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Protein

DNA ligase 3

Gene

LIG3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Isoform 3 functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair (PubMed:10207110, PubMed:24674627).2 Publications

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation2 Publications

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei506 – 5061ATPCombined sourcesCurated
Active sitei508 – 5081N6-AMP-lysine intermediatePROSITE-ProRule annotation1 Publication
Binding sitei513 – 5131ATPCombined sourcesCurated
Binding sitei528 – 5281ATPBy similarity
Metal bindingi560 – 5601Magnesium 1By similarity
Metal bindingi655 – 6551Magnesium 2By similarity
Binding sitei660 – 6601ATPCombined sourcesCurated
Binding sitei671 – 6711ATPBy similarity
Binding sitei675 – 6751ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri93 – 18593PARP-typePROSITE-ProRule annotation1 PublicationAdd
BLAST

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: InterPro
  • DNA ligase (ATP) activity Source: BHF-UCL
  • DNA ligase activity Source: BHF-UCL
  • zinc ion binding Source: InterPro

GO - Biological processi

  • base-excision repair Source: Reactome
  • base-excision repair, DNA ligation Source: BHF-UCL
  • cell cycle Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • DNA biosynthetic process Source: InterPro
  • DNA ligation Source: BHF-UCL
  • DNA recombination Source: UniProtKB-KW
  • DNA repair Source: Reactome
  • DNA replication Source: UniProtKB-KW
  • double-strand break repair Source: BHF-UCL
  • double-strand break repair via alternative nonhomologous end joining Source: BHF-UCL
  • double-strand break repair via nonhomologous end joining Source: Ensembl
  • mitochondrial DNA repair Source: BHF-UCL
  • mitochondrion organization Source: BHF-UCL
  • negative regulation of DNA recombination Source: Ensembl
  • negative regulation of mitochondrial DNA replication Source: CACAO
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, Zinc

Enzyme and pathway databases

BRENDAi6.5.1.1. 2681.
ReactomeiREACT_355367. APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
REACT_933. Resolution of AP sites via the single-nucleotide replacement pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 3 (EC:6.5.1.12 Publications)
Alternative name(s):
DNA ligase III
Polydeoxyribonucleotide synthase [ATP] 3
Gene namesi
Name:LIG3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:6600. LIG3.

Subcellular locationi

Isoform 1 :
  • Mitochondrion 2 Publications

  • Note: Contains an N-terminal mitochondrial transit peptide.1 Publication
Isoform 2 :
  • Mitochondrion 1 Publication

  • Note: Contains an N-terminal mitochondrial transit peptide.1 Publication
Isoform 3 :
  • Nucleus 1 Publication

  • Note: Lacks the N-terminal mitochondrial transit peptide.1 Publication
Isoform 4 :
  • Nucleus 1 Publication

  • Note: Lacks the N-terminal mitochondrial transit peptide.1 Publication

GO - Cellular componenti

  • DNA ligase III-XRCC1 complex Source: BHF-UCL
  • mitochondrion Source: BHF-UCL
  • nucleoplasm Source: HPA
  • nucleus Source: BHF-UCL
  • synaptonemal complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi410 – 4101K → E: Nearly abolishes ligase activity with blunt-ended DNA, but not with nicked DNA. 1 Publication
Mutagenesisi414 – 4141R → E: Abolishes ligase activity with blunt-ended DNA, but not with nicked DNA. 1 Publication

Organism-specific databases

PharmGKBiPA30374.

Chemistry

DrugBankiDB00290. Bleomycin.

Polymorphism and mutation databases

BioMutaiLIG3.
DMDMi251757259.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4242MitochondrionSequence AnalysisAdd
BLAST
Chaini43 – 1009967DNA ligase 3PRO_0000059574Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei210 – 2101Phosphoserine3 Publications
Modified residuei227 – 2271Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP49916.
PaxDbiP49916.
PRIDEiP49916.

PTM databases

PhosphoSiteiP49916.

Expressioni

Tissue specificityi

Testis, thymus, prostate and heart.

Gene expression databases

BgeeiP49916.
CleanExiHS_LIG3.
ExpressionAtlasiP49916. baseline and differential.
GenevestigatoriP49916.

