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Protein

DNA ligase 1

Gene

LIG1

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

Functioni

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.

Catalytic activityi

ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.PROSITE-ProRule annotation

Cofactori

Mg2+1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei566ATPCombined sources1 Publication1
Active sitei568N6-AMP-lysine intermediatePROSITE-ProRule annotation1
Binding sitei573ATPCombined sources1 Publication1
Binding sitei589ATP1
Metal bindingi621Magnesium 1Curated1
Metal bindingi720Magnesium 2Curated1
Binding sitei725ATPCombined sources1 Publication1
Binding sitei738ATPBy similarity1
Binding sitei744ATPCombined sources1 Publication1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: ProtInc
  • DNA ligase (ATP) activity Source: GO_Central
  • DNA ligase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi6.5.1.1 2681
ReactomeiR-HSA-110362 POLB-Dependent Long Patch Base Excision Repair
R-HSA-162594 Early Phase of HIV Life Cycle
R-HSA-174414 Processive synthesis on the C-strand of the telomere
R-HSA-5358565 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
R-HSA-5358606 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
R-HSA-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-HSA-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-69183 Processive synthesis on the lagging strand
SIGNORiP18858

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 1 (EC:6.5.1.1PROSITE-ProRule annotation)
Alternative name(s):
DNA ligase I
Polydeoxyribonucleotide synthase [ATP] 1
Gene namesi
Name:LIG1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

EuPathDBiHostDB:ENSG00000105486.13
HGNCiHGNC:6598 LIG1
MIMi126391 gene
neXtProtiNX_P18858

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi3978
OpenTargetsiENSG00000105486
PharmGKBiPA30372

Chemistry databases

ChEMBLiCHEMBL5694
DrugBankiDB00290 Bleomycin

Polymorphism and mutation databases

BioMutaiLIG1
DMDMi118773

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000595701 – 919DNA ligase 1Add BLAST919

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei47PhosphoserineCombined sources1
Modified residuei49PhosphoserineCombined sources1
Modified residuei51PhosphoserineCombined sources1
Modified residuei66PhosphoserineCombined sources1
Modified residuei76PhosphoserineCombined sources1
Modified residuei141PhosphoserineCombined sources1
Modified residuei195PhosphothreonineCombined sources1
Modified residuei199PhosphoserineCombined sources1
Modified residuei201PhosphoserineCombined sources1
Modified residuei207PhosphothreonineCombined sources1
Modified residuei226N6-acetyllysineBy similarity1
Modified residuei229PhosphoserineCombined sources1
Modified residuei230PhosphoserineCombined sources1
Modified residuei233PhosphothreonineCombined sources1
Modified residuei798PhosphothreonineCombined sources1
Modified residuei801PhosphoserineCombined sources1
Modified residuei819PhosphoserineCombined sources1
Modified residuei911PhosphoserineCombined sources1
Modified residuei913PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP18858
MaxQBiP18858
PaxDbiP18858
PeptideAtlasiP18858
PRIDEiP18858
ProteomicsDBi53617

PTM databases

iPTMnetiP18858
PhosphoSitePlusiP18858

Expressioni

Gene expression databases

BgeeiENSG00000105486 Expressed in 149 organ(s), highest expression level in right uterine tube
CleanExiHS_LIG1
ExpressionAtlasiP18858 baseline and differential
GenevisibleiP18858 HS

Organism-specific databases

HPAiCAB037015
HPA041431
HPA048071

Interactioni

Subunit structurei

Interacts with PCNA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei305Interaction with target DNA1
Sitei590Interaction with target DNA1
Sitei770Interaction with target DNA1
Sitei795Interaction with target DNA1

Protein-protein interaction databases

BioGridi110166, 19 interactors
CORUMiP18858
DIPiDIP-24215N
ELMiP18858
IntActiP18858, 7 interactors
MINTiP18858
STRINGi9606.ENSP00000263274

Chemistry databases

BindingDBiP18858

Structurei

Secondary structure

1919
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP18858
SMRiP18858
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP18858

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni449 – 458Interaction with target DNA10
Regioni642 – 644Interaction with target DNA3

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated

Phylogenomic databases

eggNOGiKOG0967 Eukaryota
COG1793 LUCA
GeneTreeiENSGT00860000133792
HOGENOMiHOG000036006
HOVERGENiHBG005514
InParanoidiP18858
KOiK10747
OMAiWIKYKRD
OrthoDBiEOG091G06OS
PhylomeDBiP18858
TreeFamiTF300342

