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Protein

DNA ligase

Gene

ligA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.

Catalytic activityi

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).1 Publication

Cofactori

Mg2+1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei113NADUniRule annotation1 Publication1
Active sitei115N6-AMP-lysine intermediateUniRule annotation1 Publication1
Binding sitei136NADUniRule annotation1 Publication1
Binding sitei173NADUniRule annotation1
Binding sitei290NADUniRule annotation1 Publication1
Binding sitei314NADUniRule annotation1
Metal bindingi408ZincUniRule annotation1 Publication1
Metal bindingi411ZincUniRule annotation1 Publication1
Metal bindingi426ZincUniRule annotation1 Publication1
Metal bindingi432ZincUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi32 – 36NADUniRule annotation5
Nucleotide bindingi81 – 82NADUniRule annotation1 Publication2

GO - Molecular functioni

  • DNA binding Source: EcoCyc
  • DNA ligase (NAD+) activity Source: EcoliWiki
  • metal ion binding Source: UniProtKB-KW
  • NAD+ binding Source: EcoCyc

GO - Biological processi

  • base-excision repair, DNA ligation Source: EcoCyc
  • DNA ligation Source: EcoCyc
  • DNA replication Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Metal-binding, NAD, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10534-MONOMER.
ECOL316407:JW2403-MONOMER.
MetaCyc:EG10534-MONOMER.
BRENDAi6.5.1.2. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase (EC:6.5.1.2)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]
Gene namesi
Name:ligA
Synonyms:dnaL, lig, lop, pdeC
Ordered Locus Names:b2411, JW2403
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10534. ligA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi10E → A: No effect. 1 Publication1
Mutagenesisi22Y → A or S: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi22Y → F: Reduces nick joining activity by 91%. 1 Publication1
Mutagenesisi23H → A or Y: Reduces nick joining activity by 90%. 1 Publication1
Mutagenesisi32D → A or E: Reduces nick joining activity by 99%. 1 Publication1
Mutagenesisi32D → N: Reduces nick joining activity by 91%. 1 Publication1
Mutagenesisi35Y → A: Reduces nick joining activity by 98%. 1 Publication1
Mutagenesisi35Y → F: Reduces nick joining activity by 77%. 1 Publication1
Mutagenesisi35Y → S: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi36D → A: Reduces nick joining activity by 99.8%. 1 Publication1
Mutagenesisi36D → E: Reduces nick joining activity by 96%. 1 Publication1
Mutagenesisi36D → N: Reduces nick joining activity by 88%. 1 Publication1
Mutagenesisi115K → Q or R: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi117D → E: Reduces nick joining activity by 97%. 1 Publication1
Mutagenesisi117D → N: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi118G → A: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi138D → A: Reduces nick joining activity by 63%. 1 Publication1
Mutagenesisi143E → A: Reduces nick joining activity by 48%. 1 Publication1
Mutagenesisi172G → A: Reduces nick joining activity by 64%. 1 Publication1
Mutagenesisi173E → A, D or Q: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi198N → A: Reduces nick joining activity by 74%. 1 Publication1
Mutagenesisi200R → A, K or Q: Reduces nick joining activity by 99.9%. 1 Publication1
Mutagenesisi208R → A, K or Q: Reduces nick joining activity by 99%. 1 Publication1
Mutagenesisi277R → A: Reduces nick joining activity by 99%. 1 Publication1
Mutagenesisi285D → E: Reduces nick joining activity by 96%. 1 Publication1
Mutagenesisi285D → N: Reduces nick joining activity by 99%. 1 Publication1
Mutagenesisi286G → A: Reduces nick joining activity by 86%. 1 Publication1
Mutagenesisi288V → A: Reduces nick joining activity by 25%. 1 Publication1
Mutagenesisi290K → A: Reduces nick joining activity by 87%. 1 Publication1
Mutagenesisi314K → Q: Reduces nick joining activity by 99%. 1 Publication1
Mutagenesisi314K → R: Reduces nick joining activity by 95%. 1 Publication1
Mutagenesisi333R → A or Q: Reduces nick joining activity by over 95%. Abolishes nick joining activity; when associated with A-334. 1 Publication1
Mutagenesisi334T → A: Abolishes nick joining activity; when associated with A-333. 1 Publication1
Mutagenesisi342R → A: Reduces nick joining activity by 80%. 1 Publication1
Mutagenesisi379R → A or Q: Reduces nick joining activity by over 95%. 1 Publication1
Mutagenesisi383 – 384VI → AA: Reduces nick joining activity by 95%. 1 Publication2
Mutagenesisi446 – 447RR → AA: Reduces nick joining activity by 95%. 1 Publication2
Mutagenesisi455G → A: Reduces nick joining activity by 50%. 1 Publication1
Mutagenesisi455G → D or V: Reduces nick joining activity by 95%. 1 Publication1
Mutagenesisi487R → A: Reduces nick joining activity by over 90%. 1 Publication1
Mutagenesisi489G → D or V: Reduces nick joining activity by 95%. 1 Publication1
Mutagenesisi521G → A: Reduces nick joining activity by 95%. 1 Publication1
Mutagenesisi521G → D or V: Loss of nick joining activity. 1 Publication1
Mutagenesisi553G → D or V: Reduces nick joining activity by 95%. 1 Publication1
Mutagenesisi614R → A: Reduces nick joining activity by 85%. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001617451 – 671DNA ligaseAdd BLAST671

