Reviewed, UniProtKB/Swiss-Prot Q660X2 (DNLJ_BORGA)

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:	BG0562

Organism

Borrelia garinii [Complete proteome] [HAMAP]

Taxonomic identifier

29519 [NCBI]

Taxonomic lineage

Bacteria › Spirochaetes › Spirochaetales › Spirochaetaceae › Borrelia › Borrelia burgdorferi group

Protein attributes

Sequence length	660 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

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	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 – 660	660	DNA ligase HAMAP MF_01588		PRO_0000313148
Regions
	Domain	583 – 660	78	BRCT
	Nucleotide binding	33 – 37	5	NAD By similarity
	Nucleotide binding	82 – 83	2	NAD By similarity
Sites
	Active site	112	1	N6-AMP-lysine intermediate By similarity
	Metal binding	396	1	Zinc By similarity
	Metal binding	399	1	Zinc By similarity
	Metal binding	412	1	Zinc By similarity
	Metal binding	417	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	281	1	NAD By similarity
	Binding site	305	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q660X2-1 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 1D0434D83D4C4DE2	FASTA	660	75,525
	10 20 30 40 50 60 MSIKIQQEIE DLKKLIRKWD KEYYVDSLPS VEDFVYDNHI LRLKELESRH PEYKTLDSPT 70 80 90 100 110 120 LKFGSDLLNN FEEVEHSVPI LSLDKVYDLD LLKSWIDKID FNNSFNISVE PKIDGCSIVL 130 140 150 160 170 180 YYKDGILEKA LTRGNGKFGN DVTKNIRTIR HIPLFLDEKV DLVLRGEVYI TKENFFKINK 190 200 210 220 230 240 FLEKPYTSSR NLASGILRRV DSREVANFPL NIFIYDFLNA ELELKTNDLA IAKLKKLGFK 250 260 270 280 290 300 VDPLIRFFDQ KSSIIEVLNY IADITKKRNS FEYEIDGVVL KVSEFVLREK LGYTSHHPKW 310 320 330 340 350 360 AMAYKFEALS GFSRVNSIVV QVGRSGKITP VANIDKVFVS GAFITNATLH NQDYIISIGL 370 380 390 400 410 420 NVGDVVKVSR RGDVIPAVEM VINKCSKGVF KVPDNCPACK TVLVKEGAHF FCTNNSCPSV 430 440 450 460 470 480 AVERIKYFCS KNCMDIEGFS DKTISFLFEK EFISSEIDLY TFNFYKLLKF KGFKDRKVYN 490 500 510 520 530 540 LINSIEASKK KPFSKLLLSI GIKELGENAI RLLFLNNLNS FSKLFRLCQD RNFAFSTLLK 550 560 570 580 590 600 IKGIGEKIAL NIIEAFNDST MLNKFKFFEN LGFKMEESIL IDDENRLLAG KKFCITGTFN 610 620 630 640 650 660 GYSRSIIIDK LKNKGAIFKT CVTEGLDFLI VGEKAGSKLE KALNLNVKIM SFEDIKSYLN

References

[1]

"Comparative analysis of the Borrelia garinii genome." Gloeckner G., Lehmann R., Romualdi A., Pradella S., Schulte-Spechtel U., Schilhabel M., Wilske B., Suehnel J., Platzer M. Nucleic Acids Res. 32:6038-6046(2004) [PubMed: 15547252] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: PBi.

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000013 Genomic DNA. Translation: AAU07399.1.
RefSeq	YP_072991.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	2957884.
GenomeReviews	Gene locus BG0562 in contig CP000013_GR.
KEGG	bga:BG0562.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q660X2.
OMA	GERITAN.
Enzyme and pathway databases
BioCyc	BGAR290434:BG0562-MON.
BRENDA	6.5.1.2. 294970.
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. 2 hits. SM00532. LIGANc. 1 hit. [Graphical view]
TIGRFAMs	TIGR00575. dnlj. 1 hit.
PROSITE	PS50172. BRCT. 1 hit. PS01055. DNA_LIGASE_N1. False negative. PS01056. DNA_LIGASE_N2. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ_BORGA

Accession

Primary (citable) accession number: Q660X2

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 11, 2004
Last modified:	November 3, 2009
This is version 38 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)