Organism-specific databases

HPAiHPA006723.

Interactioni

Subunit structurei

Isoform 3 interacts (via BRCT domain) with the nuclear DNA-repair protein XRCC1.2 Publications

Protein-protein interaction databases

BioGridi110168. 39 interactions.
IntActiP49916. 11 interactions.
MINTiMINT-4531178.
STRINGi9606.ENSP00000367787.

Structurei

Secondary structure

1
1009
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi92 – 976Combined sources
Beta strandi117 – 1248Combined sources
Helixi140 – 14910Combined sources
Beta strandi152 – 1543Combined sources
Beta strandi161 – 1655Combined sources
Turni166 – 1683Combined sources
Helixi171 – 18515Combined sources
Beta strandi188 – 1903Combined sources
Helixi259 – 2613Combined sources
Helixi263 – 27412Combined sources
Helixi279 – 29113Combined sources
Helixi303 – 3108Combined sources
Turni312 – 3143Combined sources
Helixi323 – 33412Combined sources
Helixi338 – 3447Combined sources
Helixi345 – 3473Combined sources
Helixi350 – 35910Combined sources
Beta strandi362 – 3643Combined sources
Helixi374 – 38512Combined sources
Helixi390 – 40112Combined sources
Helixi407 – 41610Combined sources
Beta strandi421 – 4233Combined sources
Helixi426 – 4316Combined sources
Helixi437 – 4437Combined sources
Helixi447 – 45913Combined sources
Beta strandi485 – 4884Combined sources
Helixi492 – 4987Combined sources
Beta strandi503 – 5075Combined sources
Beta strandi511 – 5199Combined sources
Beta strandi522 – 5265Combined sources
Helixi535 – 5373Combined sources
Turni538 – 5403Combined sources
Helixi541 – 5433Combined sources
Helixi545 – 5484Combined sources
Beta strandi553 – 56412Combined sources
Turni566 – 5683Combined sources
Helixi574 – 5774Combined sources
Helixi579 – 5846Combined sources
Beta strandi590 – 60011Combined sources
Helixi610 – 62011Combined sources
Turni625 – 6273Combined sources
Beta strandi628 – 6303Combined sources
Beta strandi633 – 6364Combined sources
Helixi639 – 65113Combined sources
Beta strandi657 – 6637Combined sources
Beta strandi671 – 6766Combined sources
Turni678 – 6803Combined sources
Beta strandi688 – 69811Combined sources
Beta strandi710 – 7167Combined sources
Turni718 – 7203Combined sources
Beta strandi721 – 7299Combined sources
Helixi735 – 7406Combined sources
Turni741 – 7433Combined sources
Beta strandi780 – 7878Combined sources
Beta strandi789 – 7913Combined sources
Beta strandi795 – 7973Combined sources
Beta strandi800 – 8045Combined sources
Beta strandi816 – 8194Combined sources
Helixi822 – 8309Combined sources
Helixi924 – 9274Combined sources
Turni930 – 9323Combined sources
Beta strandi936 – 9383Combined sources
Beta strandi942 – 9443Combined sources
Helixi952 – 96110Combined sources
Helixi969 – 9746Combined sources
Beta strandi976 – 9805Combined sources
Beta strandi982 – 9843Combined sources
Beta strandi988 – 9914Combined sources
Helixi993 – 100210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IMONMR-A924-1009[»]
1IN1NMR-A924-1009[»]
1UW0NMR-A88-204[»]
3L2PX-ray3.00A257-833[»]
3PC7X-ray1.65A/B924-1009[»]
3PC8X-ray2.31C/D924-1008[»]
3QVGX-ray2.26A/C924-1008[»]
ProteinModelPortaliP49916.
SMRiP49916. Positions 88-204, 257-833, 928-1008.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP49916.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini933 – 100977BRCTPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni277 – 2804Interaction with DNA1 Publication
Regioni318 – 3236Interaction with DNA1 Publication
Regioni388 – 3914Interaction with DNA1 Publication
Regioni421 – 4277Interaction with DNA1 Publication

