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C6A2U9 (C6A2U9_THESM) Unreviewed, UniProtKB/TrEMBL

Last modified June 11, 2014. Version 37. Feed History...

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

Names and origin

Protein namesRecommended name:
DNA ligase HAMAP-Rule MF_00407 RuleBase RU000617

EC=6.5.1.1 HAMAP-Rule MF_00407 RuleBase RU000617
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP] HAMAP-Rule MF_00407
Gene names
Name:lig HAMAP-Rule MF_00407
Ordered Locus Names:TSIB_0885 EMBL ACS89944.1
OrganismThermococcus sibiricus (strain MM 739 / DSM 12597) [Complete proteome] [HAMAP] EMBL ACS89944.1
Taxonomic identifier604354 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus

Protein attributes

Sequence length560 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair By similarity. HAMAP-Rule MF_00407

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_00407

Cofactor

Divalent metal cations By similarity. HAMAP-Rule MF_00407

Sequence similarities

Belongs to the ATP-dependent DNA ligase family. HAMAP-Rule MF_00407 RuleBase RU004196

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Nucleotide binding248 – 2514AMP PDB 4EQ5

Sites

Active site2501N6-AMP-lysine intermediate By similarity HAMAP-Rule MF_00407
Binding site2481ATP By similarity HAMAP-Rule MF_00407
Binding site2551ATP By similarity HAMAP-Rule MF_00407
Binding site2701AMP PDB 4EQ5
Binding site2701ATP By similarity HAMAP-Rule MF_00407
Binding site3001AMP PDB 4EQ5
Binding site3001ATP By similarity HAMAP-Rule MF_00407
Binding site3401AMP PDB 4EQ5
Binding site3401ATP By similarity HAMAP-Rule MF_00407
Binding site4041AMP PDB 4EQ5
Binding site4151AMP PDB 4EQ5
Binding site4151ATP By similarity HAMAP-Rule MF_00407
Binding site4211ATP By similarity HAMAP-Rule MF_00407

Sequences

Sequence LengthMass (Da)Tools
C6A2U9 [UniParc].

Last modified September 1, 2009. Version 1.
Checksum: 3B20F1C68A04EDA8

FASTA56063,448
        10         20         30         40         50         60 
MLYKELVELY KRLEKTTLKT LKTKFVSDFL KSVEKPELLE VIPYLILGKV FPDWDERELG 

        70         80         90        100        110        120 
IGEKLLIKAV SMATGINSEE IENSVRDTGD LGESIALALN KRKQKSFFSQ PLTIERVYNT 

       130        140        150        160        170        180 
LVKIAEASGA GSQDRKLKYL ANLFMDASPD EGKYLARTVL GIMRTGVAEG LLRDALADAF 

       190        200        210        220        230        240 
KVRVELVERA YMLTSDFGFV AKVAKLEGDE GLAKVKIQVG KPIKPMLAQM AANVREALVE 

       250        260        270        280        290        300 
MGGEAEFEIK YDGARVQVHK NGNKVLIYSR RLENVTKSIP EVVERVKEAL KPEKVIVEGE 

       310        320        330        340        350        360 
LVAVEETGRP RPFQYVLRRF RRKYNIEEMI EKIPLELNLF DILYVDGQNM IDTPFMERRK 

       370        380        390        400        410        420 
VLESVVNSNE WIKSAENLIT KSPEEAEAFY HKALDLGHEG LMAKRLDSTY EPGNRGKKWL 

       430        440        450        460        470        480 
KIKPTMENLD LVVLGAEWGE GRRSGVLSSF LLGAYDPVKG DFVPVGKVGS GFTDEDLVEF 

       490        500        510        520        530        540 
TKMLKPLIKK EHGKEVELEP KVVIEVAYQE IQKSPKYESG FALRFPRYIA LREDKGPEDA 

       550        560 
DTVQRLAELY QFQERLKGGR 

« Hide

References

« Hide 'large scale' references
[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 12597.
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001463 Genomic DNA. Translation: ACS89944.1.
RefSeqYP_002994293.1. NC_012883.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4EQ5X-ray2.85A2-560[»]
ProteinModelPortalC6A2U9.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING604354.TSIB_0885.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACS89944; ACS89944; TSIB_0885.
GeneID8095876.
KEGGtsi:TSIB_0885.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1793.
HOGENOMHOG000036008.
KOK10747.
OMAARVQVHK.

Enzyme and pathway databases

BioCycTSIB604354:GHMS-909-MONOMER.

Family and domain databases

Gene3D1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPMF_00407. DNA_ligase.
InterProIPR022865. 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]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameC6A2U9_THESM
AccessionPrimary (citable) accession number: C6A2U9
Entry history
Integrated into UniProtKB/TrEMBL: September 1, 2009
Last sequence update: September 1, 2009
Last modified: June 11, 2014
This is version 37 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)