Proteomic databases

PaxDbiP15042.
PRIDEiP15042.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei487Interaction with target DNA1 Publication1
Sitei492Interaction with target DNA1 Publication1

Protein-protein interaction databases

BioGridi4259672. 128 interactors.
DIPiDIP-10098N.
IntActiP15042. 20 interactors.
MINTiMINT-204717.
STRINGi511145.b2411.

Structurei

Secondary structure

1671
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 24Combined sources21
Beta strandi28 – 30Combined sources3
Helixi34 – 48Combined sources15
Helixi50 – 52Combined sources3
Helixi58 – 60Combined sources3
Beta strandi72 – 74Combined sources3
Beta strandi83 – 85Combined sources3
Helixi88 – 100Combined sources13
Beta strandi102 – 104Combined sources3
Beta strandi110 – 126Combined sources17
Beta strandi129 – 135Combined sources7
Beta strandi139 – 144Combined sources6
Helixi146 – 149Combined sources4
Beta strandi161 – 163Combined sources3
Beta strandi166 – 175Combined sources10
Helixi178 – 190Combined sources13
Helixi199 – 207Combined sources9
Helixi212 – 216Combined sources5
Beta strandi221 – 233Combined sources13
Helixi239 – 248Combined sources10
Beta strandi258 – 262Combined sources5
Helixi263 – 276Combined sources14
Helixi277 – 279Combined sources3
Beta strandi280 – 282Combined sources3
Beta strandi284 – 293Combined sources10
Helixi294 – 300Combined sources7
Beta strandi304 – 313Combined sources10
Beta strandi319 – 331Combined sources13
Beta strandi335 – 348Combined sources14
Beta strandi351 – 357Combined sources7
Helixi361 – 367Combined sources7
Beta strandi374 – 380Combined sources7
Turni381 – 383Combined sources3
Beta strandi384 – 390Combined sources7
Helixi392 – 394Combined sources3
Turni409 – 411Combined sources3
Beta strandi414 – 416Combined sources3
Beta strandi425 – 427Combined sources3
Helixi429 – 431Combined sources3
Helixi433 – 444Combined sources12
Turni446 – 449Combined sources4
Helixi456 – 464Combined sources9
Helixi471 – 475Combined sources5
Helixi479 – 483Combined sources5
Helixi490 – 503Combined sources14
Helixi508 – 514Combined sources7
Helixi522 – 532Combined sources11
Helixi535 – 540Combined sources6
Helixi543 – 546Combined sources4
Helixi554 – 565Combined sources12
Helixi567 – 578Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OWOX-ray2.30A1-671[»]
4GLXX-ray1.90A1-586[»]
ProteinModelPortaliP15042.
SMRiP15042.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP15042.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini593 – 671BRCTAdd BLAST79

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni330 – 334Interaction with target DNA1 Publication5
Regioni453 – 458Interaction with target DNA1 Publication6
Regioni519 – 524Interaction with target DNA1 Publication6
Regioni551 – 556Interaction with target DNA1 Publication6

