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Protein

DNA ligase

Gene

dnll

Organism
Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / M1) (Methanobacterium ruminantium)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei246 – 2461ATPUniRule annotation
Active sitei248 – 2481N6-AMP-lysine intermediateUniRule annotation
Binding sitei253 – 2531ATPUniRule annotation
Binding sitei268 – 2681ATPUniRule annotation
Binding sitei298 – 2981ATPUniRule annotation
Binding sitei414 – 4141ATPUniRule annotation
Binding sitei420 – 4201ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

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, Nucleotide-binding

Enzyme and pathway databases

BioCyciMRUM634498:GHDG-468-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.1UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]UniRule annotation
Gene namesi
Name:dnllImported
Synonyms:ligUniRule annotation
Ordered Locus Names:mru_0445Imported
OrganismiMethanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / M1) (Methanobacterium ruminantium)Imported
Taxonomic identifieri634498 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanobrevibacter
ProteomesiUP000008680 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi634498.mru_0445.

Structurei

3D structure databases

ProteinModelPortaliD3E0Q0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

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.

D3E0Q0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKYEELVNVY EALGATTKRL EKTEILADFL KTVELEDLQK ITLMALGRVF
60 70 80 90 100
PPWSEEEQGI GDKLVMKAVG DAVGVSVAVV EDAIRDEGDI GAAAEKLYGK
110 120 130 140 150
KTQMTFFSQP LTVNFVYNQL RKLAKITGNR STAKKISNIL ELLSSASALE
160 170 180 190 200
AKYICRTILE ELRIGVGEGI IRDAISQAFG VDKALAERAH MLTNDLGLVA
210 220 230 240 250
KVAKEEGEDG LKKLSLIPGR PVKPMLAQLS EGIEISINEM GCALCETKYD
260 270 280 290 300
GIRMQVHKKD DEITIFTRRL ENVTMALPEA VDLIREAFPD EDFIAEGEII
310 320 330 340 350
AIRDGKPTTF QNILQRVRRK HNIEEAMEKV PIKIYLYDLL YFKEPTIDEP
360 370 380 390 400
IIKRREILES VVDCSNPNLA LSSLVKVGPD NIDDAVDLFN KSIEGGHEGI
410 420 430 440 450
MIKDCDEPYI PGIRGKKMLK LKAEPETLDA VVIGGVKGIG KRGDFIGSYV
460 470 480 490 500
IALRDENDQL QPIAHVGTGL SDDDLANLTE KMEALKITEK GTRITVHPKI
510 520 530 540 550
VFEIAYSEIV KSPEYSAGYS LRFPVVKRIR DDKGVDDIDT IERLESMFKG
Length:550
Mass (Da):61,113
Last modified:March 23, 2010 - v1
Checksum:i5C33843B98B80B05
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001719 Genomic DNA. Translation: ADC46296.1.
RefSeqiWP_012955247.1. NC_013790.1.
YP_003423188.1. NC_013790.1.

Genome annotation databases

EnsemblBacteriaiADC46296; ADC46296; mru_0445.
GeneIDi8770085.
KEGGimru:mru_0445.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001719 Genomic DNA. Translation: ADC46296.1.
RefSeqiWP_012955247.1. NC_013790.1.
YP_003423188.1. NC_013790.1.

3D structure databases

ProteinModelPortaliD3E0Q0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi634498.mru_0445.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADC46296; ADC46296; mru_0445.
GeneIDi8770085.
KEGGimru:mru_0445.

Phylogenomic databases

HOGENOMiHOG000036008.
KOiK10747.
OMAiGRPRPFQ.

Enzyme and pathway databases

BioCyciMRUM634498:GHDG-468-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

  1. "The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions."
    Leahy S.C., Kelly W.J., Altermann E., Ronimus R.S., Yeoman C.J., Pacheco D.M., Li D., Kong Z., McTavish S., Sang C., Lambie S.C., Janssen P.H., Dey D., Attwood G.T.
    PLoS ONE 5:E8926-E8926(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 35063 / DSM 1093 / JCM 13430 / M1Imported.

Entry informationi

Entry nameiD3E0Q0_METRM
AccessioniPrimary (citable) accession number: D3E0Q0
Entry historyi
Integrated into UniProtKB/TrEMBL: March 23, 2010
Last sequence update: March 23, 2010
Last modified: June 24, 2015
This is version 38 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference 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.