Domaini

The PARP-type zinc finger is required for DNA ligase activity.1 Publication

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 1 BRCT domain.PROSITE-ProRule annotation
Contains 1 PARP-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri93 – 18593PARP-typePROSITE-ProRule annotation1 PublicationAdd
BLAST

Keywords - Domaini

Transit peptide, Zinc-finger

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00780000121970.
HOGENOMiHOG000007653.
HOVERGENiHBG005515.
InParanoidiP49916.
KOiK10776.
OMAiLFSEMKH.
OrthoDBiEOG7BKCT2.
PhylomeDBiP49916.
TreeFamiTF316220.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.30.1740.10. 1 hit.
3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR012340. NA-bd_OB-fold.
IPR001510. Znf_PARP.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF00645. zf-PARP. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. 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]

Sequences (4)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 4 isoformsi produced by alternative splicing and alternative initiation. AlignAdd to basket

Isoform 1 (identifier: P49916-1) [UniParc]FASTAAdd to basket

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.

« Hide

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

RKRRLVAPC

Note: Produced by alternative splicing.

Length:1,009
Mass (Da):112,907
Last modified:July 7, 2009 - v2
Checksum:i0E4057E33C3F19A6
GO
Isoform 2 (identifier: P49916-2) [UniParc]FASTAAdd to basket

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

Note: Produced by alternative splicing.

Show »
Length:949
Mass (Da):106,018
Checksum:i0C10E40E0686DB77
GO
Isoform 3 (identifier: P49916-3) [UniParc]FASTAAdd to basket

Also known as: Alpha

The sequence of this isoform differs from the canonical sequence as follows:
     1-87: Missing.

Note: Produced by alternative initiation of isoform 1.

Show »
Length:922
Mass (Da):102,691
Checksum:iFC3C60F988868808
GO
Isoform 4 (identifier: P49916-4) [UniParc]FASTAAdd to basket

Also known as: Beta

The sequence of this isoform differs from the canonical sequence as follows:
     1-87: Missing.
     933-1009: VLLDIFTGVR...IRKRRLVAPC → RRPASEQRGRTVPAGRR

Note: Produced by alternative initiation of isoform 2.

Show »
Length:862
Mass (Da):95,802
Checksum:iF6A3C6B1422FD895
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti224 – 2241R → W.
Corresponds to variant rs3744356 [ dbSNP | Ensembl ].
VAR_020196
Natural varianti717 – 7171D → N in a colorectal cancer sample; somatic mutation. 1 Publication
VAR_036513
Natural varianti768 – 7681Y → H.1 Publication
VAR_072387
Natural varianti867 – 8671R → H.1 Publication
Corresponds to variant rs3136025 [ dbSNP | Ensembl ].
VAR_018807
Natural varianti898 – 8981K → T.
Corresponds to variant rs4986974 [ dbSNP | Ensembl ].
VAR_021938
Natural varianti986 – 9861P → S.
Corresponds to variant rs4986973 [ dbSNP | Ensembl ].
VAR_020197

