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Protein

DNA ligase

Gene

lig

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-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 sitei247 – 2471ATPUniRule annotation
Active sitei249 – 2491N6-AMP-lysine intermediateUniRule annotation
Binding sitei254 – 2541ATPUniRule annotation
Binding sitei269 – 2691ATPUniRule annotation
Binding sitei299 – 2991ATPUniRule annotation
Binding sitei339 – 3391ATPUniRule annotation
Binding sitei414 – 4141ATPUniRule annotation
Binding sitei420 – 4201ATPUniRule 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, Metal-binding, Nucleotide-binding

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:ligUniRule annotation
Ordered Locus Names:PYRAB05430
ORF Names:PAB2002
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000000810: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 559559DNA ligasePRO_0000407282Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliP0CL75.
SMRiP0CL75. Positions 1-559.
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.

P0CL75-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MRYIELAQLY QKLEKTTMKL IKTRLVADFL KKVPEDHLEF IPYLILGDVF
60 70 80 90 100
PEWDERELGV GEKLLIKAVS MATGIDSKEI ENSVKDTGDL GESIALAVKK
110 120 130 140 150
RKQKSFFSQP LTIKRVYQTL VKVAETTGEG SQDKKMKYLA NLFMDAEPIE
160 170 180 190 200
AKYIARTVLG TMRTGVAEGL LRDAISLAFN VKVELVERAY MLTSDFGFVA
210 220 230 240 250
KIAKTEGNDG LAKVTIQIGK PIKPMLAQQA ANIKEALLEM GGEAEFEIKY
260 270 280 290 300
DGARVQVHKD GEKVTIYSRR LENVTRAIPE IVEAIKEALK PTKAIVEGEL
310 320 330 340 350
VAIGEDGRPL PFQYVLRRFR RKYNIEEMME KIPLELNLFD VLYVDGVSLI
360 370 380 390 400
DTKFMERRKK LEEIVETNGK VKIAENLITK NVEEAEQFYK RALEMGHEGL
410 420 430 440 450
MAKRLDAVYE PGNRGKKWLK IKPTMENLDL VIIGAEWGEG RRAHLLGSFI
460 470 480 490 500
LGAYDPETGE FLEVGKVGSG FTDDDLVEFT KMLKPLIIKE EGKRVWIQPK
510 520 530 540 550
VVIEVTYQEI QKSPKYRSGF ALRFPRYVAL REDKGPEDAD TIERIAQLYE

LQERMKGKV
Length:559
Mass (Da):63,553
Last modified:April 5, 2011 - v1
Checksum:i64CDBA1BBD188433
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49465.1.
HE613800 Genomic DNA. Translation: CCE69932.1.
PIRiB75173.
RefSeqiNP_126234.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49465; CAB49465; PAB2002.
GeneIDi1495445.
KEGGipab:PAB2002.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49465.1.
HE613800 Genomic DNA. Translation: CCE69932.1.
PIRiB75173.
RefSeqiNP_126234.1. NC_000868.1.

3D structure databases

ProteinModelPortaliP0CL75.
SMRiP0CL75. Positions 1-559.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49465; CAB49465; PAB2002.
GeneIDi1495445.
KEGGipab:PAB2002.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: GE5 / Orsay.
  2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
    Gao J., Wang J.
    Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: GE5 / Orsay.

Entry informationi

Entry nameiDNLI_PYRAB
AccessioniPrimary (citable) accession number: P0CL75
Secondary accession number(s): G8ZGQ3, Q9HH10, Q9V185
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 5, 2011
Last sequence update: April 5, 2011
Last modified: February 4, 2015
This is version 28 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

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.