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Protein

DNA ligase

Gene

ligA

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.UniRule annotation

Catalytic activityi

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei118NADUniRule annotation1 Publication1
Active sitei120N6-AMP-lysine intermediateUniRule annotation1
Binding sitei141NADUniRule annotation1 Publication1
Binding sitei175NADUniRule annotation1 Publication1
Binding sitei291NADUniRule annotation1 Publication1
Binding sitei315NADUniRule annotation1 Publication1
Metal bindingi409ZincUniRule annotation1
Metal bindingi412ZincUniRule annotation1
Metal bindingi427ZincUniRule annotation1
Metal bindingi432ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi39 – 43NADUniRule annotation1 Publication5
Nucleotide bindingi88 – 91NADUniRule annotation1 Publication4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD, Zinc

Enzyme and pathway databases

BRENDAi6.5.1.2. 2095.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.2UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]UniRule annotation
Gene namesi
Name:ligAUniRule annotation
Ordered Locus Names:EF_0722
OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)
Taxonomic identifieri226185 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
Proteomesi
  • UP000001415 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003132281 – 676DNA ligaseAdd BLAST676

Interactioni

Protein-protein interaction databases

STRINGi226185.EF0722.

Structurei

Secondary structure

1676
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 30Combined sources23
Beta strandi31 – 33Combined sources3
Helixi39 – 55Combined sources17
Helixi57 – 59Combined sources3
Helixi65 – 67Combined sources3
Beta strandi79 – 81Combined sources3
Helixi95 – 109Combined sources15
Beta strandi115 – 121Combined sources7
Beta strandi123 – 131Combined sources9
Beta strandi134 – 140Combined sources7
Beta strandi144 – 149Combined sources6
Helixi151 – 155Combined sources5
Beta strandi165 – 167Combined sources3
Beta strandi170 – 177Combined sources8
Helixi180 – 192Combined sources13
Helixi201 – 209Combined sources9
Helixi214 – 219Combined sources6
Beta strandi223 – 230Combined sources8
Helixi240 – 250Combined sources11
Beta strandi259 – 263Combined sources5
Helixi264 – 277Combined sources14
Helixi278 – 280Combined sources3
Beta strandi281 – 283Combined sources3
Beta strandi285 – 294Combined sources10
Helixi295 – 301Combined sources7
Beta strandi305 – 315Combined sources11
Helixi319 – 321Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TA8X-ray1.80A1-323[»]
1TAEX-ray2.70A/B/C/D1-324[»]
3BA8X-ray1.90A1-324[»]
3BA9X-ray1.90A1-324[»]
3BAAX-ray1.90A1-324[»]
3BABX-ray2.50A1-324[»]
4EEQX-ray2.10A1-323[»]
4EFBX-ray2.20A1-323[»]
4EFEX-ray2.00A1-323[»]
4LH6X-ray1.65A1-323[»]
4LH7X-ray1.90A1-323[»]
DisProtiDP00326.
ProteinModelPortaliQ837V6.
SMRiQ837V6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ837V6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini595 – 676BRCTUniRule annotationAdd BLAST82

Sequence similaritiesi

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.UniRule annotation
Contains 1 BRCT domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
KOiK01972.
OMAiFTAKSPR.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q837V6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQQPLTLTA ATTRAQELRK QLNQYSHEYY VKDQPSVEDY VYDRLYKELV
60 70 80 90 100
DIETEFPDLI TPDSPTQRVG GKVLSGFEKA PHDIPMYSLN DGFSKEDIFA
110 120 130 140 150
FDERVRKAIG KPVAYCCELK IDGLAISLRY ENGVFVRGAT RGDGTVGENI
160 170 180 190 200
TENLRTVRSV PMRLTEPISV EVRGECYMPK QSFVALNEER EENGQDIFAN
210 220 230 240 250
PRNAAAGSLR QLDTKIVAKR NLNTFLYTVA DFGPMKAKTQ FEALEELSAI
260 270 280 290 300
GFRTNPERQL CQSIDEVWAY IEEYHEKRST LPYEIDGIVI KVNEFALQDE
310 320 330 340 350
LGFTVKAPRW AIAYKFPPEE AETVVEDIEW TIGRTGVVTP TAVMAPVRVA
360 370 380 390 400
GTTVSRASLH NADFIQMKDI RLNDHVIIYK AGDIIPEVAQ VLVEKRAADS
410 420 430 440 450
QPYEMPTHCP ICHSELVHLD EEVALRCINP KCPAQIKEGL NHFVSRNAMN
460 470 480 490 500
IDGLGPRVLA QMYDKGLVKD VADLYFLTEE QLMTLDKIKE KSANNIYTAI
510 520 530 540 550
QGSKENSVER LIFGLGIRHV GAKAAKILAE HFGDLPTLSR ATAEEIVALD
560 570 580 590 600
SIGETIADSV VTYFENEEVH ELMAELEKAQ VNLTYKGLRT EQLAEVESPF
610 620 630 640 650
KDKTVVLTGK LAQYTREEAK EKIENLGGKV TGSVSKKTDI VVAGEDAGSK
660 670
LTKAESLGVT VWNEQEMVDA LDASHF
Length:676
Mass (Da):75,584
Last modified:June 1, 2003 - v1
Checksum:i9B6B93FD8DBB8E3B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016830 Genomic DNA. Translation: AAO80542.1.
RefSeqiNP_814472.1. NC_004668.1.
WP_002361258.1. NZ_KE136527.1.

Genome annotation databases

EnsemblBacteriaiAAO80542; AAO80542; EF_0722.
GeneIDi1199621.
KEGGiefa:EF0722.
PATRICi21851834. VBIEntFae7065_0667.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016830 Genomic DNA. Translation: AAO80542.1.
RefSeqiNP_814472.1. NC_004668.1.
WP_002361258.1. NZ_KE136527.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TA8X-ray1.80A1-323[»]
1TAEX-ray2.70A/B/C/D1-324[»]
3BA8X-ray1.90A1-324[»]
3BA9X-ray1.90A1-324[»]
3BAAX-ray1.90A1-324[»]
3BABX-ray2.50A1-324[»]
4EEQX-ray2.10A1-323[»]
4EFBX-ray2.20A1-323[»]
4EFEX-ray2.00A1-323[»]
4LH6X-ray1.65A1-323[»]
4LH7X-ray1.90A1-323[»]
DisProtiDP00326.
ProteinModelPortaliQ837V6.
SMRiQ837V6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi226185.EF0722.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO80542; AAO80542; EF_0722.
GeneIDi1199621.
KEGGiefa:EF0722.
PATRICi21851834. VBIEntFae7065_0667.

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
KOiK01972.
OMAiFTAKSPR.

Enzyme and pathway databases

BRENDAi6.5.1.2. 2095.

Miscellaneous databases

EvolutionaryTraceiQ837V6.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNLJ_ENTFA
AccessioniPrimary (citable) accession number: Q837V6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 1, 2003
Last modified: November 30, 2016
This is version 105 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, 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.