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 8787Missing in isoform 3 and isoform 4. CuratedVSP_057464Add
BLAST
Alternative sequencei933 – 100977VLLDI…LVAPC → RRPASEQRGRTVPAGRR in isoform 2 and isoform 4. 1 PublicationCuratedVSP_001302Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X84740 mRNA. Translation: CAA59230.1.
U40671 mRNA. Translation: AAA85022.1.
HQ204826 Genomic DNA. Translation: ADP89974.1.
HQ204826 Genomic DNA. Translation: ADP89975.1.
HQ204827 Genomic DNA. Translation: ADP89976.1.
HQ204827 Genomic DNA. Translation: ADP89977.1.
HQ204828 Genomic DNA. Translation: ADP89978.1.
HQ204828 Genomic DNA. Translation: ADP89979.1.
HQ204829 Genomic DNA. Translation: ADP89980.1.
HQ204829 Genomic DNA. Translation: ADP89981.1.
HQ204830 Genomic DNA. Translation: ADP89982.1.
HQ204830 Genomic DNA. Translation: ADP89983.1.
HQ204831 Genomic DNA. Translation: ADP89984.1.
HQ204831 Genomic DNA. Translation: ADP89985.1.
HQ204832 Genomic DNA. Translation: ADP89986.1.
HQ204832 Genomic DNA. Translation: ADP89987.1.
HQ204833 Genomic DNA. Translation: ADP89988.1.
HQ204833 Genomic DNA. Translation: ADP89989.1.
HQ204834 Genomic DNA. Translation: ADP89990.1.
HQ204834 Genomic DNA. Translation: ADP89991.1.
HQ204835 Genomic DNA. Translation: ADP89992.1.
HQ204835 Genomic DNA. Translation: ADP89993.1.
HQ204836 Genomic DNA. Translation: ADP89994.1.
HQ204836 Genomic DNA. Translation: ADP89995.1.
HQ204837 Genomic DNA. Translation: ADP89996.1.
HQ204837 Genomic DNA. Translation: ADP89997.1.
HQ204838 Genomic DNA. Translation: ADP89998.1.
HQ204838 Genomic DNA. Translation: ADP89999.1.
HQ204839 Genomic DNA. Translation: ADP90000.1.
HQ204839 Genomic DNA. Translation: ADP90001.1.
HQ204840 Genomic DNA. Translation: ADP90002.1.
HQ204840 Genomic DNA. Translation: ADP90003.1.
HQ204841 Genomic DNA. Translation: ADP90004.1.
HQ204841 Genomic DNA. Translation: ADP90005.1.
HQ204842 Genomic DNA. Translation: ADP90006.1.
HQ204842 Genomic DNA. Translation: ADP90007.1.
HQ204843 Genomic DNA. Translation: ADP90008.1.
HQ204843 Genomic DNA. Translation: ADP90009.1.
HQ204844 Genomic DNA. Translation: ADP90010.1.
HQ204844 Genomic DNA. Translation: ADP90011.1.
HQ204845 Genomic DNA. Translation: ADP90012.1.
HQ204845 Genomic DNA. Translation: ADP90013.1.
HQ204846 Genomic DNA. Translation: ADP90014.1.
HQ204846 Genomic DNA. Translation: ADP90015.1.
HQ204847 Genomic DNA. Translation: ADP90016.1.
HQ204847 Genomic DNA. Translation: ADP90017.1.
HQ204848 Genomic DNA. Translation: ADP90018.1.
HQ204848 Genomic DNA. Translation: ADP90019.1.
HQ204849 Genomic DNA. Translation: ADP90020.1.
HQ204849 Genomic DNA. Translation: ADP90021.1.
HQ204850 Genomic DNA. Translation: ADP90022.1.
HQ204850 Genomic DNA. Translation: ADP90023.1.
HQ204851 Genomic DNA. Translation: ADP90024.1.
HQ204851 Genomic DNA. Translation: ADP90025.1.
HQ204852 Genomic DNA. Translation: ADP90026.1.
HQ204852 Genomic DNA. Translation: ADP90027.1.
HQ204853 Genomic DNA. Translation: ADP90028.1.
HQ204853 Genomic DNA. Translation: ADP90029.1.
HQ204854 Genomic DNA. Translation: ADP90030.1.
HQ204854 Genomic DNA. Translation: ADP90031.1.
HQ204855 Genomic DNA. Translation: ADP90032.1.
HQ204855 Genomic DNA. Translation: ADP90033.1.
HQ204856 Genomic DNA. Translation: ADP90034.1.
HQ204856 Genomic DNA. Translation: ADP90035.1.
HQ204857 Genomic DNA. Translation: ADP90036.1.
HQ204857 Genomic DNA. Translation: ADP90037.1.
HQ204858 Genomic DNA. Translation: ADP90038.1.
HQ204858 Genomic DNA. Translation: ADP90039.1.
HQ204859 Genomic DNA. Translation: ADP90040.1.
HQ204859 Genomic DNA. Translation: ADP90041.1.
HQ204860 Genomic DNA. Translation: ADP90042.1.
HQ204860 Genomic DNA. Translation: ADP90043.1.
HQ204861 Genomic DNA. Translation: ADP90044.1.
HQ204861 Genomic DNA. Translation: ADP90045.1.
HQ204862 Genomic DNA. Translation: ADP90046.1.
HQ204862 Genomic DNA. Translation: ADP90047.1.
HQ204863 Genomic DNA. Translation: ADP90048.1.
HQ204863 Genomic DNA. Translation: ADP90049.1.
HQ204864 Genomic DNA. Translation: ADP90050.1.
HQ204864 Genomic DNA. Translation: ADP90051.1.
HQ204865 Genomic DNA. Translation: ADP90052.1.
HQ204865 Genomic DNA. Translation: ADP90053.1.
AF491645 Genomic DNA. Translation: AAL91592.1.
AC004223 Genomic DNA. No translation available.
AC022903 Genomic DNA. No translation available.
CH471147 Genomic DNA. Translation: EAW80197.1.
CH471147 Genomic DNA. Translation: EAW80199.1.
BC068005 mRNA. Translation: AAH68005.1.
CCDSiCCDS11284.2. [P49916-1]
CCDS11285.2. [P49916-2]
PIRiI37292.
RefSeqiNP_002302.2. NM_002311.4. [P49916-2]
NP_039269.2. NM_013975.3. [P49916-1]
UniGeneiHs.100299.

