Reviewed, UniProtKB/Swiss-Prot A1K713 (DNLJ_AZOSB)

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:	azo2001

Organism

Azoarcus sp. (strain BH72) [Complete proteome] [HAMAP]

Taxonomic identifier

62928 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Rhodocyclales › Rhodocyclaceae › Azoarcus

Protein attributes

Sequence length	693 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 – 693	693	DNA ligase HAMAP MF_01588		PRO_0000313119
Regions
	Domain	601 – 690	90	BRCT
	Nucleotide binding	35 – 39	5	NAD By similarity
	Nucleotide binding	84 – 85	2	NAD By similarity
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	436	1	Zinc By similarity
	Metal binding	442	1	Zinc By similarity
	Binding site	121	1	NAD By similarity
	Binding site	144	1	NAD By similarity
	Binding site	180	1	NAD By similarity
	Binding site	297	1	NAD By similarity
	Binding site	321	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1K713-1 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: C7E0ACC4BBA89768	FASTA	693	74,907
	10 20 30 40 50 60 MPLFADAAAR AATLRAEIAR HNHAYYVLDT PTIPDAEYDR LFRELQDIEA AHPELLTPDS 70 80 90 100 110 120 PTQRVGGAPL PELVPVRHAV PMLSIRTETD TTAQGVRNFD TRVRNALGLG DGDPAVEYLS 130 140 150 160 170 180 ELKFDGLAIS LRYEHGVLVR AATRGDGETG EDVTHNVRTI QQIPLRLHGA APAVIEVRGE 190 200 210 220 230 240 IYMRRDDFEA LNNRQREAGD KVFVNPRNAA AGAVRQLDPR IAARRPLSFF AYGLGEHAGF 250 260 270 280 290 300 DLPATQAELL TRLAAFGVPV CEHREVSSGP EGLIAFHDRI AALRNELPYD IDGVVYKVNR 310 320 330 340 350 360 VDLQRELGFV TREPRWAVAH KYPAQEEITR LAGIDVQVGR TGALTPVARL EPVFVGGVTV 370 380 390 400 410 420 TNATLHNQDE IDRKDVRVGD WVIVRRAGDV IPEVVGPVLE RRVGEPPRFN LLASYPTCPV 430 440 450 460 470 480 CGSHVVRGED EAVARCSGGL FCPAQRKQAL LHFAGRRAMD IEGLGDKLVE QLVDASIVKT 490 500 510 520 530 540 PADLYKLGIL ALANLERMGE KSAQNLLAAI EKSRNTTLAR FIFALGIRNV GEATAKDLAR 550 560 570 580 590 600 HFGSLDALLA ADEGALQQVP DVGPVVAKCI AEFFAEAHNV EVVEQLRAAG LRWEEGAPAA 610 620 630 640 650 660 PASGSVAGLT FVITGTLPTL SRDEAKALIE AHGGKVSGSV SKKTDYLVAG AEAGSKLAKA 670 680 690 QDLGVDIVDE DGLRRLLESG EQSPINNKDG VPE

References

[1]

"Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72." Krause A., Ramakumar A., Bartels D., Battistoni F., Bekel T., Boch J., Boehm M., Friedrich F., Hurek T., Krause L., Linke B., McHardy A.C., Sarkar A., Schneiker S., Syed A.A., Thauer R., Vorhoelter F.-J., Weidner S. , Puehler A., Reinhold-Hurek B., Kaiser O., Goesmann A. Nat. Biotechnol. 24:1385-1391(2006) [PubMed: 17057704] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AM406670 Genomic DNA. Translation: CAL94618.1.
RefSeq	YP_933505.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	A1K713.
Genome annotation databases
GeneID	4608857.
GenomeReviews	Gene locus azo2001 in contig AM406670_GR.
KEGG	azo:azo2001.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	YKFPAQE.
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. IPR000445. HhH_motif. 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. PF00633. HHH. 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. 4 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...

Entry information

Entry name

DNLJ_AZOSB

Accession

Primary (citable) accession number: A1K713

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	February 6, 2007
Last modified:	November 3, 2009
This is version 22 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)