P15042 (DNLJ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA ligase
EC=6.5.1.2

Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]

Gene names

Name:	ligA
Synonyms:	dnaL, lig, lop, pdeC
Ordered Locus Names:	b2411, JW2403

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	671 AA.
Sequence status	Complete.
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. HAMAP-Rule MF_01588
Catalytic activity	NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m). Ref.7
Cofactor	Magnesium. Ref.7
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 Metal-binding NAD Zinc
Molecular function	Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activity Inferred from direct assay PubMed 15583169. Source: EcoliWiki metal 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 – 671

671

DNA ligase HAMAP-Rule MF_01588

PRO_0000161745

Regions

Domain

593 – 671

79

BRCT

Nucleotide binding

32 – 36

5

NAD Probable

Nucleotide binding

81 – 82

2

NAD HAMAP-Rule MF_01588

Region

330 – 334

5

Interaction with target DNA HAMAP-Rule MF_01588

Region

453 – 458

6

Interaction with target DNA HAMAP-Rule MF_01588

Region

519 – 524

6

Interaction with target DNA HAMAP-Rule MF_01588

Region

551 – 556

6

Interaction with target DNA HAMAP-Rule MF_01588

Sites

Active site

115

1

N6-AMP-lysine intermediate Ref.7

Metal binding

408

1

Zinc

Metal binding

411

1

Zinc

Metal binding

426

1

Zinc

Metal binding

432

1

Zinc

Binding site

113

1

NAD

Binding site

136

1

NAD

Binding site

173

1

NAD By similarity

Binding site

290

1

NAD

Binding site

314

1

NAD Probable

Site

487

1

Interaction with target DNA

Site

492

1

Interaction with target DNA

Experimental info

Mutagenesis

10

1

E → A: No effect. Ref.7

Mutagenesis

22

1

Y → A or S: Reduces nick joining activity by 99.9%. Ref.7

Mutagenesis

22

1

Y → F: Reduces nick joining activity by 91%. Ref.7

Mutagenesis

23

1

H → A or Y: Reduces nick joining activity by 90%. Ref.7

Mutagenesis

32

1

D → A or E: Reduces nick joining activity by 99%. Ref.7

Mutagenesis

32

1

D → N: Reduces nick joining activity by 91%. Ref.7

Mutagenesis

35

1

Y → A: Reduces nick joining activity by 98%. Ref.7

Mutagenesis

35

1

Y → F: Reduces nick joining activity by 77%. Ref.7

Mutagenesis

35

1

Y → S: Reduces nick joining activity by 99.9%. Ref.7

Mutagenesis

36

1

D → A: Reduces nick joining activity by 99.8%. Ref.7

Mutagenesis

36

1

D → E: Reduces nick joining activity by 96%. Ref.7

Mutagenesis

36

1

D → N: Reduces nick joining activity by 88%. Ref.7

Mutagenesis

115

1

K → Q or R: Reduces nick joining activity by 99.9%. Ref.8

Mutagenesis

117

1

D → E: Reduces nick joining activity by 97%. Ref.8

Mutagenesis

117

1

D → N: Reduces nick joining activity by 99.9%. Ref.8

Mutagenesis

118

1

G → A: Reduces nick joining activity by 99.9%. Ref.8

Mutagenesis

138

1

D → A: Reduces nick joining activity by 63%. Ref.8

Mutagenesis

143

1

E → A: Reduces nick joining activity by 48%. Ref.8

Mutagenesis

172

1

G → A: Reduces nick joining activity by 64%. Ref.8

Mutagenesis

173

1

E → A, D or Q: Reduces nick joining activity by 99.9%. Ref.8

Mutagenesis

198

1

N → A: Reduces nick joining activity by 74%. Ref.8

Mutagenesis

200

1

R → A, K or Q: Reduces nick joining activity by 99.9%. Ref.8

Mutagenesis

208

1

R → A, K or Q: Reduces nick joining activity by 99%. Ref.8

Mutagenesis

277

1

R → A: Reduces nick joining activity by 99%. Ref.8

Mutagenesis

285

1

D → E: Reduces nick joining activity by 96%. Ref.8

Mutagenesis

285

1

D → N: Reduces nick joining activity by 99%. Ref.8

Mutagenesis

286

1

G → A: Reduces nick joining activity by 86%. Ref.8

Mutagenesis

288

1

V → A: Reduces nick joining activity by 25%. Ref.8

Mutagenesis

290

1

K → A: Reduces nick joining activity by 87%. Ref.8

Mutagenesis

314

1

K → Q: Reduces nick joining activity by 99%. Ref.8

Mutagenesis

314

1

K → R: Reduces nick joining activity by 95%. Ref.8

Mutagenesis

333

1

R → A or Q: Reduces nick joining activity by over 95%. Abolishes nick joining activity; when associated with A-334. Ref.9

Mutagenesis

334

1

T → A: Abolishes nick joining activity; when associated with A-333. Ref.9

Mutagenesis

342

1

R → A: Reduces nick joining activity by 80%. Ref.9

Mutagenesis

379

1

R → A or Q: Reduces nick joining activity by over 95%. Ref.9

Mutagenesis

383 – 384

2

VI → AA: Reduces nick joining activity by 95%.