Genome annotation databases

EnsembliENST00000262327; ENSP00000262327; ENSG00000005156. [P49916-2]
ENST00000378526; ENSP00000367787; ENSG00000005156. [P49916-1]
GeneIDi3980.
KEGGihsa:3980.
UCSCiuc002hik.2. human. [P49916-1]

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Wikipedia

DNA ligase entry

NIEHS-SNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X84740 mRNA. Translation: CAA59230.1.
U40671 mRNA. Translation: AAA85022.1.
HQ204826 Genomic DNA. Translation: ADP89974.1.
HQ204826 Genomic DNA. Translation: ADP89975.1.
HQ204827 Genomic DNA. Translation: ADP89976.1.
HQ204827 Genomic DNA. Translation: ADP89977.1.
HQ204828 Genomic DNA. Translation: ADP89978.1.
HQ204828 Genomic DNA. Translation: ADP89979.1.
HQ204829 Genomic DNA. Translation: ADP89980.1.
HQ204829 Genomic DNA. Translation: ADP89981.1.
HQ204830 Genomic DNA. Translation: ADP89982.1.
HQ204830 Genomic DNA. Translation: ADP89983.1.
HQ204831 Genomic DNA. Translation: ADP89984.1.
HQ204831 Genomic DNA. Translation: ADP89985.1.
HQ204832 Genomic DNA. Translation: ADP89986.1.
HQ204832 Genomic DNA. Translation: ADP89987.1.
HQ204833 Genomic DNA. Translation: ADP89988.1.
HQ204833 Genomic DNA. Translation: ADP89989.1.
HQ204834 Genomic DNA. Translation: ADP89990.1.
HQ204834 Genomic DNA. Translation: ADP89991.1.
HQ204835 Genomic DNA. Translation: ADP89992.1.
HQ204835 Genomic DNA. Translation: ADP89993.1.
HQ204836 Genomic DNA. Translation: ADP89994.1.
HQ204836 Genomic DNA. Translation: ADP89995.1.
HQ204837 Genomic DNA. Translation: ADP89996.1.
HQ204837 Genomic DNA. Translation: ADP89997.1.
HQ204838 Genomic DNA. Translation: ADP89998.1.
HQ204838 Genomic DNA. Translation: ADP89999.1.
HQ204839 Genomic DNA. Translation: ADP90000.1.
HQ204839 Genomic DNA. Translation: ADP90001.1.
HQ204840 Genomic DNA. Translation: ADP90002.1.
HQ204840 Genomic DNA. Translation: ADP90003.1.
HQ204841 Genomic DNA. Translation: ADP90004.1.
HQ204841 Genomic DNA. Translation: ADP90005.1.
HQ204842 Genomic DNA. Translation: ADP90006.1.
HQ204842 Genomic DNA. Translation: ADP90007.1.
HQ204843 Genomic DNA. Translation: ADP90008.1.
HQ204843 Genomic DNA. Translation: ADP90009.1.
HQ204844 Genomic DNA. Translation: ADP90010.1.
HQ204844 Genomic DNA. Translation: ADP90011.1.
HQ204845 Genomic DNA. Translation: ADP90012.1.
HQ204845 Genomic DNA. Translation: ADP90013.1.
HQ204846 Genomic DNA. Translation: ADP90014.1.
HQ204846 Genomic DNA. Translation: ADP90015.1.
HQ204847 Genomic DNA. Translation: ADP90016.1.
HQ204847 Genomic DNA. Translation: ADP90017.1.
HQ204848 Genomic DNA. Translation: ADP90018.1.