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
InterProiView protein in InterPro
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
IPR036599 DNA_ligase_N_sf
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF04675 DNA_ligase_A_N, 1 hit
SUPFAMiSSF117018 SSF117018, 1 hit
SSF50249 SSF50249, 1 hit
TIGRFAMsiTIGR00574 dnl1, 1 hit
PROSITEiView protein in PROSITE
PS00697 DNA_LIGASE_A1, 1 hit
PS00333 DNA_LIGASE_A2, 1 hit
PS50160 DNA_LIGASE_A3, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 7 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: P18858-1) [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
MQRSIMSFFH PKKEGKAKKP EKEASNSSRE TEPPPKAALK EWNGVVSESD
60 70 80 90 100
SPVKRPGRKA ARVLGSEGEE EDEALSPAKG QKPALDCSQV SPPRPATSPE
110 120 130 140 150
NNASLSDTSP MDSSPSGIPK RRTARKQLPK RTIQEVLEEQ SEDEDREAKR
160 170 180 190 200
KKEEEEEETP KESLTEAEVA TEKEGEDGDQ PTTPPKPLKT SKAETPTESV
210 220 230 240 250
SEPEVATKQE LQEEEEQTKP PRRAPKTLSS FFTPRKPAVK KEVKEEEPGA
260 270 280 290 300
PGKEGAAEGP LDPSGYNPAK NNYHPVEDAC WKPGQKVPYL AVARTFEKIE
310 320 330 340 350
EVSARLRMVE TLSNLLRSVV ALSPPDLLPV LYLSLNHLGP PQQGLELGVG
360 370 380 390 400
DGVLLKAVAQ ATGRQLESVR AEAAEKGDVG LVAENSRSTQ RLMLPPPPLT
410 420 430 440 450
ASGVFSKFRD IARLTGSAST AKKIDIIKGL FVACRHSEAR FIARSLSGRL
460 470 480 490 500
RLGLAEQSVL AALSQAVSLT PPGQEFPPAM VDAGKGKTAE ARKTWLEEQG
510 520 530 540 550
MILKQTFCEV PDLDRIIPVL LEHGLERLPE HCKLSPGIPL KPMLAHPTRG
560 570 580 590 600
ISEVLKRFEE AAFTCEYKYD GQRAQIHALE GGEVKIFSRN QEDNTGKYPD
610 620 630 640 650
IISRIPKIKL PSVTSFILDT EAVAWDREKK QIQPFQVLTT RKRKEVDASE
660 670 680 690 700
IQVQVCLYAF DLIYLNGESL VREPLSRRRQ LLRENFVETE GEFVFATSLD
710 720 730 740 750
TKDIEQIAEF LEQSVKDSCE GLMVKTLDVD ATYEIAKRSH NWLKLKKDYL
760 770 780 790 800
DGVGDTLDLV VIGAYLGRGK RAGRYGGFLL ASYDEDSEEL QAICKLGTGF
810 820 830 840 850
SDEELEEHHQ SLKALVLPSP RPYVRIDGAV IPDHWLDPSA VWEVKCADLS
860 870 880 890 900
LSPIYPAARG LVDSDKGISL RFPRFIRVRE DKQPEQATTS AQVACLYRKQ
910
SQIQNQQGED SGSDPEDTY
Length:919
Mass (Da):101,736
Last modified:November 1, 1990 - v1
Checksum:iB2854DAE38A8D4AD
GO
Isoform 2 (identifier: P18858-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     796-801: LGTGFS → VLGNWG
     802-919: Missing.

Note: No experimental confirmation available.
Show »
Length:801
Mass (Da):88,516
Checksum:i1AC26C5FB793684F
GO
Isoform 3 (identifier: P18858-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     7-36: Missing.
     153-153: Missing.

