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P56709

- DNLI_PYRFU

UniProt

P56709 - DNLI_PYRFU

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Protein
DNA ligase
Gene
lig, PF1635
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.UniRule annotation

Catalytic activityi

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

Cofactori

Magnesium Inferred.1 Publication

Temperature dependencei

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

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 – 4141ATP By 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
Complete GO annotation...

GO - Biological processi

  1. DNA ligation involved in DNA repair Source: InterPro
  2. DNA recombination Source: UniProtKB-HAMAP
  3. DNA replication Source: UniProtKB-HAMAP
  4. cell cycle Source: UniProtKB-KW
  5. cell division Source: UniProtKB-KW
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 ligaseUniRule annotation
PRO_0000059613Add
BLAST

Proteomic databases

PRIDEiP56709.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

DIPiDIP-48778N.
STRINGi186497.PF1635.

Structurei

Secondary structure

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

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.

Miscellaneous databases

EvolutionaryTraceiP56709.

Family & Domainsi

Sequence similaritiesi

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

MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF    50
PEWDERELGV GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK 100
KKQKSFFSQP LTIKRVYQTL VKVAETTGEG SQDKKVKYLA DLFMDAEPLE 150
AKYLARTILG TMRTGVAEGL LRDAIAMAFH VKVELVERAY MLTSDFGYVA 200
KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM GGEAEFEIKY 250
DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL 300
VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI 350
DTKFIDRRRT LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL 400
MAKRLDAVYE PGNRGKKWLK IKPTMENLDL VIIGAEWGEG RRAHLFGSFI 450
LGAYDPETGE FLEVGKVGSG FTDDDLVEFT KMLKPLIIKE EGKRVWLQPK 500
VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD TIERIAQLYE 550
LQEKMKGKVE S 561
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.
WP_011012782.1. 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.
WP_011012782.1. 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...

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: September 3, 2014
This is version 99 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

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