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Protein

DNA ligase

Gene

lig

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
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 ADP, but not 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

Cofactori

Mg2+1 Publication, Mn2+1 PublicationNote: Less active with Ca(2+) or Co(2+). Not active with Cu(2+), Zn(2+), Sr(2+) or Ni2+.1 Publication

Enzyme regulationi

Inhibited in the presence of 100 mM KCl, NaCl or NH4Cl.1 Publication

pH dependencei

Optimum pH is 7.5.1 Publication

Temperature dependencei

Optimum temperature is 70 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei262 – 2621ATPUniRule annotation
Active sitei264 – 2641N6-AMP-lysine intermediateUniRule annotation
Binding sitei269 – 2691ATPUniRule annotation
Binding sitei284 – 2841ATPUniRule annotation
Binding sitei314 – 3141ATPUniRule annotation
Binding sitei354 – 3541ATPUniRule annotation
Binding sitei431 – 4311ATPUniRule annotation
Binding sitei437 – 4371ATPUniRule 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, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciAPER272557:GJD6-774-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase1 PublicationUniRule annotation (EC:6.5.1.-1 Publication)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP/ADP]Curated
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:APE_1094.1
OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Taxonomic identifieri272557 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
ProteomesiUP000002518: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 602602DNA ligasePRO_0000059600Add
BLAST

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi272557.APE_1094.1.

Structurei

3D structure databases

ProteinModelPortaliQ9YD18.
SMRiQ9YD18. Positions 1-594.
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.

Q9YD18-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPFKPVAEAF ASMERITSRT QLTLLLTRLF KSTPPGAIGI VVYLIQGKLG
60 70 80 90 100
PDWKGLPELG VGEKLLVKAI ALAYKATEER VERLYKSVGD LGSVAERLSR
110 120 130 140 150
EYRSRAARAV TLEAFMAGGG EALTVRRVYN TLYRIAMAQG EGSRDIKLRL
160 170 180 190 200
LAGLLADAEP VEAKYIVRFV EGRLRVGVGD ATVLDALAMA FGGGAHARPV
210 220 230 240 250
IERAYNLRAD LGYIAEVVAR EGVDALRGVK PQVGVPIRPM LAERGRDPAE
260 270 280 290 300
ILRKVGGRAV VEYKYDGERA QIHKKDGEVY IYSRRLENIT RMFPDVVEMA
310 320 330 340 350
RKGLKAGEAI VEGEIVAVDP DNYEIQPFQV LMQRKRKHDI HRVMREVPVA
360 370 380 390 400
VFLFDALYVD GEDLTSKPLP ERRRRLKEIV VETPLWRLAE SIETSDPEEL
410 420 430 440 450
WTFFLKAIEE GAEGVMVKAV HRDSVYTAGV RGWLWVKLKR DYKSEMMDTV
460 470 480 490 500
DLVVVGAFYG RGKRGGKLSS LLMAAYDPDR DVFPTVCKVA TGFTDEELDR
510 520 530 540 550
MNEMLKKHII PRKHPRVESR IEPDVWVEPA LVAEILGAEL TLSPMHTCCL
560 570 580 590 600
NTVRPGVGIS IRFPRFIRWR DDKSPEDATT THELLEMYKR QLRRVEEPAE

QV
Length:602
Mass (Da):67,748
Last modified:June 20, 2001 - v2
Checksum:iAD1DC7521FAFD814
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA80079.2.
PIRiG72709.
RefSeqiNP_147713.2. NC_000854.2.
WP_010866170.1. NC_000854.2.

Genome annotation databases

EnsemblBacteriaiBAA80079; BAA80079; APE_1094.1.
GeneIDi1445787.
KEGGiape:APE_1094.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA80079.2.
PIRiG72709.
RefSeqiNP_147713.2. NC_000854.2.
WP_010866170.1. NC_000854.2.

3D structure databases

ProteinModelPortaliQ9YD18.
SMRiQ9YD18. Positions 1-594.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272557.APE_1094.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA80079; BAA80079; APE_1094.1.
GeneIDi1445787.
KEGGiape:APE_1094.1.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiLACYDEQ.

Enzyme and pathway databases

BioCyciAPER272557:GJD6-774-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.
  2. "A novel ADP-dependent DNA ligase from Aeropyrum pernix K1."
    Jeon S.J., Ishikawa K.
    FEBS Lett. 550:69-73(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.

Entry informationi

Entry nameiDNLI_AERPE
AccessioniPrimary (citable) accession number: Q9YD18
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: June 20, 2001
Last modified: February 4, 2015
This is version 96 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, 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.