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Protein

DNA ligase

Gene

lig

Organism
Hyperthermus butylicus (strain DSM 5456 / JCM 9403)
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 ATP, ADP and GTP, but not CTP, TTP or NAD+.1 Publication

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).1 PublicationUniRule annotation
ADP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + phosphate + (deoxyribonucleotide)(n+m).1 Publication
GTP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = GMP + diphosphate + (deoxyribonucleotide)(n+m).1 Publication

Cofactori

Mg2+1 Publication, Mn2+1 Publication

pH dependencei

Optimum pH is 8.0.1 Publication

Temperature dependencei

Optimum temperature is 75 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei266 – 2661ATPUniRule annotation
Active sitei268 – 2681N6-AMP-lysine intermediateUniRule annotation
Binding sitei273 – 2731ATPUniRule annotation
Binding sitei288 – 2881ATPUniRule annotation
Binding sitei318 – 3181ATPUniRule annotation
Binding sitei358 – 3581ATPUniRule annotation
Binding sitei435 – 4351ATPUniRule annotation
Binding sitei441 – 4411ATPUniRule 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, GTP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciHBUT415426:GC56-421-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase1 PublicationUniRule annotation (EC:6.5.1.71 Publication)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP/ADP/GTP]Curated
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:Hbut_0421
OrganismiHyperthermus butylicus (strain DSM 5456 / JCM 9403)
Taxonomic identifieri415426 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesPyrodictiaceaeHyperthermus
ProteomesiUP000002593: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 608608DNA ligasePRO_0000365248Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi415426.Hbut_0421.

Structurei

3D structure databases

ProteinModelPortaliA2BJX6.
SMRiA2BJX6. Positions 3-598.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiLACYDEQ.

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.

A2BJX6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSMPFSVLAE TFEKLERVTA RTQMLLYLVE LFKKTPPEII DKVVYFIQGK
60 70 80 90 100
LWPDWKGLPE LGIGEKMLIK AASIALHVSE KQIEQLVKKL GDTGKAIEMI
110 120 130 140 150
KREKQQKQKA VGLLAFMQKP SGGESTLTVE KVYDTLARIA LVQGEGSRDI
160 170 180 190 200
KLKLLAGLLA EASPREAKYI ARFVEGRLRL GVGDATIMEA LAVVYGGSAA
210 220 230 240 250
MRSVVERAYN LRADLGMVAK ILATQGIDAL KNIKPEVGVP IRPMLAERLN
260 270 280 290 300
DPVEIIKKLG GRALVEYKYD GERAQIHKKG DKIWIFSRRL ENITHMYPDV
310 320 330 340 350
VEMAKKGIKA EEAIVEGEIV AIDPETGEFR PFQVLMHRRR KKDVHAVLSE
360 370 380 390 400
IPVAVFLFDT LYVNGEDLTL KPLPARHEVL EKIIEQSDTW RIAEGIVTSD
410 420 430 440 450
PQELESFFLK AIEDGAEGVM AKAIHDRSIY QAGARGWLWI KYKRDYKSEM
460 470 480 490 500
SDTVDLVVIG AFYGKGRRGG KFGALLMAAY DPDTDTFKSV CKVGSGFTDE
510 520 530 540 550
DLERLDDMLK PYISDKKPAR VDSQMKPDVW VEPTLVAEII GAELTLSPIH
560 570 580 590 600
TCCYGWVKSG AGISIRFPRF IRWRPDKGPE DATTTKELYE MYKRQLRRIK

EEEAPTGV
Length:608
Mass (Da):68,330
Last modified:February 20, 2007 - v1
Checksum:i7D16CF4AEB60771E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000493 Genomic DNA. Translation: ABM80287.1.
RefSeqiWP_011821605.1. NC_008818.1.
YP_001012632.1. NC_008818.1.

Genome annotation databases

EnsemblBacteriaiABM80287; ABM80287; Hbut_0421.
GeneIDi4781994.
KEGGihbu:Hbut_0421.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000493 Genomic DNA. Translation: ABM80287.1.
RefSeqiWP_011821605.1. NC_008818.1.
YP_001012632.1. NC_008818.1.

3D structure databases

ProteinModelPortaliA2BJX6.
SMRiA2BJX6. Positions 3-598.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi415426.Hbut_0421.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABM80287; ABM80287; Hbut_0421.
GeneIDi4781994.
KEGGihbu:Hbut_0421.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiLACYDEQ.

Enzyme and pathway databases

BioCyciHBUT415426:GC56-421-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. "The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C."
    Bruegger K., Chen L., Stark M., Zibat A., Redder P., Ruepp A., Awayez M., She Q., Garrett R.A., Klenk H.-P.
    Archaea 2:127-135(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 5456 / JCM 9403.
  2. "Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance."
    Kim J.H., Lee K.K., Sun Y., Seo G.J., Cho S.S., Kwon S.H., Kwon S.T.
    Extremophiles 17:515-522(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: DSM 5456 / JCM 9403.

Entry informationi

Entry nameiDNLI_HYPBU
AccessioniPrimary (citable) accession number: A2BJX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 3, 2009
Last sequence update: February 20, 2007
Last modified: February 4, 2015
This is version 65 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, 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.