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Protein

DNA ligase

Gene

lig

Organism
Thermococcus sibiricus (strain MM 739 / DSM 12597)
Status
Unreviewed-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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei248 – 2481ATPUniRule annotation
Active sitei250 – 2501N6-AMP-lysine intermediateUniRule annotation
Binding sitei255 – 2551ATPUniRule annotation
Binding sitei270 – 2701AMPCombined sources
Binding sitei270 – 2701ATPUniRule annotation
Binding sitei300 – 3001AMPCombined sources
Binding sitei300 – 3001ATPUniRule annotation
Binding sitei340 – 3401AMPCombined sources
Binding sitei340 – 3401ATPUniRule annotation
Binding sitei404 – 4041AMPCombined sources
Binding sitei415 – 4151AMPCombined sources
Binding sitei415 – 4151ATPUniRule annotation
Binding sitei421 – 4211ATPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi248 – 2514AMPCombined sources

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

LigaseUniRule annotation

Keywords - Biological processi

Cell cycle, Cell divisionUniRule annotation, DNA damage, DNA recombinationUniRule annotation, DNA repairUniRule annotation, DNA replicationUniRule annotation

Keywords - Ligandi

ATP-bindingUniRule annotation, MagnesiumUniRule annotation, Metal-bindingUniRule annotation, NADUniRule annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciTSIB604354:GHMS-909-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.1UniRule annotation, EC:6.5.1.6UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP/NAD(+)]UniRule annotation
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:TSIB_0885Imported
OrganismiThermococcus sibiricus (strain MM 739 / DSM 12597)Imported
Taxonomic identifieri604354 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000009079: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi604354.TSIB_0885.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EQ5X-ray2.85A2-560[»]
ProteinModelPortaliC6A2U9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiGRPRPFQ.

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.

C6A2U9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLYKELVELY KRLEKTTLKT LKTKFVSDFL KSVEKPELLE VIPYLILGKV
60 70 80 90 100
FPDWDERELG IGEKLLIKAV SMATGINSEE IENSVRDTGD LGESIALALN
110 120 130 140 150
KRKQKSFFSQ PLTIERVYNT LVKIAEASGA GSQDRKLKYL ANLFMDASPD
160 170 180 190 200
EGKYLARTVL GIMRTGVAEG LLRDALADAF KVRVELVERA YMLTSDFGFV
210 220 230 240 250
AKVAKLEGDE GLAKVKIQVG KPIKPMLAQM AANVREALVE MGGEAEFEIK
260 270 280 290 300
YDGARVQVHK NGNKVLIYSR RLENVTKSIP EVVERVKEAL KPEKVIVEGE
310 320 330 340 350
LVAVEETGRP RPFQYVLRRF RRKYNIEEMI EKIPLELNLF DILYVDGQNM
360 370 380 390 400
IDTPFMERRK VLESVVNSNE WIKSAENLIT KSPEEAEAFY HKALDLGHEG
410 420 430 440 450
LMAKRLDSTY EPGNRGKKWL KIKPTMENLD LVVLGAEWGE GRRSGVLSSF
460 470 480 490 500
LLGAYDPVKG DFVPVGKVGS GFTDEDLVEF TKMLKPLIKK EHGKEVELEP
510 520 530 540 550
KVVIEVAYQE IQKSPKYESG FALRFPRYIA LREDKGPEDA DTVQRLAELY
560
QFQERLKGGR
Length:560
Mass (Da):63,448
Last modified:September 1, 2009 - v1
Checksum:i3B20F1C68A04EDA8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001463 Genomic DNA. Translation: ACS89944.1.
RefSeqiWP_015849163.1. NC_012883.1.
YP_002994293.1. NC_012883.1.

Genome annotation databases

EnsemblBacteriaiACS89944; ACS89944; TSIB_0885.
GeneIDi8095876.
KEGGitsi:TSIB_0885.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001463 Genomic DNA. Translation: ACS89944.1.
RefSeqiWP_015849163.1. NC_012883.1.
YP_002994293.1. NC_012883.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EQ5X-ray2.85A2-560[»]
ProteinModelPortaliC6A2U9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi604354.TSIB_0885.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACS89944; ACS89944; TSIB_0885.
GeneIDi8095876.
KEGGitsi:TSIB_0885.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiGRPRPFQ.

Enzyme and pathway databases

BioCyciTSIB604354:GHMS-909-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. "Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis."
    Mardanov A.V., Ravin N.V., Svetlitchnyi V.A., Beletsky A.V., Miroshnichenko M.L., Bonch-Osmolovskaya E.A., Skryabin K.G.
    Appl. Environ. Microbiol. 75:4580-4588(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MM 739 / DSM 12597Imported.
  2. "Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus."
    Petrova T.E., Bezsudnova E.Y., Dorokhov B.D., Slutskaya E.S., Polyakov K.M., Dorovatovskiy P.V., Ravin N.V., Skryabin K.G., Kovalchuk M.V., Popov V.O.
    Acta Crystallogr. F 68:163-165(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 2-560 IN COMPLEX WITH AMP.

Entry informationi

Entry nameiC6A2U9_THESM
AccessioniPrimary (citable) accession number: C6A2U9
Entry historyi
Integrated into UniProtKB/TrEMBL: September 1, 2009
Last sequence update: September 1, 2009
Last modified: February 4, 2015
This is version 42 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteomeImported

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.