Reviewed, UniProtKB/Swiss-Prot Q837V6 (DNLJ_ENTFA)

Names and origin

Protein names

Recommended name:
    DNA ligase
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+]

Gene names

Name:	ligA
Ordered Locus Names:	EF_0722

Organism

Enterococcus faecalis (Streptococcus faecalis) [Complete proteome] [HAMAP]

Taxonomic identifier

1351 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Enterococcaceae › Enterococcus

Protein attributes

Sequence length	676 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 By similarity.
Catalytic activity	NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588
Cofactor	Magnesium or manganese By similarity.
Sequence similarities	Belongs to the NAD-dependent DNA ligase family. LigA subfamily. Contains 1 BRCT domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication
Ligand	Magnesium Manganese Metal-binding NAD Zinc
Molecular function	Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 676

676

DNA ligase HAMAP MF_01588

PRO_0000313228

Regions

Domain

595 – 676

82

BRCT

Nucleotide binding

39 – 43

5

NAD HAMAP MF_01588

Nucleotide binding

88 – 91

4

NAD HAMAP MF_01588

Sites

Active site

120

1

N6-AMP-lysine intermediate HAMAP MF_01588

Metal binding

409

1

Zinc By similarity

Metal binding

412

1

Zinc By similarity

Metal binding

427

1

Zinc By similarity

Metal binding

432

1

Zinc By similarity

Binding site

118

1

NAD HAMAP MF_01588

Binding site

141

1

NAD HAMAP MF_01588

Binding site

175

1

NAD HAMAP MF_01588

Binding site

291

1

NAD HAMAP MF_01588

Binding site

315

1

NAD HAMAP MF_01588

Secondary structure

1

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676

Helix Strand Turn

Details...

Helix

8 – 30

23

Helix

39 – 55

17

Helix

57 – 59

3

Helix

65 – 69

5

Beta strand

79 – 81

3

Helix

95 – 109

15

Beta strand

115 – 121

7

Beta strand

123 – 131

9

Beta strand

134 – 140

7

Beta strand

144 – 149

6

Helix

151 – 154

4

Beta strand

170 – 177

8

Helix

180 – 192

13

Helix

201 – 209

9

Helix

214 – 218

5

Beta strand

223 – 230

8

Helix

240 – 249

10

Beta strand

259 – 263

5

Helix

264 – 276

13

Helix

278 – 280

3

Beta strand

281 – 283

3

Beta strand

285 – 294

10

Helix

295 – 301

7

Beta strand

305 – 315

11

Helix

319 – 322

4

Sequences

	Sequence		Length	Mass (Da)
	Q837V6-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 9B6B93FD8DBB8E3B	FASTA	676	75,584
	10 20 30 40 50 60 MEQQPLTLTA ATTRAQELRK QLNQYSHEYY VKDQPSVEDY VYDRLYKELV DIETEFPDLI 70 80 90 100 110 120 TPDSPTQRVG GKVLSGFEKA PHDIPMYSLN DGFSKEDIFA FDERVRKAIG KPVAYCCELK 130 140 150 160 170 180 IDGLAISLRY ENGVFVRGAT RGDGTVGENI TENLRTVRSV PMRLTEPISV EVRGECYMPK 190 200 210 220 230 240 QSFVALNEER EENGQDIFAN PRNAAAGSLR QLDTKIVAKR NLNTFLYTVA DFGPMKAKTQ 250 260 270 280 290 300 FEALEELSAI GFRTNPERQL CQSIDEVWAY IEEYHEKRST LPYEIDGIVI KVNEFALQDE 310 320 330 340 350 360 LGFTVKAPRW AIAYKFPPEE AETVVEDIEW TIGRTGVVTP TAVMAPVRVA GTTVSRASLH 370 380 390 400 410 420 NADFIQMKDI RLNDHVIIYK AGDIIPEVAQ VLVEKRAADS QPYEMPTHCP ICHSELVHLD 430 440 450 460 470 480 EEVALRCINP KCPAQIKEGL NHFVSRNAMN IDGLGPRVLA QMYDKGLVKD VADLYFLTEE 490 500 510 520 530 540 QLMTLDKIKE KSANNIYTAI QGSKENSVER LIFGLGIRHV GAKAAKILAE HFGDLPTLSR 550 560 570 580 590 600 ATAEEIVALD SIGETIADSV VTYFENEEVH ELMAELEKAQ VNLTYKGLRT EQLAEVESPF 610 620 630 640 650 660 KDKTVVLTGK LAQYTREEAK EKIENLGGKV TGSVSKKTDI VVAGEDAGSK LTKAESLGVT 670 VWNEQEMVDA LDASHF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis." Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R., Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H., Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C., DeBoy R.T., Durkin S.A. , Kolonay J.F., Madupu R., Nelson W.C., Vamathevan J.J., Tran B., Upton J., Hansen T., Shetty J., Khouri H.M., Utterback T.R., Radune D., Ketchum K.A., Dougherty B.A., Fraser C.M. Science 299:2071-2074(2003) [PubMed: 12663927] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: V583 / ATCC 700802.
[2]	"Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal." Gajiwala K.S., Pinko C. Structure 12:1449-1459(2004) [PubMed: 15296738] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-325 IN COMPLEXES WITH NAD AND NICOTINAMIDE NUCLEOTIDE.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AE016830 Genomic DNA. Translation: AAO80542.1.

RefSeq

NP_814472.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TA8	X-ray	1.80	A	1-325	[»]
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	[»]

ModBase

Search...

Genome annotation databases

GeneID

1199621.

GenomeReviews

Gene locus EF_0722 in contig AE016830_GR.

KEGG

efa:EF0722.

NMPDR

fig|226185.1.peg.657.

TIGR

EF_0722.

Phylogenomic databases

HOGENOM

Q837V6.

OMA

YKFPAQE.

Enzyme and pathway databases

BioCyc

EFAE226185:EF_0722-MON.

BRENDA

6.5.1.2. 704.

Family and domain databases

HAMAP

MF_01588.
[Tree]

InterPro

IPR001357. BRCT.
IPR018239. DNA_ligase_AS.
IPR004150. DNA_ligase_OB.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004149. Znf_DNAligase_C4.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.

Pfam

PF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]

PIRSF

PIRSF001604. LigA. 1 hit.

ProDom

PD003944. DNAligase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00292. BRCT. 1 hit.
SM00278. HhH1. 3 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00575. dnlj. 1 hit.

PROSITE

PS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DNLJ_ENTFA

Accession

Primary (citable) accession number: Q837V6

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	June 1, 2003
Last modified:	November 3, 2009
This is version 53 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)