLREFRKLC AMVADNPSYN TKTQIIQDFL RKGSAGDGFH 310 320 330 340 350 360 GDVYLTVKLL LPGVIKTVYN LNDKQIVKLF SRIFNCNPDD MARDLEQGDV SETIRVFFEQ 370 380 390 400 410 420 SKSFPPAAKS LLTIQEVDEF LLRLSKLTKE DEQQQALQDI ASRCTANDLK CIIRLIKHDL 430 440 450 460 470 480 KMNSGAKHVL DALDPNAYEA FKASRNLQDV VERVLHNAQE VEKEPGQRRA LSVQASLMTP 490 500 510 520 530 540 VQPMLAEACK SVEYAMKKCP NGMFSEIKYD GERVQVHKNG DHFSYFSRSL KPVLPHKVAH 550 560 570 580 590 600 FKDYIPQAFP GGHSMILDSE VLLIDNKTGK PLPFGTLGVH KKAAFQDANV CLFVFDCIYF 610 620 630 640 650 660 NDVSLMDRPL CERRKFLHDN MVEIPNRIMF SEMKRVTKAL DLADMITRVI QEGLEGLVLK 670 680 690 700 710 720 DVKGTYEPGK RHWLKVKKDY LNEGAMADTA DLVVLGAFYG QGSKGGMMSI FLMGCYDPGS 730 740 750 760 770 780 QKWCTVTKCA GGHDDATLAR LQNELDMVKI SKDPSKIPSW LKVNKIYYPD FIVPDPKKAA 790 800 810 820 830 840 VWEITGAEFS KSEAHTADGI SIRFPRCTRI RDDKDWKSAT NLPQLKELYQ LSKEKADFTV 850 860 870 880 890 900 VAGDEGSSTT GGSSEENKGP SGSAVSRKAP SKPSASTKKA EGKLSNSNSK DGNMQTAKPS 910 920 930 940 AMKVGEKLAT KSSPVKVGEK RKAADETLCQ TKRRPASEQR GRTVPAGRR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination." Wei Y.-F., Robins P., Carter K., Caldecott K., Pappin D.J.C., Yu G.-L., Wang R.-P., Shell B.K., Nash R.A., Schar P., Barnes D.E., Haseltine W.A., Lindahl T. Mol. Cell. Biol. 15:3206-3216(1995) [PubMed: 7760816] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA). Tissue: Prostate.
[2]	"Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination." Chen J., Tomkinson A.E., Ramos W., Mackey Z.B., Danehower S., Walter C.A., Schultz R.A., Besterman J.M., Husain I. Mol. Cell. Biol. 15:5412-5422(1995) [PubMed: 7565692] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM BETA). Tissue: Testis.
[3]	NIEHS SNPs program Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT HIS-867.
[4]	"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage." Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C. Nature 440:1045-1049(2006) [PubMed: 16625196] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM ALPHA). Tissue: Pancreas.
[7]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, MASS SPECTROMETRY. Tissue: Epithelium.
[8]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed: 16964243] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, MASS SPECTROMETRY. Tissue: Epithelium.
[9]	"Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column." Imami K., Sugiyama N., Kyono Y., Tomita M., Ishihama Y. Anal. Sci. 24:161-166(2008) [PubMed: 18187866] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, MASS SPECTROMETRY.
[10]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-227 AND SER-242, MASS SPECTROMETRY.
[11]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[12]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, MASS SPECTROMETRY. Tissue: T-cell.
[13]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-316, MASS SPECTROMETRY.
[14]	"Expression, purification, and biophysical characterization of the BRCT domain of human DNA ligase IIIalpha." Thornton K.H., Krishnan V.V., West M.G., Popham J., Ramirez M., Thelen M.P., Cosman M. Protein Expr. Purif. 21:401-411(2001) [PubMed: 11281714] [Abstract] Cited for: STRUCTURE BY NMR OF 924-1009.
[15]	"Solution structure and DNA binding of the zinc-finger domain from DNA ligase IIIalpha." Kulczyk A.W., Yang J.C., Neuhaus D. J. Mol. Biol. 341:723-738(2004) [PubMed: 15288782] [Abstract] Cited for: STRUCTURE BY NMR OF 1-204.
[16]	"The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. Science 314:268-274(2006) [PubMed: 16959974] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] ASN-717.
+	Additional computationally mapped references.

Web resources

Wikipedia

DNA ligase entry

NIEHS-SNPs

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X84740 mRNA. Translation: CAA59230.1. Different initiation.
U40671 mRNA. Translation: AAA85022.1. Different initiation.
AF491645 Genomic DNA. Translation: AAL91592.1. Different initiation.
AC004223 Genomic DNA. No translation available.
AC022903 Genomic DNA. No translation available.
CH471147 Genomic DNA. Translation: EAW80199.1.
BC068005 mRNA. Translation: AAH68005.1.

IPI

IPI00000156.
IPI00029081.

PIR

I37292.

RefSeq

NP_002302.2.
NP_039269.2.

UniGene

Hs.100299

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IMO	NMR	-	A	924-1009	[»]
1IN1	NMR	-	A	924-1009	[»]
1UW0	NMR	-	A	88-204	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P49916. 7 interactions.

STRING

P49916.

PTM databases

PhosphoSite

P49916.

Proteomic databases

PRIDE

P49916.

Genome annotation databases

Ensembl

ENST00000378526; ENSP00000367787; ENSG00000005156; Homo sapiens. [Genome view]

GeneID

3980.

KEGG

hsa:3980.

UCSC

uc002hij.1. human.
uc002hik.1. human.

Organism-specific databases

CTD

3980.

GeneCards

GC17P030331.

H-InvDB

HIX0027160.

HGNC

HGNC:6600. LIG3.

MIM

600940. gene.

PharmGKB

PA30374.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

HBG357148.

HOVERGEN

P49916.

InParanoid

P49916.

OMA

RKAADET.

OrthoDB

EOG9J403C.

PhylomeDB

P49916.

Enzyme and pathway databases

BRENDA

6.5.1.1. 247.

Reactome

REACT_216. DNA Repair.

Gene expression databases

ArrayExpress

P49916.

Bgee

P49916.

CleanEx

HS_LIG3.

Genevestigator

P49916.

GermOnline

ENSG00000005156. Homo sapiens.

Family and domain databases

InterPro

IPR001357. BRCT.
IPR000977. DNA_ligase.
IPR012309. DNA_ligase_A_C.
IPR012310. DNA_ligase_A_M.
IPR016059. DNA_ligase_CS.
IPR012340. NA-bd_OB-fold.
IPR001510. Znf_PARP.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
G3DSA:3.30.1740.10. Znf_PARP. 1 hit.

Pfam

PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF00645. zf-PARP. 1 hit.
[Graphical view]

SMART

SM00292. BRCT. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00574. dnl1. 1 hit.

PROSITE

PS50172. BRCT. 1 hit.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
PS00347. PARP_ZN_FINGER_1. 1 hit.
PS50064. PARP_ZN_FINGER_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00290. Bleomycin.

NextBio

15598.

SOURCE

Search...

Entry information

Entry name

DNLI3_HUMAN

Accession

Primary (citable) accession number: P49916
Secondary accession number(s): Q16714, Q6NVK3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	July 7, 2009
Last modified:	February 9, 2010
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.