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Protein

DNA ligase

Gene

lig

Organism
Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1)
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 use both ATP and ADP.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 Publication

Enzyme regulationi

Inhibited by Ca2+ and Zn2+.1 Publication

pH dependencei

Optimum pH is 6.5.1 Publication

Temperature dependencei

Optimum temperature is 75 degrees Celsius. Activity declines at temperatures from 75 to 80 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

BioCyciSMAR399550:GHK2-1370-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:Smar_1318
OrganismiStaphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1)
Taxonomic identifieri399550 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeStaphylothermus
ProteomesiUP000000254: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 597597DNA ligasePRO_0000365264Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi399550.Smar_1318.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.

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.

A3DP49-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPFRELADTF ERIEIITSRT QMTVLLVNLF KKTPPEIIDK VVYLLQGRLW
60 70 80 90 100
PDWKGLPELG VGEKMLIKAI ALATQSTESE VESLYKSLGD LGKAAEKLKA
110 120 130 140 150
IYEEKLKKGA MSILAFVPVK RELTVSQVYE TLSRVALATG EGSRDIKLKL
160 170 180 190 200
LAGLLSDASP KEAKYIIRFV EGRLRLGIGD ATIMDALAIV YGGGAHARPI
210 220 230 240 250
VERAYNLRAD LGHIAKILAT QGLNALKGIK PQVGIPIRPM LAERLNNPVE
260 270 280 290 300
ILKKVGGIAF VEYKYDGERA QIHKLGDKIW IYSRRLENIT HQYPDVVDYA
310 320 330 340 350
RKYIKANEAI VEGEIVAYDP DTGELRPFQE LMHRKRKHDI HIAIKEVPVK
360 370 380 390 400
VYLFDLLYVD GEDYTLKPLP ERRAKLVEII EQTETFQIAE YIRTNNPDEL
410 420 430 440 450
EKFFLKAIED GAEGVMIKAL HKNAIYQAGT RGWLWIKYKR DYKSEMIDTV
460 470 480 490 500
DLVVIGAFYG RGRRGGKYGA LLMASYNPDK DVFESVCKVG SGFKDEDIDK
510 520 530 540 550
LPEMLKPYII EHKHPRVVAR MKPDVWVTPA LVAEIIGAEL TLSPLHTCCL
560 570 580 590
DIIKPGVGIS IRFPRFIRWR PDKGPEDATT SQELLEMYKR QLKKLSE
Length:597
Mass (Da):67,627
Last modified:March 3, 2009 - v2
Checksum:iCA4E62C8890515D6
GO

Sequence cautioni

The sequence ABE27150.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence ABN70409.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ451010 Genomic DNA. Translation: ABE27150.1. Different initiation.
CP000575 Genomic DNA. Translation: ABN70409.1. Different initiation.
RefSeqiYP_001041317.1. NC_009033.1.

Genome annotation databases

EnsemblBacteriaiABN70409; ABN70409; Smar_1318.
GeneIDi4906593.
KEGGismr:Smar_1318.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ451010 Genomic DNA. Translation: ABE27150.1. Different initiation.
CP000575 Genomic DNA. Translation: ABN70409.1. Different initiation.
RefSeqiYP_001041317.1. NC_009033.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi399550.Smar_1318.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABN70409; ABN70409; Smar_1318.
GeneIDi4906593.
KEGGismr:Smar_1318.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.

Enzyme and pathway databases

BioCyciSMAR399550:GHK2-1370-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. "Cloning and expression of a DNA ligase from the hyperthermophilic archaeon Staphylothermus marinus and properties of the enzyme."
    Seo M.S., Kim Y.J., Choi J.J., Lee M.S., Kim J.H., Lee J.H., Kwon S.T.
    J. Biotechnol. 128:519-530(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: ATCC 43588 / DSM 3639 / F1.
  2. "The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota."
    Anderson I.J., Dharmarajan L., Rodriguez J., Hooper S., Porat I., Ulrich L.E., Elkins J.G., Mavromatis K., Sun H., Land M., Lapidus A., Lucas S., Barry K., Huber H., Zhulin I.B., Whitman W.B., Mukhopadhyay B., Woese C., Bristow J., Kyrpides N.
    BMC Genomics 10:145-145(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43588 / DSM 3639 / F1.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43588 / DSM 3639 / F1.

Entry informationi

Entry nameiDNLI_STAMF
AccessioniPrimary (citable) accession number: A3DP49
Secondary accession number(s): A3E0P8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 3, 2009
Last sequence update: March 3, 2009
Last modified: February 4, 2015
This is version 63 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.