Note: No experimental confirmation available.
Show »
Length:888
Mass (Da):98,228
Checksum:i6A59D9975C259D9F
GO

Computationally mapped potential isoform sequencesi

There are 7 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F5GZ28F5GZ28_HUMAN
DNA ligase
LIG1
851Annotation score:
M0R0Q7M0R0Q7_HUMAN
DNA ligase
LIG1
800Annotation score:
B4E135B4E135_HUMAN
DNA ligase 1
LIG1
415Annotation score:
M0QY71M0QY71_HUMAN
DNA ligase 1
LIG1
145Annotation score:
M0R1G7M0R1G7_HUMAN
DNA ligase 1
LIG1
149Annotation score:
M0R1S4M0R1S4_HUMAN
DNA ligase 1
LIG1
28Annotation score:
M0R254M0R254_HUMAN
DNA ligase 1
LIG1
36Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01880224A → V1 PublicationCorresponds to variant dbSNP:rs3730855Ensembl.1
Natural variantiVAR_02019452P → L. Corresponds to variant dbSNP:rs4987181Ensembl.1
Natural variantiVAR_01880362R → W1 PublicationCorresponds to variant dbSNP:rs3730863Ensembl.1
Natural variantiVAR_02019572D → G. Corresponds to variant dbSNP:rs4987070Ensembl.1
Natural variantiVAR_036511152K → E in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs780748107Ensembl.1
Natural variantiVAR_016766249G → E1 PublicationCorresponds to variant dbSNP:rs3730911Ensembl.1
Natural variantiVAR_016767267N → S1 PublicationCorresponds to variant dbSNP:rs3730933Ensembl.1
Natural variantiVAR_018804349V → M1 PublicationCorresponds to variant dbSNP:rs3730947Ensembl.1
Natural variantiVAR_018805369V → I1 PublicationCorresponds to variant dbSNP:rs3730966Ensembl.1
Natural variantiVAR_016768409R → H. Corresponds to variant dbSNP:rs4987068Ensembl.1
Natural variantiVAR_016769480M → V1 PublicationCorresponds to variant dbSNP:rs3730980Ensembl.1
Natural variantiVAR_002262566E → K Found in a patient with a syndrome of immunodeficiency and increased cellular sensitivity to DNA-damaging agents due to LIG1 deficiency; compound heterozygote carrying W-771. 1 PublicationCorresponds to variant dbSNP:rs121434560EnsemblClinVar.1
Natural variantiVAR_036512612S → L in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs780324684Ensembl.1
Natural variantiVAR_016770614T → I1 PublicationCorresponds to variant dbSNP:rs3731003Ensembl.1
Natural variantiVAR_018806677R → L1 PublicationCorresponds to variant dbSNP:rs3731008Ensembl.1
Natural variantiVAR_002263771R → W Found in a patient with a syndrome of immunodeficiency and increased cellular sensitivity to DNA-damaging agents due to LIG1 deficiency; compound heterozygote carrying K-566. 1 PublicationCorresponds to variant dbSNP:rs121434561EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0573207 – 36Missing in isoform 3. 1 PublicationAdd BLAST30
Alternative sequenceiVSP_057321153Missing in isoform 3. 1 Publication1
Alternative sequenceiVSP_056139796 – 801LGTGFS → VLGNWG in isoform 2. 1 Publication6
Alternative sequenceiVSP_056140802 – 919Missing in isoform 2. 1 PublicationAdd BLAST118

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M36067 mRNA Translation: AAA59518.1
AF527418 Genomic DNA Translation: AAM77697.1
AK300370 mRNA Translation: BAG62106.1
AK314210 mRNA Translation: BAG36885.1
AC011466 Genomic DNA No translation available.
KC877741 Genomic DNA No translation available.
CH471177 Genomic DNA Translation: EAW52316.1
BC108318 mRNA Translation: AAI08319.1
BC110622 mRNA Translation: AAI10623.1
CCDSiCCDS12711.1 [P18858-1]
CCDS74409.1 [P18858-3]
PIRiA36048 A41275
RefSeqiNP_000225.1, NM_000234.2 [P18858-1]
NP_001275992.1, NM_001289063.1 [P18858-3]
NP_001275993.1, NM_001289064.1
NP_001307899.1, NM_001320970.1
NP_001307900.1, NM_001320971.1
UniGeneiHs.1770

Genome annotation databases

EnsembliENST00000263274; ENSP00000263274; ENSG00000105486 [P18858-1]
ENST00000427526; ENSP00000442841; ENSG00000105486 [P18858-3]
ENST00000601091; ENSP00000471836; ENSG00000105486 [P18858-2]
ENST00000613670; ENSP00000483027; ENSG00000105486 [P18858-2]
GeneIDi3978
KEGGihsa:3978
UCSCiuc002pia.2 human [P18858-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

