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Protein

DNA ligase

Gene

lig

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
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.UniRule annotation

Catalytic activityi

ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation1 Publication

Temperature dependencei

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei247ATPUniRule annotationCombined sources1 Publication1
Active sitei249N6-AMP-lysine intermediateUniRule annotation1 Publication1
Binding sitei254ATPUniRule annotationCombined sources1 Publication1
Binding sitei269ATPUniRule annotationCombined sources1 Publication1
Binding sitei299ATPUniRule annotationCombined sources1 Publication1
Binding sitei339ATPUniRule annotationCombined sources1 Publication1
Binding sitei414ATPUniRule annotation1
Binding sitei420ATPUniRule annotationCombined sources1 Publication1

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

BRENDAi6.5.1.1. 5243.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.1UniRule annotation1 Publication)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]UniRule annotation
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:PF1635
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi249K → A: Loss of N6-AMP-lysine intermediate. 1 Publication1
Mutagenesisi531R → A: Reduced ATP binding and enzyme activity; when associated with A-534. 1 Publication1
Mutagenesisi534K → A: Reduced ATP binding and enzyme activity; when associated with A-531. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000596131 – 561DNA ligaseAdd BLAST561

Proteomic databases

PRIDEiP56709.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

DIPiDIP-48778N.
STRINGi186497.PF1635.

Structurei

Secondary structure

1561
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 14Combined sources12
Helixi19 – 32Combined sources14
Helixi35 – 37Combined sources3
Turni38 – 40Combined sources3
Helixi41 – 45Combined sources5
Helixi62 – 73Combined sources12
Helixi77 – 87Combined sources11
Helixi90 – 101Combined sources12
Turni102 – 104Combined sources3
Helixi113 – 125Combined sources13
Beta strandi128 – 130Combined sources3
Helixi131 – 143Combined sources13
Helixi148 – 159Combined sources12
Helixi168 – 178Combined sources11
Helixi183 – 193Combined sources11
Helixi196 – 213Combined sources18
Beta strandi226 – 231Combined sources6
Helixi233 – 239Combined sources7
Beta strandi244 – 249Combined sources6
Beta strandi252 – 260Combined sources9
Beta strandi263 – 267Combined sources5
Helixi275 – 277Combined sources3
Helixi279 – 288Combined sources10
Beta strandi291 – 303Combined sources13
Beta strandi307 – 309Combined sources3
Helixi313 – 320Combined sources8
Helixi325 – 331Combined sources7
Beta strandi334 – 344Combined sources11
Helixi354 – 364Combined sources11
Beta strandi369 – 373Combined sources5
Beta strandi376 – 380Combined sources5
Helixi382 – 394Combined sources13
Beta strandi399 – 403Combined sources5
Beta strandi414 – 421Combined sources8
Beta strandi428 – 437Combined sources10
Helixi440 – 442Combined sources3
Beta strandi445 – 454Combined sources10
Turni456 – 458Combined sources3
Beta strandi461 – 467Combined sources7
Helixi473 – 483Combined sources11
Helixi484 – 486Combined sources3
Beta strandi487 – 491Combined sources5
Beta strandi494 – 497Combined sources4
Beta strandi502 – 506Combined sources5
Beta strandi508 – 511Combined sources4
Beta strandi514 – 516Combined sources3
Beta strandi521 – 524Combined sources4
Beta strandi526 – 530Combined sources5
Helixi536 – 538Combined sources3
Helixi542 – 557Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CFMX-ray1.80A1-561[»]
ProteinModelPortaliP56709.
SMRiP56709.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP56709.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG01347. Archaea.
COG1793. LUCA.
HOGENOMiHOG000036008.
KOiK10747.
OMAiRKHNIEE.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
HAMAPiMF_00407. DNA_ligase. 1 hit.
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:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81759.1.
RefSeqiWP_011012782.1. NC_003413.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81759.1.
RefSeqiWP_011012782.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CFMX-ray1.80A1-561[»]
ProteinModelPortaliP56709.
SMRiP56709.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48778N.
STRINGi186497.PF1635.

Proteomic databases

PRIDEiP56709.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiarCOG01347. Archaea.
COG1793. LUCA.
HOGENOMiHOG000036008.
KOiK10747.
OMAiRKHNIEE.

Enzyme and pathway databases

BRENDAi6.5.1.1. 5243.

Miscellaneous databases

EvolutionaryTraceiP56709.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
HAMAPiMF_00407. DNA_ligase. 1 hit.
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...

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: November 30, 2016
This is version 115 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

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 one 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.