Q9AIU7 (DNLJ_STAAU) 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

Organism

Staphylococcus aureus

Taxonomic identifier

1280 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Staphylococcus

Protein attributes

Sequence length	667 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 MF_01588
Catalytic activity	NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588
Cofactor	Magnesium or manganese By similarity. HAMAP MF_01588
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
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: EC 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 – 667

667

DNA ligase HAMAP MF_01588

PRO_0000161762

Regions

Domain

586 – 667

82

BRCT

Nucleotide binding

32 – 36

5

NAD By similarity

Nucleotide binding

81 – 82

2

NAD By similarity

Sites

Active site

112

1

N6-AMP-lysine intermediate By similarity

Metal binding

401

1

Zinc By similarity

Metal binding

404

1

Zinc By similarity

Metal binding

419

1

Zinc By similarity

Metal binding

424

1

Zinc By similarity

Binding site

110

1

NAD By similarity

Binding site

133

1

NAD By similarity

Binding site

167

1

NAD By similarity

Binding site

283

1

NAD By similarity

Binding site

307

1

NAD By similarity

Secondary structure

1

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667

Helix Strand Turn

Details...

Helix

5 – 23

19

Helix

32 – 48

17

Helix

50 – 52

3

Helix

58 – 61

4

Helix

88 – 101

14

Beta strand

107 – 110

4

Beta strand

118 – 122

5

Beta strand

127 – 129

3

Helix

143 – 146

4

Beta strand

162 – 165

4

Beta strand

167 – 169

3

Helix

172 – 182

11

Turn

183 – 186

4

Helix

193 – 197

5

Helix

206 – 211

6

Beta strand

215 – 222

8

Helix

232 – 241

10

Beta strand

251 – 255

5

Helix

260 – 269

10

Helix

270 – 272

3

Beta strand

273 – 275

3

Beta strand

281 – 286

6

Helix

287 – 292

6

Beta strand

297 – 299

3

Beta strand

303 – 306

4

Sequences

	Sequence		Length	Mass (Da)
	Q9AIU7 [UniParc]. Last modified June 1, 2001. Version 1. Checksum: F599F7BC8AB59D67	FASTA	667	75,081
	10 20 30 40 50 60 MADLSSRVNE LHDLLNQYSY EYYVEDNPSV PDSEYDKLLH ELIKIEEEHP EYKTVDSPTV 70 80 90 100 110 120 RVGGEAQASF NKVNHDTPML SLGNAFNEDD LRKFDQRIRE QIGNVEYMCE LKIDGLAVSL 130 140 150 160 170 180 KYVDGYFVQG LTRGDGTTGE DITENLKTIH AIPLKMKEPL NVEVRGEAYM PRRSFLRLNE 190 200 210 220 230 240 EKEKNDEQLF ANPRNAAAGS LRQLDSKLTA KRKLSVFIYS VNDFTDFNAR SQSEALDELD 250 260 270 280 290 300 KLGFTTNKNR ARVNNIDGVL EYIEKWTSQR ESLPYDIDGI VIKVNDLDQQ DEMGFTQKSP 310 320 330 340 350 360 RWAIAYKFPA EEVVTKLLDI ELSIGRTGVV TPTAILEPVK VAGTTVSRAS LHNEDLIHDR 370 380 390 400 410 420 DIRIGDSVVV KKAGDIIPEV VRSIPERRPE DAVTYHMPTH CPSCGHELVR IEGEVALRCI 430 440 450 460 470 480 NPKCQAQLVE GLIHFVSRQA MNIDGLGTKI IQQLYQSELI KDVADIFYLT EEDLLPLDRM 490 500 510 520 530 540 GQKKVDNLLA AIQQAKDNSL ENLLFGLGIR HLGVKASQVL AEKYETIDRL LTVTEAELVE 550 560 570 580 590 600 IHDIGDKVAQ SVVTYLENED IRALIQKLKD KHVNMIYKGI KTSDIEGHPE FSGKTIVLTG 610 620 630 640 650 660 KLHQMTRNEA SKWLASQGAK VTSSVTKNTD VVIAGEDAGS KLTKAQSLGI EIWTEQQFVD KQNELNS

References

[1]

"Cloning and functional characterization of an NAD(+)-dependent DNA ligase from Staphylococcus aureus." Kaczmarek F.S., Zaniewski R.P., Gootz T.D., Danley D.E., Mansour M.N., Griffor M., Kamath A.V., Cronan M., Mueller J., Sun D., Martin P.K., Benton B., McDowell L., Biek D., Schmid M.B. J. Bacteriol. 183:3016-3024(2001) [PubMed: 11325928] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: NT64.

+

Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF234833 Genomic DNA. Translation: AAK15020.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3JSL	X-ray	1.80	A/B	1-312	[»]
3JSN	X-ray	1.90	A	1-312	[»]

ProteinModelPortal

Q9AIU7.

SMR

Q9AIU7. Positions 7-311.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

HAMAP

MF_01588. DNA_ligase_A.
[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.
IPR016027. NA-bd_OB-fold-like.
IPR010994. RuvA_2-like.
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.

SMART

SM00292. BRCT. 1 hit.
SM00278. HhH1. 3 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...

Entry information

Entry name

DNLJ_STAAU

Accession

Primary (citable) accession number: Q9AIU7

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	June 1, 2001
Last modified:	September 21, 2011
This is version 53 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program