LIG1base

LIG1 mutation db

NIEHS-SNPs
Wikipedia

DNA ligase entry

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M36067 mRNA Translation: AAA59518.1
AF527418 Genomic DNA Translation: AAM77697.1
AK300370 mRNA Translation: BAG62106.1
AK314210 mRNA Translation: BAG36885.1
AC011466 Genomic DNA No translation available.
KC877741 Genomic DNA No translation available.
CH471177 Genomic DNA Translation: EAW52316.1
BC108318 mRNA Translation: AAI08319.1
BC110622 mRNA Translation: AAI10623.1
CCDSiCCDS12711.1 [P18858-1]
CCDS74409.1 [P18858-3]
PIRiA36048 A41275
RefSeqiNP_000225.1, NM_000234.2 [P18858-1]
NP_001275992.1, NM_001289063.1 [P18858-3]
NP_001275993.1, NM_001289064.1
NP_001307899.1, NM_001320970.1
NP_001307900.1, NM_001320971.1
UniGeneiHs.1770

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X9NX-ray3.00A233-919[»]
ProteinModelPortaliP18858
SMRiP18858
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110166, 19 interactors
CORUMiP18858
DIPiDIP-24215N
ELMiP18858
IntActiP18858, 7 interactors
MINTiP18858
STRINGi9606.ENSP00000263274

Chemistry databases

BindingDBiP18858
ChEMBLiCHEMBL5694
DrugBankiDB00290 Bleomycin

PTM databases

iPTMnetiP18858
PhosphoSitePlusiP18858

Polymorphism and mutation databases

BioMutaiLIG1
DMDMi118773

Proteomic databases

EPDiP18858
MaxQBiP18858
PaxDbiP18858
PeptideAtlasiP18858
PRIDEiP18858
ProteomicsDBi53617

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263274; ENSP00000263274; ENSG00000105486 [P18858-1]
ENST00000427526; ENSP00000442841; ENSG00000105486 [P18858-3]
ENST00000601091; ENSP00000471836; ENSG00000105486 [P18858-2]
ENST00000613670; ENSP00000483027; ENSG00000105486 [P18858-2]
GeneIDi3978
KEGGihsa:3978
UCSCiuc002pia.2 human [P18858-1]

Organism-specific databases

CTDi3978
DisGeNETi3978
EuPathDBiHostDB:ENSG00000105486.13
GeneCardsiLIG1
HGNCiHGNC:6598 LIG1
HPAiCAB037015
HPA041431
HPA048071
MIMi126391 gene
neXtProtiNX_P18858
OpenTargetsiENSG00000105486
PharmGKBiPA30372
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0967 Eukaryota
COG1793 LUCA
GeneTreeiENSGT00860000133792
HOGENOMiHOG000036006
HOVERGENiHBG005514
InParanoidiP18858
KOiK10747
OMAiWIKYKRD
OrthoDBiEOG091G06OS
PhylomeDBiP18858
TreeFamiTF300342

Enzyme and pathway databases

BRENDAi6.5.1.1 2681
ReactomeiR-HSA-110362 POLB-Dependent Long Patch Base Excision Repair
R-HSA-162594 Early Phase of HIV Life Cycle
R-HSA-174414 Processive synthesis on the C-strand of the telomere
R-HSA-5358565 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
R-HSA-5358606 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
R-HSA-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-HSA-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-69183 Processive synthesis on the lagging strand
SIGNORiP18858

Miscellaneous databases

ChiTaRSiLIG1 human
EvolutionaryTraceiP18858
GeneWikiiLIG1
GenomeRNAii3978
PROiPR:P18858
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000105486 Expressed in 149 organ(s), highest expression level in right uterine tube
CleanExiHS_LIG1
ExpressionAtlasiP18858 baseline and differential
GenevisibleiP18858 HS

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
InterProiView protein in InterPro
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
IPR036599 DNA_ligase_N_sf
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF04675 DNA_ligase_A_N, 1 hit
SUPFAMiSSF117018 SSF117018, 1 hit
SSF50249 SSF50249, 1 hit
TIGRFAMsiTIGR00574 dnl1, 1 hit
PROSITEiView protein in PROSITE
PS00697 DNA_LIGASE_A1, 1 hit
PS00333 DNA_LIGASE_A2, 1 hit
PS50160 DNA_LIGASE_A3, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDNLI1_HUMAN
AccessioniPrimary (citable) accession number: P18858
Secondary accession number(s): B2RAI8
, B4DTU4, Q2TB12, Q32P23
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: September 12, 2018
This is version 197 of the entry and version 1 of the sequence. See 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
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