Reviewed, UniProtKB/Swiss-Prot A1R4P6 (DNLJ_ARTAT)

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:	AAur_1434

Organism

Arthrobacter aurescens (strain TC1) [Complete proteome] [HAMAP]

Taxonomic identifier

290340 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Micrococcineae › Micrococcaceae › Arthrobacter

Protein attributes

Sequence length	768 AA.
Sequence status	Complete.
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. 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	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 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 – 768	768	DNA ligase HAMAP MF_01588		PRO_0000313116
Regions
	Domain	661 – 750	90	BRCT
	Nucleotide binding	61 – 65	5	NAD By similarity
	Nucleotide binding	110 – 111	2	NAD By similarity
Sites
	Active site	148	1	N6-AMP-lysine intermediate By similarity
	Metal binding	443	1	Zinc By similarity
	Metal binding	446	1	Zinc By similarity
	Metal binding	462	1	Zinc By similarity
	Metal binding	468	1	Zinc By similarity
	Binding site	146	1	NAD By similarity
	Binding site	169	1	NAD By similarity
	Binding site	206	1	NAD By similarity
	Binding site	322	1	NAD By similarity
	Binding site	346	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1R4P6-1 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: 7F92736417DC2050	FASTA	768	83,412
	10 20 30 40 50 60 MSTPENPDPV DTTTQDAAAA IVAEEGTPPS ESLRDEYEQL ADLVRKYRYA YYQEDSPTVS 70 80 90 100 110 120 DAEFDELYRR LEELEALHPE LVSNDSPTQE VGGEVSSAFA AVEHLQRMYS LDDVFSLDEL 130 140 150 160 170 180 EAWVRKAEAS VAKLGDSVPP IAWLTELKID GLAVNLLYRD GKLVRAATRG DGTTGEDITH 190 200 210 220 230 240 NVLTIKEIPR QLSGSGYPSE VEIRGEVFIP SKAFLEFNES LVAAGKAPLA NPRNAAAGSL 250 260 270 280 290 300 RQKDPAETAK RPLSMFVHGI GAREGLDAKS QSESYKLLEE WGLPVSPYLK VLETFDDVLK 310 320 330 340 350 360 FIADYGERRH KLVHEIDGIV VKIDDFATQR ALGYTSRVPR WAAAYKYPPE EVHTKLLDIA 370 380 390 400 410 420 VNVGRTGRVT PFGLMEPVKV AGSTVGMATL HNQDVVKAKG VMIGDIVILR KAGDVIPEIV 430 440 450 460 470 480 GPVLALRDKQ EPPVREFVMP TECPSCGTPL APAKESDVDI RCPNAKSCPS QLRERVFHVA 490 500 510 520 530 540 SRGAFDIEAL GWEAAVALTQ PAEPETPPLT SEARLFSLTR EDLADVLIRR EKRSKGVGTG 550 560 570 580 590 600 EYELVPYFYT KGTAKSPSKP TATTEKLFAE LEKAKQQPLW RVLVALSIRH VGPTASRALA 610 620 630 640 650 660 TAFGSMDAIR NATEEQMAHV DGVGPTIAVA LKEWFAVDWH NEIVDSWAAA GVRMEDERDA 670 680 690 700 710 720 SVPRTLEGLT VVVTGTLPNF SRDEAKEAII IRGGKASGSV SKNTSYLVAG ESAGTKLDKA 730 740 750 760 EQLGVPVLDE DGFRELLANG PAQTGTEAEA ATDEATVVDE TAAEAATE

References

[1]

"Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1." Mongodin E.F., Shapir N., Daugherty S.C., DeBoy R.T., Emerson J.B., Shvartzbeyn A., Radune D., Vamathevan J., Riggs F., Grinberg V., Khouri H.M., Wackett L.P., Nelson K.E., Sadowsky M.J. PLoS Genet. 2:2094-2106(2006) [PubMed: 17194220] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000474 Genomic DNA. Translation: ABM07125.1.
RefSeq	YP_947208.1.
3D structure databases
SMR	A1R4P6. Positions 32-350, 663-744.
ModBase	Search...
Protein-protein interaction databases
STRING	A1R4P6.
Genome annotation databases
GeneID	4639882.
GenomeReviews	Gene locus AAur_1434 in contig CP000474_GR.
KEGG	aau:AAur_1434.
TIGR	AAur_1434.
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	IKHFASR.
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. 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. 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...

Entry information

Entry name

DNLJ_ARTAT

Accession

Primary (citable) accession number: A1R4P6

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	February 6, 2007
Last modified:	February 9, 2010
This is version 27 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)