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Protein

DNA ligase

Gene

lig

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 5 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 also use NAD, but less efficiently than ATP.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+UniRule annotation1 Publication

pH dependencei

Optimum pH is 8.0.1 Publication

Temperature dependencei

Still active at 100 degrees Celsius. Thermostable.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei247 – 2471ATPUniRule annotation
Active sitei249 – 2491N6-AMP-lysine intermediateUniRule annotation
Binding sitei254 – 2541ATPUniRule annotation
Binding sitei269 – 2691ATPUniRule annotation
Binding sitei299 – 2991ATPUniRule annotation
Binding sitei339 – 3391ATPUniRule annotation
Binding sitei414 – 4141ATPUniRule annotation
Binding sitei420 – 4201ATPUniRule 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

Enzyme and pathway databases

BioCyciTKOD69014:GH72-2184-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase1 PublicationUniRule annotation (EC:6.5.1.6UniRule annotation1 Publication)
Alternative name(s):
Lig(Tk)1 Publication
Polydeoxyribonucleotide synthase [ATP/NAD(+)]UniRule annotationCurated
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:TK2140
OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 559559DNA ligasePRO_0000059615Add
BLAST

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi69014.TK2140.

Structurei

3D structure databases

ProteinModelPortaliQ9HHC4.
SMRiQ9HHC4. Positions 1-558.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
InParanoidiQ9HHC4.
KOiK10747.

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.

Q9HHC4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRYSELADLY RRLEKTTLKT LKTKFVADFL KKTPDELLEI VPYLILGKVF
60 70 80 90 100
PDWDERELGV GEKLLIKAVS MATGVPEKEI EDSVRDTGDL GESVALAIKK
110 120 130 140 150
KKQKSFFSQP LTIKRVYDTF VKIAEAQGEG SQDRKMKYLA NLFMDAEPEE
160 170 180 190 200
GKYLARTVLG TMRTGVAEGI LRDAIAEAFR VKPELVERAY MLTSDFGYVA
210 220 230 240 250
KIAKLEGNEG LSKVRIQIGK PIRPMLAQNA ASVKDALIEM GGEAAFEIKY
260 270 280 290 300
DGARVQVHKD GDKVIVYSRR LENVTRSIPE VIEAIKAALK PEKAIVEGEL
310 320 330 340 350
VAVGENGRPR PFQYVLRRFR RKYNIDEMIE KIPLELNLFD VMFVDGESLI
360 370 380 390 400
ETKFIDRRNK LEEIVKESEK IKLAEQLITK KVEEAEAFYR RALELGHEGL
410 420 430 440 450
MAKRLDSIYE PGNRGKKWLK IKPTMENLDL VIIGAEWGEG RRAHLLGSFL
460 470 480 490 500
VAAYDPHSGE FLPVGKVGSG FTDEDLVEFT KMLKPYIVRQ EGKFVEIEPK
510 520 530 540 550
FVIEVTYQEI QKSPKYKSGF ALRFPRYVAL REDKSPEEAD TIERVAELYE

LQERFKAKK
Length:559
Mass (Da):63,749
Last modified:June 20, 2001 - v2
Checksum:i91AB32542E03D20D
GO

Sequence cautioni

The sequence BAB15949.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence BAD86329.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB042527 Genomic DNA. Translation: BAB15949.1. Different initiation.
AP006878 Genomic DNA. Translation: BAD86329.1. Different initiation.
RefSeqiYP_184553.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD86329; BAD86329; TK2140.
GeneIDi3235455.
KEGGitko:TK2140.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB042527 Genomic DNA. Translation: BAB15949.1. Different initiation.
AP006878 Genomic DNA. Translation: BAD86329.1. Different initiation.
RefSeqiYP_184553.1. NC_006624.1.

3D structure databases

ProteinModelPortaliQ9HHC4.
SMRiQ9HHC4. Positions 1-558.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi69014.TK2140.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD86329; BAD86329; TK2140.
GeneIDi3235455.
KEGGitko:TK2140.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
InParanoidiQ9HHC4.
KOiK10747.

Enzyme and pathway databases

BioCyciTKOD69014:GH72-2184-MONOMER.

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. "A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity."
    Nakatani M., Ezaki S., Atomi H., Imanaka T.
    J. Bacteriol. 182:6424-6433(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.
  2. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
    Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
    Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Entry informationi

Entry nameiDNLI_THEKO
AccessioniPrimary (citable) accession number: Q9HHC4
Secondary accession number(s): Q5JHF2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: June 20, 2001
Last modified: February 4, 2015
This is version 101 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

Complete proteome, Direct protein sequencing, Reference 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.