DNA ligase - Staphylococcus aureus

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

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Protein attributes

Sequence length	667 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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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.

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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: 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...

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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

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9AIU7-1 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: F599F7BC8AB59D67
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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

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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.

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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	[»]

SMR

Q9AIU7. Positions 7-311, 589-662.

ModBase

Search...

Enzyme and pathway databases

BRENDA

6.5.1.2. 95.

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]

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...

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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:	February 9, 2010
This is version 46 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)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families