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P15042 (DNLJ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 144. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase

EC=6.5.1.2
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]
Gene names
Name:ligA
Synonyms:dnaL, lig, lop, pdeC
Ordered Locus Names:b2411, JW2403
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length671 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_01588

Catalytic activity

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m). Ref.7

Cofactor

Magnesium. Ref.7

Sequence similarities

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.

Contains 1 BRCT domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 671671DNA ligase HAMAP-Rule MF_01588
PRO_0000161745

Regions

Domain593 – 67179BRCT
Nucleotide binding32 – 365NAD Probable
Nucleotide binding81 – 822NAD HAMAP-Rule MF_01588
Region330 – 3345Interaction with target DNA HAMAP-Rule MF_01588
Region453 – 4586Interaction with target DNA HAMAP-Rule MF_01588
Region519 – 5246Interaction with target DNA HAMAP-Rule MF_01588
Region551 – 5566Interaction with target DNA HAMAP-Rule MF_01588

Sites

Active site1151N6-AMP-lysine intermediate Ref.7
Metal binding4081Zinc
Metal binding4111Zinc
Metal binding4261Zinc
Metal binding4321Zinc
Binding site1131NAD
Binding site1361NAD
Binding site1731NAD By similarity
Binding site2901NAD
Binding site3141NAD Probable
Site4871Interaction with target DNA
Site4921Interaction with target DNA

Experimental info

Mutagenesis101E → A: No effect. Ref.7
Mutagenesis221Y → A or S: Reduces nick joining activity by 99.9%. Ref.7
Mutagenesis221Y → F: Reduces nick joining activity by 91%. Ref.7
Mutagenesis231H → A or Y: Reduces nick joining activity by 90%. Ref.7
Mutagenesis321D → A or E: Reduces nick joining activity by 99%. Ref.7
Mutagenesis321D → N: Reduces nick joining activity by 91%. Ref.7
Mutagenesis351Y → A: Reduces nick joining activity by 98%. Ref.7
Mutagenesis351Y → F: Reduces nick joining activity by 77%. Ref.7
Mutagenesis351Y → S: Reduces nick joining activity by 99.9%. Ref.7
Mutagenesis361D → A: Reduces nick joining activity by 99.8%. Ref.7
Mutagenesis361D → E: Reduces nick joining activity by 96%. Ref.7
Mutagenesis361D → N: Reduces nick joining activity by 88%. Ref.7
Mutagenesis1151K → Q or R: Reduces nick joining activity by 99.9%. Ref.8
Mutagenesis1171D → E: Reduces nick joining activity by 97%. Ref.8
Mutagenesis1171D → N: Reduces nick joining activity by 99.9%. Ref.8
Mutagenesis1181G → A: Reduces nick joining activity by 99.9%. Ref.8
Mutagenesis1381D → A: Reduces nick joining activity by 63%. Ref.8
Mutagenesis1431E → A: Reduces nick joining activity by 48%. Ref.8
Mutagenesis1721G → A: Reduces nick joining activity by 64%. Ref.8
Mutagenesis1731E → A, D or Q: Reduces nick joining activity by 99.9%. Ref.8
Mutagenesis1981N → A: Reduces nick joining activity by 74%. Ref.8
Mutagenesis2001R → A, K or Q: Reduces nick joining activity by 99.9%. Ref.8
Mutagenesis2081R → A, K or Q: Reduces nick joining activity by 99%. Ref.8
Mutagenesis2771R → A: Reduces nick joining activity by 99%. Ref.8
Mutagenesis2851D → E: Reduces nick joining activity by 96%. Ref.8
Mutagenesis2851D → N: Reduces nick joining activity by 99%. Ref.8
Mutagenesis2861G → A: Reduces nick joining activity by 86%. Ref.8
Mutagenesis2881V → A: Reduces nick joining activity by 25%. Ref.8
Mutagenesis2901K → A: Reduces nick joining activity by 87%. Ref.8
Mutagenesis3141K → Q: Reduces nick joining activity by 99%. Ref.8
Mutagenesis3141K → R: Reduces nick joining activity by 95%. Ref.8
Mutagenesis3331R → A or Q: Reduces nick joining activity by over 95%. Abolishes nick joining activity; when associated with A-334. Ref.9
Mutagenesis3341T → A: Abolishes nick joining activity; when associated with A-333. Ref.9
Mutagenesis3421R → A: Reduces nick joining activity by 80%. Ref.9
Mutagenesis3791R → A or Q: Reduces nick joining activity by over 95%. Ref.9
Mutagenesis383 – 3842VI → AA: Reduces nick joining activity by 95%.
Mutagenesis446 – 4472RR → AA: Reduces nick joining activity by 95%.
Mutagenesis4551G → A: Reduces nick joining activity by 50%. Ref.9
Mutagenesis4551G → D or V: Reduces nick joining activity by 95%. Ref.9
Mutagenesis4871R → A: Reduces nick joining activity by over 90%. Ref.9
Mutagenesis4891G → D or V: Reduces nick joining activity by 95%. Ref.9
Mutagenesis5211G → A: Reduces nick joining activity by 95%. Ref.9
Mutagenesis5211G → D or V: Loss of nick joining activity. Ref.9
Mutagenesis5531G → D or V: Reduces nick joining activity by 95%. Ref.9
Mutagenesis6141R → A: Reduces nick joining activity by 85%. Ref.9
Sequence conflict691A → R in AAA24071. Ref.1

Secondary structure

................................................................................................. 671
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P15042 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: DD2BDC64D8E65256

