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P56709

- DNLI_PYRFU

UniProt

P56709 - DNLI_PYRFU

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Protein

DNA ligase

Gene

lig

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - 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.

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).1 Publication

Cofactori

Magnesium.1 Publication

Temperature dependencei

Optimum temperature is about 70 degrees Celsius. Active from 4 to 100 degrees Celsius. Thermostable.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei247 – 2471ATP
Active sitei249 – 2491N6-AMP-lysine intermediate1 Publication
Binding sitei254 – 2541ATP
Binding sitei269 – 2691ATP
Binding sitei299 – 2991ATP
Binding sitei339 – 3391ATP
Binding sitei414 – 4141ATPBy similarity
Binding sitei420 – 4201ATP

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 ligase (EC:6.5.1.1)
Alternative name(s):
Pfu DNA ligase
Polydeoxyribonucleotide synthase [ATP]
Gene namesi
Name:lig
Ordered Locus Names:PF1635
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000001013: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi249 – 2491K → A: Loss of N6-AMP-lysine intermediate. 1 Publication
Mutagenesisi531 – 5311R → A: Reduced ATP binding and enzyme activity; when associated with A-534. 1 Publication
Mutagenesisi534 – 5341K → A: Reduced ATP binding and enzyme activity; when associated with A-531. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 561561DNA ligasePRO_0000059613Add
BLAST

Proteomic databases

PRIDEiP56709.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

DIPiDIP-48778N.
STRINGi186497.PF1635.

Structurei

Secondary structure

1
561
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1412Combined sources
Helixi19 – 3214Combined sources
Helixi35 – 373Combined sources
Turni38 – 403Combined sources
Helixi41 – 455Combined sources
Helixi62 – 7312Combined sources
Helixi77 – 8711Combined sources
Helixi90 – 10112Combined sources
Turni102 – 1043Combined sources
Helixi113 – 12513Combined sources
Beta strandi128 – 1303Combined sources
Helixi131 – 14313Combined sources
Helixi148 – 15912Combined sources
Helixi168 – 17811Combined sources
Helixi183 – 19311Combined sources
Helixi196 – 21318Combined sources
Beta strandi226 – 2316Combined sources
Helixi233 – 2397Combined sources
Beta strandi244 – 2496Combined sources
Beta strandi252 – 2609Combined sources
Beta strandi263 – 2675Combined sources
Helixi275 – 2773Combined sources
Helixi279 – 28810Combined sources
Beta strandi291 – 30313Combined sources
Beta strandi307 – 3093Combined sources
Helixi313 – 3208Combined sources
Helixi325 – 3317Combined sources
Beta strandi334 – 34411Combined sources
Helixi354 – 36411Combined sources
Beta strandi369 – 3735Combined sources
Beta strandi376 – 3805Combined sources
Helixi382 – 39413Combined sources
Beta strandi399 – 4035Combined sources
Beta strandi414 – 4218Combined sources
Beta strandi428 – 43710Combined sources
Helixi440 – 4423Combined sources
Beta strandi445 – 45410Combined sources
Turni456 – 4583Combined sources
Beta strandi461 – 4677Combined sources
Helixi473 – 48311Combined sources
Helixi484 – 4863Combined sources
Beta strandi487 – 4915Combined sources
Beta strandi494 – 4974Combined sources
Beta strandi502 – 5065Combined sources
Beta strandi508 – 5114Combined sources
Beta strandi514 – 5163Combined sources
Beta strandi521 – 5244Combined sources
Beta strandi526 – 5305Combined sources
Helixi536 – 5383Combined sources
Helixi542 – 55716Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CFMX-ray1.80A1-561[»]
ProteinModelPortaliP56709.
SMRiP56709. Positions 1-561.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP56709.

Family & Domainsi

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiARVQVHK.

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.

P56709-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF
60 70 80 90 100
PEWDERELGV GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK
110 120 130 140 150
KKQKSFFSQP LTIKRVYQTL VKVAETTGEG SQDKKVKYLA DLFMDAEPLE
160 170 180 190 200
AKYLARTILG TMRTGVAEGL LRDAIAMAFH VKVELVERAY MLTSDFGYVA
210 220 230 240 250
KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM GGEAEFEIKY
260 270 280 290 300
DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL
310 320 330 340 350
VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI
360 370 380 390 400
DTKFIDRRRT LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL
410 420 430 440 450
MAKRLDAVYE PGNRGKKWLK IKPTMENLDL VIIGAEWGEG RRAHLFGSFI
460 470 480 490 500
LGAYDPETGE FLEVGKVGSG FTDDDLVEFT KMLKPLIIKE EGKRVWLQPK
510 520 530 540 550
VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD TIERIAQLYE
560
LQEKMKGKVE S
Length:561
Mass (Da):63,773
Last modified:May 30, 2000 - v1
Checksum:i534158525B9D24B2
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE009950 Genomic DNA. Translation: AAL81759.1.
RefSeqiNP_579364.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81759; AAL81759; PF1635.
GeneIDi1469512.
KEGGipfu:PF1635.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE009950 Genomic DNA. Translation: AAL81759.1 .
RefSeqi NP_579364.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2CFM X-ray 1.80 A 1-561 [» ]
ProteinModelPortali P56709.
SMRi P56709. Positions 1-561.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-48778N.
STRINGi 186497.PF1635.

Proteomic databases

PRIDEi P56709.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL81759 ; AAL81759 ; PF1635 .
GeneIDi 1469512.
KEGGi pfu:PF1635.

Phylogenomic databases

eggNOGi COG1793.
HOGENOMi HOG000036008.
KOi K10747.
OMAi ARVQVHK.

Miscellaneous databases

EvolutionaryTracei P56709.

Family and domain databases

Gene3Di 1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPi MF_00407. DNA_ligase.
InterProi IPR022865. 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 ]
Pfami PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view ]
SUPFAMi SSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsi TIGR00574. dnl1. 1 hit.
PROSITEi PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiDNLI_PYRFU
AccessioniPrimary (citable) accession number: P56709
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: October 29, 2014
This is version 101 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3