HQ204848 Genomic DNA. Translation: ADP90019.1.
HQ204849 Genomic DNA. Translation: ADP90020.1.
HQ204849 Genomic DNA. Translation: ADP90021.1.
HQ204850 Genomic DNA. Translation: ADP90022.1.
HQ204850 Genomic DNA. Translation: ADP90023.1.
HQ204851 Genomic DNA. Translation: ADP90024.1.
HQ204851 Genomic DNA. Translation: ADP90025.1.
HQ204852 Genomic DNA. Translation: ADP90026.1.
HQ204852 Genomic DNA. Translation: ADP90027.1.
HQ204853 Genomic DNA. Translation: ADP90028.1.
HQ204853 Genomic DNA. Translation: ADP90029.1.
HQ204854 Genomic DNA. Translation: ADP90030.1.
HQ204854 Genomic DNA. Translation: ADP90031.1.
HQ204855 Genomic DNA. Translation: ADP90032.1.
HQ204855 Genomic DNA. Translation: ADP90033.1.
HQ204856 Genomic DNA. Translation: ADP90034.1.
HQ204856 Genomic DNA. Translation: ADP90035.1.
HQ204857 Genomic DNA. Translation: ADP90036.1.
HQ204857 Genomic DNA. Translation: ADP90037.1.
HQ204858 Genomic DNA. Translation: ADP90038.1.
HQ204858 Genomic DNA. Translation: ADP90039.1.
HQ204859 Genomic DNA. Translation: ADP90040.1.
HQ204859 Genomic DNA. Translation: ADP90041.1.
HQ204860 Genomic DNA. Translation: ADP90042.1.
HQ204860 Genomic DNA. Translation: ADP90043.1.
HQ204861 Genomic DNA. Translation: ADP90044.1.
HQ204861 Genomic DNA. Translation: ADP90045.1.
HQ204862 Genomic DNA. Translation: ADP90046.1.
HQ204862 Genomic DNA. Translation: ADP90047.1.
HQ204863 Genomic DNA. Translation: ADP90048.1.
HQ204863 Genomic DNA. Translation: ADP90049.1.
HQ204864 Genomic DNA. Translation: ADP90050.1.
HQ204864 Genomic DNA. Translation: ADP90051.1.
HQ204865 Genomic DNA. Translation: ADP90052.1.
HQ204865 Genomic DNA. Translation: ADP90053.1.
AF491645 Genomic DNA. Translation: AAL91592.1.
AC004223 Genomic DNA. No translation available.
AC022903 Genomic DNA. No translation available.
CH471147 Genomic DNA. Translation: EAW80197.1.
CH471147 Genomic DNA. Translation: EAW80199.1.
BC068005 mRNA. Translation: AAH68005.1.
CCDSiCCDS11284.2. [P49916-1]
CCDS11285.2. [P49916-2]
PIRiI37292.
RefSeqiNP_002302.2. NM_002311.4. [P49916-2]
NP_039269.2. NM_013975.3. [P49916-1]
UniGeneiHs.100299.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IMONMR-A924-1009[»]
1IN1NMR-A924-1009[»]
1UW0NMR-A88-204[»]
3L2PX-ray3.00A257-833[»]
3PC7X-ray1.65A/B924-1009[»]
3PC8X-ray2.31C/D924-1008[»]
3QVGX-ray2.26A/C924-1008[»]
ProteinModelPortaliP49916.
SMRiP49916. Positions 88-204, 257-833, 928-1008.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110168. 39 interactions.
IntActiP49916. 11 interactions.
MINTiMINT-4531178.
STRINGi9606.ENSP00000367787.

Chemistry

DrugBankiDB00290. Bleomycin.