Mutagenesis

446 – 447

2

RR → AA: Reduces nick joining activity by 95%.

Mutagenesis

455

1

G → A: Reduces nick joining activity by 50%. Ref.9

Mutagenesis

455

1

G → D or V: Reduces nick joining activity by 95%. Ref.9

Mutagenesis

487

1

R → A: Reduces nick joining activity by over 90%. Ref.9

Mutagenesis

489

1

G → D or V: Reduces nick joining activity by 95%. Ref.9

Mutagenesis

521

1

G → A: Reduces nick joining activity by 95%. Ref.9

Mutagenesis

521

1

G → D or V: Loss of nick joining activity. Ref.9

Mutagenesis

553

1

G → D or V: Reduces nick joining activity by 95%. Ref.9

Mutagenesis

614

1

R → A: Reduces nick joining activity by 85%. Ref.9

Sequence conflict

69

1

A → R in AAA24071. Ref.1

Secondary structure

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671

Helix Strand Turn

Details...

Helix

4 – 24

21

Beta strand

28 – 30

3

Helix

34 – 48

15

Helix

50 – 52

3

Helix

58 – 60

3

Beta strand

72 – 74

3

Beta strand

83 – 85

3

Helix

88 – 100

13

Beta strand

102 – 104

3

Beta strand

110 – 126

17

Beta strand

129 – 135

7

Beta strand

139 – 144

6

Helix

146 – 149

4

Beta strand

161 – 163

3

Beta strand

166 – 175

10

Helix

178 – 190

13

Helix

199 – 207

9

Helix

212 – 216

5

Beta strand

221 – 233

13

Helix

239 – 248

10

Beta strand

258 – 262

5

Helix

263 – 276

14

Helix

277 – 279

3

Beta strand

280 – 282

3

Beta strand

284 – 293

10

Helix

294 – 300

7

Beta strand

304 – 313

10

Beta strand

319 – 331

13

Beta strand

335 – 348

14

Beta strand

351 – 357

7

Helix

361 – 367

7

Beta strand

374 – 380

7

Turn

381 – 383

3

Beta strand

384 – 390

7

Helix

392 – 394

3

Turn

409 – 411

3

Beta strand

414 – 416

3

Beta strand

425 – 427

3

Helix

429 – 431

3

Helix

433 – 444

12

Turn

446 – 449

4

Helix

456 – 464

9

Helix

471 – 475

5

Helix

479 – 483

5

Helix

490 – 503

14

Helix

508 – 514

7

Helix

522 – 532

11

Helix

535 – 540

6

Helix

543 – 546

4

Helix

554 – 565

12

Helix

567 – 578

12

Sequences

	Sequence		Length	Mass (Da)
	P15042 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: DD2BDC64D8E65256	FASTA	671	73,606
	10 20 30 40 50 60 MESIEQQLTE LRTTLRHHEY LYHVMDAPEI PDAEYDRLMR ELRELETKHP ELITPDSPTQ 70 80 90 100 110 120 RVGAAPLAAF SQIRHEVPML SLDNVFDEES FLAFNKRVQD RLKNNEKVTW CCELKLDGLA 130 140 150 160 170 180 VSILYENGVL VSAATRGDGT TGEDITSNVR TIRAIPLKLH GENIPARLEV RGEVFLPQAG 190 200 210 220 230 240 FEKINEDARR TGGKVFANPR NAAAGSLRQL DPRITAKRPL TFFCYGVGVL EGGELPDTHL 250 260 270 280 290 300 GRLLQFKKWG LPVSDRVTLC ESAEEVLAFY HKVEEDRPTL GFDIDGVVIK VNSLAQQEQL 310 320 330 340 350 360 GFVARAPRWA VAFKFPAQEQ MTFVRDVEFQ VGRTGAITPV ARLEPVHVAG VLVSNATLHN 370 380 390 400 410 420 ADEIERLGLR IGDKVVIRRA GDVIPQVVNV VLSERPEDTR EVVFPTHCPV CGSDVERVEG 430 440 450 460 470 480 EAVARCTGGL ICGAQRKESL KHFVSRRAMD VDGMGDKIID QLVEKEYVHT PADLFKLTAG 490 500 510 520 530 540 KLTGLERMGP KSAQNVVNAL EKAKETTFAR FLYALGIREV GEATAAGLAA YFGTLEALEA 550 560 570 580 590 600 ASIEELQKVP DVGIVVASHV HNFFAEESNR NVISELLAEG VHWPAPIVIN AEEIDSPFAG 610 620 630 640 650 660 KTVVLTGSLS QMSRDDAKAR LVELGAKVAG SVSKKTDLVI AGEAAGSKLA KAQELGIEVI 670 DEAEMLRLLG S

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the lig gene and primary structure of DNA ligase of Escherichia coli." Ishino Y., Shinagawa H., Makino K., Tsunasawa S., Sakiyama F., Nakata A. Mol. Gen. Genet. 204:1-7(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-13 AND 666-671. Strain: K12 / C600 / ATCC 23724 / DSM 3925 / LMG 3041 / NCIB 10222.
[2]	O'Connor M.J., Ally A., Ally D., Zhang X., Robichaud M., Backman K. Submitted (APR-1989) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Direct binding of FtsZ to ZipA, an essential component of the septal ring structure that mediates cell division in E. coli." Hale C.A., de Boer P.A.J. Cell 88:175-185(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-90. Strain: PB103.
[7]	"Conserved residues in domain Ia are required for the reaction of Escherichia coli DNA ligase with NAD+." Sriskanda V., Shuman S. J. Biol. Chem. 277:9695-9700(2002) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF GLU-10; TYR-22; HIS-23; ASP-32; TYR-35 AND ASP-36, ACTIVE SITE.
[8]	"Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA)." Zhu H., Shuman S. J. Biol. Chem. 280:12137-12144(2005) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LYS-115; ASP-117; GLY-118; ASP-138; GLU-143; GLY-172; GLU-173; ASN-198; ARG-200; ARG-208; ARG-277; ASP-285; GLY-286; VAL-288; LYS-290 AND LYS-314.
[9]	"Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase." Wang L.K., Nair P.A., Shuman S. J. Biol. Chem. 283:23343-23352(2008) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-333; THR-334; ARG-342; ARG-379; 383-VAL-ILE-384; 446-ARG-ARG-447; GLY-455; ARG-487; GLY-489; GLY-521; GLY-553 AND ARG-614.
[10]	"Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate." Nandakumar J., Nair P.A., Shuman S. Mol. Cell 26:257-271(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH ZINC IONS; AMP AND DNA.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M30255 Genomic DNA. Translation: AAA24071.1.
M24278 Genomic DNA. Translation: AAA24070.1.
U00096 Genomic DNA. Translation: AAC75464.1.
AP009048 Genomic DNA. Translation: BAA16282.2.
U74650 Genomic DNA. Translation: AAB42062.1.

PIR

LQECC6. B65015.

RefSeq

NP_416906.1. NC_000913.2.
YP_490647.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2OWO	X-ray	2.30	A	1-671	[»]
4GLX	X-ray	1.90	A	1-586	[»]

ProteinModelPortal

P15042.

SMR

P15042. Positions 1-586, 600-669.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10098N.

IntAct

P15042. 13 interactions.

STRING

511145.b2411.

Proteomic databases

PaxDb

P15042.

PRIDE

P15042.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75464; AAC75464; b2411.
BAA16282; BAA16282; BAA16282.

GeneID

12930678.
946885.

KEGG

ecj:Y75_p2372.
eco:b2411.

PATRIC

32120205. VBIEscCol129921_2505.

Organism-specific databases

EchoBASE

EB0529.

EcoGene

EG10534. ligA.

Phylogenomic databases

eggNOG

COG0272.

HOGENOM

HOG000218459.

KO

K01972.

OMA

ENVRTIR.

ProtClustDB

PRK07956.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10534-MONOMER.
ECOL316407:JW2403-MONOMER.
MetaCyc:EG10534-MONOMER.

Gene expression databases

Genevestigator

P15042.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

HAMAP

MF_01588. DNA_ligase_A.

InterPro

IPR001357. BRCT_dom.
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.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]

PANTHER

PTHR11107:SF5. PTHR11107:SF5. 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.

SMART

SM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]

SUPFAM

SSF52113. BRCT. 1 hit.
SSF50249. Nucleic_acid_OB. 1 hit.
SSF47781. RuvA_2_like. 1 hit.

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...

Other

EvolutionaryTrace

P15042.

Entry information

Entry name

DNLJ_ECOLI

Accession

Primary (citable) accession number: P15042
Secondary accession number(s): P78197, P78198

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 135 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program