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P56709 (DNLI_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
DNA ligase
EC=6.5.1.1
Alternative name(s):
Pfu DNA ligase
Polydeoxyribonucleotide synthase [ATP]
Gene names
Name:lig
Ordered Locus Names:PF1635
OrganismPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]
Taxonomic identifier186497 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus ›

Protein attributes

Sequence length561 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. HAMAP-Rule MF_00407

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). Ref.3

Cofactor

Magnesium Probable. Ref.3

Subunit structure

Monomer.

Sequence similarities

Belongs to the ATP-dependent DNA ligase family.

Biophysicochemical properties

Temperature dependence:

Optimum temperature is about 70 degrees Celsius. Active from 4 to 100 degrees Celsius. Thermostable. HAMAP-Rule MF_00407

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 561561DNA ligase HAMAP-Rule MF_00407
PRO_0000059613

Sites

Active site2491N6-AMP-lysine intermediate Ref.3
Binding site2471ATP
Binding site2541ATP
Binding site2691ATP
Binding site2991ATP
Binding site3391ATP
Binding site4141ATP By similarity
Binding site4201ATP

Experimental info

Mutagenesis2491K → A: Loss of N6-AMP-lysine intermediate. Ref.3
Mutagenesis5311R → A: Reduced ATP binding and enzyme activity; when associated with A-534. Ref.3
Mutagenesis5341K → A: Reduced ATP binding and enzyme activity; when associated with A-531. Ref.3

Secondary structure

1 ............................................................................................... 561
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P56709 [UniParc].

Last modified May 30, 2000. Version 1.
Checksum: 534158525B9D24B2

FASTA56163,773
        10         20         30         40         50         60 
MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF PEWDERELGV 

        70         80         90        100        110        120 
GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK KKQKSFFSQP LTIKRVYQTL 

       130        140        150        160        170        180 
VKVAETTGEG SQDKKVKYLA DLFMDAEPLE AKYLARTILG TMRTGVAEGL LRDAIAMAFH 

       190        200        210        220        230        240 
VKVELVERAY MLTSDFGYVA KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM 

       250        260        270        280        290        300 
GGEAEFEIKY DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL 

       310        320        330        340        350        360 
VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI DTKFIDRRRT 

       370        380        390        400        410        420 
LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL MAKRLDAVYE PGNRGKKWLK 

       430        440        450        460        470        480 
IKPTMENLDL VIIGAEWGEG RRAHLFGSFI LGAYDPETGE FLEVGKVGSG FTDDDLVEFT 

       490        500        510        520        530        540 
KMLKPLIIKE EGKRVWLQPK VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD 

       550        560 
TIERIAQLYE LQEKMKGKVE S

« Hide

References

« Hide 'large scale' references
[1]"Purified thermostable Pyrococcus furiosus DNA ligase."
Mathur E.J., Marsh E.J., Schoettlin W.E.
Patent number US5700672, 23-DEC-1997
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS.
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]"The closed structure of an archaeal DNA ligase from Pyrococcus furiosus."
Nishida H., Kiyonari S., Ishino Y., Morikawa K.
J. Mol. Biol. 360:956-967(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-534 IN COMPLEX WITH AMP, ACTIVE SITE, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF LYS-249; ARG-531 AND LYS-534.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE009950 Genomic DNA. Translation: AAL81759.1.
RefSeqNP_579364.1. NC_003413.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2CFMX-ray1.80A1-561[»]
ProteinModelPortalP56709.
SMRP56709. Positions 1-561.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-48778N.
STRING186497.PF1635.

Proteomic databases

PRIDEP56709.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL81759; AAL81759; PF1635.
GeneID1469512.
KEGGpfu:PF1635.

Phylogenomic databases

eggNOGCOG1793.
HOGENOMHOG000036008.
KOK10747.
OMAARVQVHK.
ProtClustDBPRK01109.

Family and domain databases

Gene3D1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPMF_00407. DNA_ligase.
InterProIPR022865. 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]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMSSF50249. Nucleic_acid_OB. 1 hit.
SSF117018. SSF117018. 1 hit.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP56709.

Entry information

Entry nameDNLI_PYRFU
AccessionPrimary (citable) accession number: P56709
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: May 1, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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