Sequence similaritiesi

Contains 1 BRCT domain.Curated

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
HOGENOMiHOG000218459.
InParanoidiP15042.
KOiK01972.
OMAiFTAKSPR.
PhylomeDBiP15042.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P15042-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MESIEQQLTE LRTTLRHHEY LYHVMDAPEI PDAEYDRLMR ELRELETKHP
60 70 80 90 100
ELITPDSPTQ RVGAAPLAAF SQIRHEVPML SLDNVFDEES FLAFNKRVQD
110 120 130 140 150
RLKNNEKVTW CCELKLDGLA VSILYENGVL VSAATRGDGT TGEDITSNVR
160 170 180 190 200
TIRAIPLKLH GENIPARLEV RGEVFLPQAG FEKINEDARR TGGKVFANPR
210 220 230 240 250
NAAAGSLRQL DPRITAKRPL TFFCYGVGVL EGGELPDTHL GRLLQFKKWG
260 270 280 290 300
LPVSDRVTLC ESAEEVLAFY HKVEEDRPTL GFDIDGVVIK VNSLAQQEQL
310 320 330 340 350
GFVARAPRWA VAFKFPAQEQ MTFVRDVEFQ VGRTGAITPV ARLEPVHVAG
360 370 380 390 400
VLVSNATLHN ADEIERLGLR IGDKVVIRRA GDVIPQVVNV VLSERPEDTR
410 420 430 440 450
EVVFPTHCPV CGSDVERVEG EAVARCTGGL ICGAQRKESL KHFVSRRAMD
460 470 480 490 500
VDGMGDKIID QLVEKEYVHT PADLFKLTAG KLTGLERMGP KSAQNVVNAL
510 520 530 540 550
EKAKETTFAR FLYALGIREV GEATAAGLAA YFGTLEALEA ASIEELQKVP
560 570 580 590 600
DVGIVVASHV HNFFAEESNR NVISELLAEG VHWPAPIVIN AEEIDSPFAG
610 620 630 640 650
KTVVLTGSLS QMSRDDAKAR LVELGAKVAG SVSKKTDLVI AGEAAGSKLA
660 670
KAQELGIEVI DEAEMLRLLG S
Length:671
Mass (Da):73,606
Last modified:November 1, 1997 - v2
Checksum:iDD2BDC64D8E65256
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti69A → R in AAA24071 (PubMed:3018436).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30255 Genomic DNA. Translation: AAA24071.1.
M24278 Genomic DNA. Translation: AAA24070.1.
U00096 Genomic DNA. Translation: AAC75464.1.
AP009048 Genomic DNA. Translation: BAA16282.2.
U74650 Genomic DNA. Translation: AAB42062.1.
PIRiB65015. LQECC6.
RefSeqiNP_416906.1. NC_000913.3.
WP_000443661.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75464; AAC75464; b2411.
BAA16282; BAA16282; BAA16282.
GeneIDi946885.
KEGGiecj:JW2403.
eco:b2411.
PATRICi32120205. VBIEscCol129921_2505.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30255 Genomic DNA. Translation: AAA24071.1.
M24278 Genomic DNA. Translation: AAA24070.1.
U00096 Genomic DNA. Translation: AAC75464.1.
AP009048 Genomic DNA. Translation: BAA16282.2.
U74650 Genomic DNA. Translation: AAB42062.1.
PIRiB65015. LQECC6.
RefSeqiNP_416906.1. NC_000913.3.
WP_000443661.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OWOX-ray2.30A1-671[»]
4GLXX-ray1.90A1-586[»]
ProteinModelPortaliP15042.
SMRiP15042.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259672. 128 interactors.
DIPiDIP-10098N.
IntActiP15042. 20 interactors.
MINTiMINT-204717.
STRINGi511145.b2411.

Proteomic databases

PaxDbiP15042.
PRIDEiP15042.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75464; AAC75464; b2411.
BAA16282; BAA16282; BAA16282.
GeneIDi946885.
KEGGiecj:JW2403.
eco:b2411.
PATRICi32120205. VBIEscCol129921_2505.

Organism-specific databases

EchoBASEiEB0529.
EcoGeneiEG10534. ligA.

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
HOGENOMiHOG000218459.
InParanoidiP15042.
KOiK01972.
OMAiFTAKSPR.
PhylomeDBiP15042.

Enzyme and pathway databases

BioCyciEcoCyc:EG10534-MONOMER.
ECOL316407:JW2403-MONOMER.
MetaCyc:EG10534-MONOMER.
BRENDAi6.5.1.2. 2026.

Miscellaneous databases

EvolutionaryTraceiP15042.
PROiP15042.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNLJ_ECOLI
AccessioniPrimary (citable) accession number: P15042
Secondary accession number(s): P78197, P78198
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: November 1, 1997
Last modified: November 30, 2016
This is version 164 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.