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Protein

DNA ligase

Gene

lig

Organism
Pyrobaculum calidifontis (strain JCM 11548 / VA1)
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 sitei249 – 2491ATPUniRule annotation
Active sitei251 – 2511N6-AMP-lysine intermediateUniRule annotation
Binding sitei256 – 2561ATPUniRule annotation
Binding sitei271 – 2711ATPUniRule annotation
Binding sitei301 – 3011ATPUniRule annotation
Binding sitei341 – 3411ATPUniRule annotation
Binding sitei416 – 4161ATPUniRule annotation
Binding sitei422 – 4221ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

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

Enzyme and pathway databases

BioCyciPCAL410359:GIX2-39-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:ligUniRule annotation
Ordered Locus Names:Pcal_0039
OrganismiPyrobaculum calidifontis (strain JCM 11548 / VA1)
Taxonomic identifieri410359 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaePyrobaculum
ProteomesiUP000001431 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 583583DNA ligasePRO_1000049876Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi410359.Pcal_0039.

Structurei

3D structure databases

ProteinModelPortaliA3MS62.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiPQVVIEV.

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.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A3MS62-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFGELAKVL AAVESTTQRT TMVKLLTSLF KKAKPEEIDK IVYFILGDLR
60 70 80 90 100
PPWEGVELGV AEKLCIRAIS KATGLSAAEL EGWYKKSGDV GEVARRALAA
110 120 130 140 150
GKRPTLLAFA QQKPLEVAEV YDTLLKVAKA AGEGAQDLKV SLLSSLFSRA
160 170 180 190 200
SPEEAKYIAR FVVGKLRLGV ADMTLIEALS EAFGVSKEGL ERAYHVYPDL
210 220 230 240 250
GRLARHVAEG RPLEEIKITP GVPVLPMLAQ RLSSASEILA KLGGTAICEY
260 270 280 290 300
KYDGERAQIH LREGSVKIFS RRLEDITHAY PDVAKAVKEA VKAREAILEG
310 320 330 340 350
EIVAVDPDTG EMLPFQELMH RKRKHDVAEA MEAYPAVLYL FDLLYVDGED
360 370 380 390 400
LTTQPLIYRR LRLSEVVEEG GDVYIAKWGM FDGAEDVDLF FHEAVSLGTE
410 420 430 440 450
GLICKSPTST YEMGARGWNW IKYKRDYRSE MIDTVDLVVV GAFHGRGKRA
460 470 480 490 500
GLYGAFLLAA YDPSTDMFYT VCKVGSGFTD ADLRRMYDML QPLKIPHRHP
510 520 530 540 550
RVVSKMQPDV WFVPQVVIEV IGAEITLSPL HTCCIGAVKP GVGLAIRFPR
560 570 580
FTGRYRTDKR PEDATTTKEL VEMYQRQKKV PTT
Length:583
Mass (Da):64,840
Last modified:April 3, 2007 - v1
Checksum:i3B3B4E318FC2C215
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000561 Genomic DNA. Translation: ABO07479.1.
RefSeqiWP_011848736.1. NC_009073.1.
YP_001054945.1. NC_009073.1.

Genome annotation databases

EnsemblBacteriaiABO07479; ABO07479; Pcal_0039.
GeneIDi4908550.
KEGGipcl:Pcal_0039.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000561 Genomic DNA. Translation: ABO07479.1.
RefSeqiWP_011848736.1. NC_009073.1.
YP_001054945.1. NC_009073.1.

3D structure databases

ProteinModelPortaliA3MS62.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi410359.Pcal_0039.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABO07479; ABO07479; Pcal_0039.
GeneIDi4908550.
KEGGipcl:Pcal_0039.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiPQVVIEV.

Enzyme and pathway databases

BioCyciPCAL410359:GIX2-39-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.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 11548 / VA1.

Entry informationi

Entry nameiDNLI_PYRCJ
AccessioniPrimary (citable) accession number: A3MS62
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: April 3, 2007
Last modified: May 27, 2015
This is version 61 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.