PTM databases

PhosphoSiteiP49916.

Polymorphism and mutation databases

BioMutaiLIG3.
DMDMi251757259.

Proteomic databases

MaxQBiP49916.
PaxDbiP49916.
PRIDEiP49916.

Protocols and materials databases

DNASUi3980.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000262327; ENSP00000262327; ENSG00000005156. [P49916-2]
ENST00000378526; ENSP00000367787; ENSG00000005156. [P49916-1]
GeneIDi3980.
KEGGihsa:3980.
UCSCiuc002hik.2. human. [P49916-1]

Organism-specific databases

CTDi3980.
GeneCardsiGC17P033307.
HGNCiHGNC:6600. LIG3.
HPAiHPA006723.
MIMi600940. gene.
neXtProtiNX_P49916.
PharmGKBiPA30374.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00780000121970.
HOGENOMiHOG000007653.
HOVERGENiHBG005515.
InParanoidiP49916.
KOiK10776.
OMAiLFSEMKH.
OrthoDBiEOG7BKCT2.
PhylomeDBiP49916.
TreeFamiTF316220.

Enzyme and pathway databases

BRENDAi6.5.1.1. 2681.
ReactomeiREACT_355367. APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
REACT_933. Resolution of AP sites via the single-nucleotide replacement pathway.

Miscellaneous databases

ChiTaRSiLIG3. human.
EvolutionaryTraceiP49916.
GeneWikiiLIG3.
GenomeRNAii3980.
NextBioi15598.
PROiP49916.
SOURCEiSearch...

Gene expression databases

BgeeiP49916.
CleanExiHS_LIG3.
ExpressionAtlasiP49916. baseline and differential.
GenevestigatoriP49916.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.30.1740.10. 1 hit.
3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR012340. NA-bd_OB-fold.
IPR001510. Znf_PARP.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF00645. zf-PARP. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. 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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), INTERACTION WITH XRCC1.
    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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4).
    Tissue: Testis.
  3. "Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing."
    Wang W., Shen P., Thiyagarajan S., Lin S., Palm C., Horvath R., Klopstock T., Cutler D., Pique L., Schrijver I., Davis R.W., Mindrinos M., Speed T.P., Scharfe C.
    Nucleic Acids Res. 39:44-58(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT HIS-768.
  4. NIEHS SNPs program
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT HIS-867.
  5. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Pancreas.
  8. "The human DNA ligase III gene encodes nuclear and mitochondrial proteins."
    Lakshmipathy U., Campbell C.
    Mol. Cell. Biol. 19:3869-3876(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, ALTERNATIVE INITIATION.
  9. "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] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  10. "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] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-227, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  12. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "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] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  14. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair."
    Akbari M., Keijzers G., Maynard S., Scheibye-Knudsen M., Desler C., Hickson I.D., Bohr V.A.
    DNA Repair 16:44-53(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  18. "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] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 924-1009.
  19. "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] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-204 IN COMPLEX WITH ZINC.
  20. "Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states."
    Cotner-Gohara E., Kim I.K., Hammel M., Tainer J.A., Tomkinson A.E., Ellenberger T.
    Biochemistry 49:6165-6176(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 257-833 IN COMPLEX WITH DNA AND AMP, ACTIVE SITE, FUNCTION, CATALYTIC ACTIVITY, DOMAIN, MUTAGENESIS OF LYS-410 AND ARG-414.
  21. "The structural basis for partitioning of the XRCC1/DNA ligase III-? BRCT-mediated dimer complexes."
    Cuneo M.J., Gabel S.A., Krahn J.M., Ricker M.A., London R.E.
    Nucleic Acids Res. 39:7816-7827(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 924-1009 IN COMPLEX WITH XRCC1, INTERACTION WITH XRCC1.
  22. Cited for: VARIANT [LARGE SCALE ANALYSIS] ASN-717.

Entry informationi

Entry nameiDNLI3_HUMAN
AccessioniPrimary (citable) accession number: P49916
Secondary accession number(s): E5KLB5
, E5KLB6, Q16714, Q6NVK3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 7, 2009
Last modified: May 27, 2015
This is version 168 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.