FASTA67173,606
        10         20         30         40         50         60 
MESIEQQLTE LRTTLRHHEY LYHVMDAPEI PDAEYDRLMR ELRELETKHP ELITPDSPTQ 

        70         80         90        100        110        120 
RVGAAPLAAF SQIRHEVPML SLDNVFDEES FLAFNKRVQD RLKNNEKVTW CCELKLDGLA 

       130        140        150        160        170        180 
VSILYENGVL VSAATRGDGT TGEDITSNVR TIRAIPLKLH GENIPARLEV RGEVFLPQAG 

       190        200        210        220        230        240 
FEKINEDARR TGGKVFANPR NAAAGSLRQL DPRITAKRPL TFFCYGVGVL EGGELPDTHL 

       250        260        270        280        290        300 
GRLLQFKKWG LPVSDRVTLC ESAEEVLAFY HKVEEDRPTL GFDIDGVVIK VNSLAQQEQL 

       310        320        330        340        350        360 
GFVARAPRWA VAFKFPAQEQ MTFVRDVEFQ VGRTGAITPV ARLEPVHVAG VLVSNATLHN 

       370        380        390        400        410        420 
ADEIERLGLR IGDKVVIRRA GDVIPQVVNV VLSERPEDTR EVVFPTHCPV CGSDVERVEG 

       430        440        450        460        470        480 
EAVARCTGGL ICGAQRKESL KHFVSRRAMD VDGMGDKIID QLVEKEYVHT PADLFKLTAG 

       490        500        510        520        530        540 
KLTGLERMGP KSAQNVVNAL EKAKETTFAR FLYALGIREV GEATAAGLAA YFGTLEALEA 

       550        560        570        580        590        600 
ASIEELQKVP DVGIVVASHV HNFFAEESNR NVISELLAEG VHWPAPIVIN AEEIDSPFAG 

       610        620        630        640        650        660 
KTVVLTGSLS QMSRDDAKAR LVELGAKVAG SVSKKTDLVI AGEAAGSKLA KAQELGIEVI 

       670 
DEAEMLRLLG S 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence of the lig gene and primary structure of DNA ligase of Escherichia coli."
Ishino Y., Shinagawa H., Makino K., Tsunasawa S., Sakiyama F., Nakata A.
Mol. Gen. Genet. 204:1-7(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-13 AND 666-671.
Strain: K12 / C600 / ATCC 23724 / DSM 3925 / LMG 3041 / NCIB 10222.
[2]O'Connor M.J., Ally A., Ally D., Zhang X., Robichaud M., Backman K.
Submitted (APR-1989) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. expand/collapse author list , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]"Direct binding of FtsZ to ZipA, an essential component of the septal ring structure that mediates cell division in E. coli."
Hale C.A., de Boer P.A.J.
Cell 88:175-185(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-90.
Strain: PB103.
[7]"Conserved residues in domain Ia are required for the reaction of Escherichia coli DNA ligase with NAD+."
Sriskanda V., Shuman S.
J. Biol. Chem. 277:9695-9700(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF GLU-10; TYR-22; HIS-23; ASP-32; TYR-35 AND ASP-36, ACTIVE SITE.
[8]"Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA)."
Zhu H., Shuman S.
J. Biol. Chem. 280:12137-12144(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYS-115; ASP-117; GLY-118; ASP-138; GLU-143; GLY-172; GLU-173; ASN-198; ARG-200; ARG-208; ARG-277; ASP-285; GLY-286; VAL-288; LYS-290 AND LYS-314.
[9]"Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase."
Wang L.K., Nair P.A., Shuman S.
J. Biol. Chem. 283:23343-23352(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ARG-333; THR-334; ARG-342; ARG-379; 383-VAL-ILE-384; 446-ARG-ARG-447; GLY-455; ARG-487; GLY-489; GLY-521; GLY-553 AND ARG-614.
[10]"Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate."
Nandakumar J., Nair P.A., Shuman S.
Mol. Cell 26:257-271(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH ZINC IONS; AMP AND DNA.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRLQECC6. B65015.
RefSeqNP_416906.1. NC_000913.3.
YP_490647.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2OWOX-ray2.30A1-671[»]
4GLXX-ray1.90A1-586[»]
ProteinModelPortalP15042.
SMRP15042. Positions 1-671.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10098N.
IntActP15042. 20 interactions.
MINTMINT-204717.
STRING511145.b2411.

Proteomic databases

PaxDbP15042.
PRIDEP15042.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75464; AAC75464; b2411.
BAA16282; BAA16282; BAA16282.
GeneID12930678.
946885.
KEGGecj:Y75_p2372.
eco:b2411.
PATRIC32120205. VBIEscCol129921_2505.

Organism-specific databases

EchoBASEEB0529.
EcoGeneEG10534. ligA.

Phylogenomic databases

eggNOGCOG0272.
HOGENOMHOG000218459.
KOK01972.
OMAFTAKSPR.
OrthoDBEOG6TTVM9.
PhylomeDBP15042.
ProtClustDBPRK07956.

Enzyme and pathway databases

BioCycEcoCyc:EG10534-MONOMER.
ECOL316407:JW2403-MONOMER.
MetaCyc:EG10534-MONOMER.

Gene expression databases

GenevestigatorP15042.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPMF_01588. DNA_ligase_A.
InterProIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR004150. DNA_ligase_OB.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
SMARTSM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsTIGR00575. dnlj. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP15042.
PROP15042.

Entry information

Entry nameDNLJ_ECOLI
AccessionPrimary (citable) accession number: P15042
Secondary accession number(s): P78197, P78198
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 144 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene