P63973 (DNLJ_MYCTU) 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:	lig
Ordered Locus Names:	Rv3014c, MT3094
ORF Names:	MTV012.28c

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	691 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.3
Cofactor	Magnesium. Ref.3
Sequence similarities	Belongs to the NAD-dependent DNA ligase family. LigA subfamily. Contains 1 BRCT domain.
Sequence caution	The sequence AAK47423.1 differs from that shown. Reason: Erroneous initiation.

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 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 growth Inferred from mutant phenotype PubMed 12657046PubMed 14985346. Source: MTBBASE
Cellular_component	cell wall Inferred from direct assay PubMed 15525680. Source: MTBBASE cytosol Inferred from direct assay PubMed 15525680. Source: MTBBASE plasma membrane Inferred from direct assay PubMed 15525680. Source: MTBBASE
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activity Inferred from direct assay PubMed 12696044PubMed 14985346. Source: MTBBASE magnesium ion binding Inferred from direct assay PubMed 14985346. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 691

691

DNA ligase HAMAP-Rule MF_01588

PRO_0000161752

Regions

Domain

607 – 691

85

BRCT

Nucleotide binding

41 – 45

5

NAD By similarity

Nucleotide binding

91 – 92

2

NAD HAMAP-Rule MF_01588

Sites

Active site

123

1

N6-AMP-lysine intermediate By similarity

Metal binding

418

1

Zinc By similarity

Metal binding

421

1

Zinc By similarity

Metal binding

437

1

Zinc By similarity

Metal binding

443

1

Zinc By similarity

Binding site

121

1

NAD By similarity

Binding site

144

1

NAD By similarity

Binding site

184

1

NAD By similarity

Binding site

300

1

NAD

Binding site

324

1

NAD By similarity

Secondary structure

1

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691

Helix Strand Turn

Details...

Helix

10 – 14

5

Helix

17 – 31

15

Turn

32 – 34

3

Helix

42 – 56

15

Helix

59 – 61

3

Turn

67 – 70

4

Beta strand

77 – 79

3

Beta strand

95 – 97

3

Helix

98 – 106

9

Helix

107 – 109

3

Turn

110 – 112

3

Beta strand

118 – 124

7

Beta strand

126 – 132

7

Helix

134 – 136

3

Beta strand

137 – 142

6

Beta strand

147 – 150

4

Helix

154 – 159

6

Beta strand

160 – 162

3

Beta strand

180 – 186

7

Helix

189 – 197

9

Beta strand

200 – 204

5

Helix

210 – 218

9

Helix

223 – 228

6

Beta strand

232 – 243

12

Helix

249 – 257

9

Turn

258 – 260

3

Helix

272 – 282

11

Turn

283 – 286

4

Helix

287 – 289

3

Beta strand

290 – 292

3

Beta strand

294 – 301

8

Helix

304 – 307

4

Beta strand

314 – 319

6

Beta strand

328 – 333

6

Beta strand

343 – 345

3

Beta strand

350 – 352

3

Beta strand

359 – 363

5

Turn

371 – 377

7

Beta strand

384 – 388

5

Beta strand

391 – 394

4

Sequences

	Sequence		Length	Mass (Da)
	P63973 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 94AD5AEDCD065567	FASTA	691	75,289
	10 20 30 40 50 60 MSSPDADQTA PEVLRQWQAL AEEVREHQFR YYVRDAPIIS DAEFDELLRR LEALEEQHPE 70 80 90 100 110 120 LRTPDSPTQL VGGAGFATDF EPVDHLERML SLDNAFTADE LAAWAGRIHA EVGDAAHYLC 130 140 150 160 170 180 ELKIDGVALS LVYREGRLTR ASTRGDGRTG EDVTLNARTI ADVPERLTPG DDYPVPEVLE 190 200 210 220 230 240 VRGEVFFRLD DFQALNASLV EEGKAPFANP RNSAAGSLRQ KDPAVTARRR LRMICHGLGH 250 260 270 280 290 300 VEGFRPATLH QAYLALRAWG LPVSEHTTLA TDLAGVRERI DYWGEHRHEV DHEIDGVVVK 310 320 330 340 350 360 VDEVALQRRL GSTSRAPRWA IAYKYPPEEA QTKLLDIRVN VGRTGRITPF AFMTPVKVAG 370 380 390 400 410 420 STVGQATLHN ASEIKRKGVL IGDTVVIRKA GDVIPEVLGP VVELRDGSER EFIMPTTCPE 430 440 450 460 470 480 CGSPLAPEKE GDADIRCPNA RGCPGQLRER VFHVASRNGL DIEVLGYEAG VALLQAKVIA 490 500 510 520 530 540 DEGELFALTE RDLLRTDLFR TKAGELSANG KRLLVNLDKA KAAPLWRVLV ALSIRHVGPT 550 560 570 580 590 600 AARALATEFG SLDAIAAAST DQLAAVEGVG PTIAAAVTEW FAVDWHREIV DKWRAAGVRM 610 620 630 640 650 660 VDERDESVPR TLAGLTIVVT GSLTGFSRDD AKEAIVARGG KAAGSVSKKT NYVVAGDSPG 670 680 690 SKYDKAVELG VPILDEDGFR RLLADGPASR T

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors." Srivastava S.K., Tripathi R.P., Ramachandran R. J. Biol. Chem. 280:30273-30281(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS) OF 1-328 IN COMPLEX WITH AMP, CATALYTIC ACTIVITY, COFACTOR.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842581 Genomic DNA. Translation: CAA16099.1.
AE000516 Genomic DNA. Translation: AAK47423.1. Different initiation.
AL123456 Genomic DNA. Translation: CCP45820.1.

PIR

A70857.

RefSeq

NP_217530.1. NC_000962.3.
NP_337609.2. NC_002755.2.
YP_006516472.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZAU	X-ray	3.15	A	1-328	[»]
3SGI	X-ray	3.50	A	2-605	[»]

ProteinModelPortal

P63973.

SMR

P63973. Positions 8-600, 612-683.

ModBase

Search...

Protein-protein interaction databases

STRING

83332.Rv3014c.

Proteomic databases

PRIDE

P63973.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK47423; AAK47423; MT3094.

GeneID

13317815.
887354.
923055.

KEGG

mtc:MT3094.
mtu:Rv3014c.

PATRIC

18128568. VBIMycTub22151_3382.

Organism-specific databases

TubercuList

Rv3014c.

Phylogenomic databases

eggNOG

COG0272.

HOGENOM

HOG000218459.

KO

K01972.

OMA

ENVRTIR.

ProtClustDB

PRK07956.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.
3.40.50.10190. 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:SF8. PTHR11107:SF8. 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. 2 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

BindingDB

P63973.

EvolutionaryTrace

P63973.

Entry information

Entry name

DNLJ_MYCTU

Accession

Primary (citable) accession number: P63973
Secondary accession number(s): L0TBA8, O53261

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 29, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program