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Q837V6

- DNLJ_ENTFA

UniProt

Q837V6 - DNLJ_ENTFA

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Protein

DNA ligase

Gene

ligA

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Reviewed - 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei118 – 1181NAD
Active sitei120 – 1201N6-AMP-lysine intermediate
Binding sitei141 – 1411NAD
Binding sitei175 – 1751NAD
Binding sitei291 – 2911NAD
Binding sitei315 – 3151NAD
Metal bindingi409 – 4091ZincUniRule annotation
Metal bindingi412 – 4121ZincUniRule annotation
Metal bindingi427 – 4271ZincUniRule annotation
Metal bindingi432 – 4321ZincUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi39 – 435NAD
Nucleotide bindingi88 – 914NAD

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. DNA ligase (NAD+) activity Source: UniProtKB-HAMAP
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA repair Source: UniProtKB-KW
  2. DNA replication Source: UniProtKB-KW
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

BioCyciEFAE226185:GHI1-709-MONOMER.

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
ProteomesiUP000001415: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 676676DNA ligasePRO_0000313228Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi226185.EF0722.

Structurei

Secondary structure

1
676
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi8 – 3023Combined sources
Beta strandi31 – 333Combined sources
Helixi39 – 5517Combined sources
Helixi57 – 593Combined sources
Helixi65 – 673Combined sources
Beta strandi79 – 813Combined sources
Helixi95 – 10915Combined sources
Beta strandi115 – 1217Combined sources
Beta strandi123 – 1319Combined sources
Beta strandi134 – 1407Combined sources
Beta strandi144 – 1496Combined sources
Helixi151 – 1555Combined sources
Beta strandi165 – 1673Combined sources
Beta strandi170 – 1778Combined sources
Helixi180 – 19213Combined sources
Helixi201 – 2099Combined sources
Helixi214 – 2196Combined sources
Beta strandi223 – 2308Combined sources
Helixi240 – 25011Combined sources
Beta strandi259 – 2635Combined sources
Helixi264 – 27714Combined sources
Helixi278 – 2803Combined sources
Beta strandi281 – 2833Combined sources
Beta strandi285 – 29410Combined sources
Helixi295 – 3017Combined sources
Beta strandi305 – 31511Combined sources
Helixi319 – 3213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 4-324.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ837V6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini595 – 67682BRCTUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0272.
KOiK01972.
OMAiPVEYLCE.
OrthoDBiEOG6TTVM9.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
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.
SM00278. HhH1. 3 hits.
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.

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 .
RefSeqi NP_814472.1. NC_004668.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1TA8 X-ray 1.80 A 1-323 [» ]
1TAE X-ray 2.70 A/B/C/D 1-324 [» ]
3BA8 X-ray 1.90 A 1-324 [» ]
3BA9 X-ray 1.90 A 1-324 [» ]
3BAA X-ray 1.90 A 1-324 [» ]
3BAB X-ray 2.50 A 1-324 [» ]
4EEQ X-ray 2.10 A 1-323 [» ]
4EFB X-ray 2.20 A 1-323 [» ]
4EFE X-ray 2.00 A 1-323 [» ]
4LH6 X-ray 1.65 A 1-323 [» ]
4LH7 X-ray 1.90 A 1-323 [» ]
DisProti DP00326.
ProteinModelPortali Q837V6.
SMRi Q837V6. Positions 4-324.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 226185.EF0722.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAO80542 ; AAO80542 ; EF_0722 .
GeneIDi 1199621.
KEGGi efa:EF0722.
PATRICi 21851834. VBIEntFae7065_0667.

Phylogenomic databases

eggNOGi COG0272.
KOi K01972.
OMAi PVEYLCE.
OrthoDBi EOG6TTVM9.

Enzyme and pathway databases

BioCyci EFAE226185:GHI1-709-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q837V6.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPi MF_01588. DNA_ligase_A.
InterProi IPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view ]
Pfami PF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view ]
PIRSFi PIRSF001604. LigA. 1 hit.
SMARTi SM00292. BRCT. 1 hit.
SM00278. HhH1. 3 hits.
SM00532. LIGANc. 1 hit.
[Graphical view ]
SUPFAMi SSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsi TIGR00575. dnlj. 1 hit.
PROSITEi PS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700802 / V583.
  2. "Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal."
    Gajiwala K.S., Pinko C.
    Structure 12:1449-1459(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-325 IN COMPLEXES WITH NAD AND NICOTINAMIDE NUCLEOTIDE.

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 26, 2014
This is version 90 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

External Data

Dasty 3