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Protein

DNA ligase

Gene

lig

Organism
Thermococcus onnurineus (strain NA1)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. Can use both ATP and NAD+, but NAD+ may be a preferred nucleotide cofactor.1 Publication

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).UniRule annotation1 Publication
NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation1 Publication

Cofactori

Mg2+1 Publication, Zn2+1 PublicationNote: Not stimulated by Ca(2+), Mn(2+) and Ni2+.1 Publication

pH dependencei

Optimum pH is 7.5.1 Publication

Temperature dependencei

Optimum temperature is 80 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei250 – 2501ATPUniRule annotation
Active sitei252 – 2521N6-AMP-lysine intermediateUniRule annotation
Binding sitei257 – 2571ATPUniRule annotation
Binding sitei272 – 2721ATPUniRule annotation
Binding sitei302 – 3021ATPUniRule annotation
Binding sitei342 – 3421ATPUniRule annotation
Binding sitei417 – 4171ATPUniRule annotation
Binding sitei423 – 4231ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: InterPro
  3. DNA ligase (ATP) activity Source: UniProtKB-HAMAP
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. DNA biosynthetic process Source: InterPro
  4. DNA ligation involved in DNA repair Source: InterPro
  5. DNA recombination Source: UniProtKB-HAMAP
  6. DNA replication Source: UniProtKB-HAMAP
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, NAD, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciTONN523850:GC7X-1562-MONOMER.
BRENDAi6.5.1.1. 289156.
6.5.1.2. 289156.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase1 PublicationUniRule annotation (EC:6.5.1.6UniRule annotation1 Publication)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP/NAD(+)]UniRule annotationCurated
TNA1_lig1 Publication
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:TON_1515Imported
OrganismiThermococcus onnurineus (strain NA1)
Taxonomic identifieri523850 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000002727: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 562562DNA ligasePRO_0000431840Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi523850.TON_1515.

Structurei

3D structure databases

ProteinModelPortaliB6YTR4.
SMRiB6YTR4. Positions 4-561.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.UniRule annotationCurated

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiARVQVHK.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPiMF_00407. DNA_ligase.
InterProiIPR022865. DNA_ligae_ATP-dep_bac/arc.
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.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B6YTR4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGDMKYTELS DLYRRLEKTT LKTLKTKFVA DFLKKTPDEL LEVVPYLILG
60 70 80 90 100
KVFPDWDERE LGVGEKLLIK AVSMATGVQE REIENSVKDT GDLGESVALA
110 120 130 140 150
LKKKKQKSFF SQPLTIKRVY QTFIKIAEAS GEGSQDRKLK YLANIFMDAQ
160 170 180 190 200
PEEGKYIART VLGMMRTGVA EGILRDAIAE AFKVKAELVE RAYMLTSDFG
210 220 230 240 250
YVAKVAKLEG NDGLGKVHIQ IGKPIRPMLA QNAASVKEAL LEMGAEAAFE
260 270 280 290 300
IKYDGARVQV HKDGDRVVIY SRRLENVTRS IPEVVDAIKA SIKSEKAIVE
310 320 330 340 350
GELVAVGEGG RPRPFQYVLR RFRRKYNIEE MIEKIPLELN LFDVLYVDGE
360 370 380 390 400
PLIDTPFRER RAKLEEIVEE GEKLKLAQQL VTKKVEEAEE FYKKALELGH
410 420 430 440 450
EGLMAKRLDS VYEPGNRGKK WLKIKPTMED LDLVIIGAEW GEGRRAHLLG
460 470 480 490 500
SFLVAAYDPH SGEFVPVGKV GSGFTDEDLV EFTKMLKPLI IGGEGKFVEI
510 520 530 540 550
EPKVVIQVTY QEIQKSPKYR SGFALRFPRY VALREDKSPE EADTIERIAQ
560
LYEFQERFKA KK
Length:562
Mass (Da):63,655
Last modified:January 20, 2009 - v1
Checksum:iA54BDEB51585437D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ223722 Genomic DNA. Translation: ABC11973.1.
CP000855 Genomic DNA. Translation: ACJ17005.1.
RefSeqiWP_012572477.1. NC_011529.1.
YP_002307902.1. NC_011529.1.

Genome annotation databases

EnsemblBacteriaiACJ17005; ACJ17005; TON_1515.
GeneIDi7018552.
KEGGiton:TON_1515.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ223722 Genomic DNA. Translation: ABC11973.1.
CP000855 Genomic DNA. Translation: ACJ17005.1.
RefSeqiWP_012572477.1. NC_011529.1.
YP_002307902.1. NC_011529.1.

3D structure databases

ProteinModelPortaliB6YTR4.
SMRiB6YTR4. Positions 4-561.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi523850.TON_1515.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACJ17005; ACJ17005; TON_1515.
GeneIDi7018552.
KEGGiton:TON_1515.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiARVQVHK.

Enzyme and pathway databases

BioCyciTONN523850:GC7X-1562-MONOMER.
BRENDAi6.5.1.1. 289156.
6.5.1.2. 289156.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPiMF_00407. DNA_ligase.
InterProiIPR022865. DNA_ligae_ATP-dep_bac/arc.
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.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp."
    Kim Y.J., Lee H.S., Bae S.S., Jeon J.H., Yang S.H., Lim J.K., Kang S.G., Kwon S.T., Lee J.H.
    Biotechnol. Lett. 28:401-407(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: NA1.
  2. "The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism."
    Lee H.S., Kang S.G., Bae S.S., Lim J.K., Cho Y., Kim Y.J., Jeon J.H., Cha S.-S., Kwon K.K., Kim H.-T., Park C.-J., Lee H.-W., Kim S.I., Chun J., Colwell R.R., Kim S.-J., Lee J.-H.
    J. Bacteriol. 190:7491-7499(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NA1.

Entry informationi

Entry nameiDNLI_THEON
AccessioniPrimary (citable) accession number: B6YTR4
Secondary accession number(s): Q2Q452
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 4, 2015
Last sequence update: January 20, 2009
Last modified: March 4, 2015
This is version 46 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. 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.