Reviewed, UniProtKB/Swiss-Prot A7Z261 (DNLJ_BACA2)

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:	RBAM_007020

Organism

Bacillus amyloliquefaciens (strain FZB42) [Complete proteome] [HAMAP]

Taxonomic identifier

326423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	669 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 regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro
Cellular component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro 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 transcription factor binding Inferred from electronic annotation. Source: InterPro 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 – 669	669	DNA ligase HAMAP MF_01588		PRO_0000313121
Regions
	Domain	591 – 669	79	BRCT
	Nucleotide binding	35 – 39	5	NAD By similarity
	Nucleotide binding	84 – 85	2	NAD By similarity
Sites
	Active site	116	1	N6-AMP-lysine intermediate By similarity
	Metal binding	405	1	Zinc By similarity
	Metal binding	408	1	Zinc By similarity
	Metal binding	423	1	Zinc By similarity
	Metal binding	428	1	Zinc By similarity
	Binding site	114	1	NAD By similarity
	Binding site	137	1	NAD By similarity
	Binding site	171	1	NAD By similarity
	Binding site	287	1	NAD By similarity
	Binding site	311	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A7Z261-1 [UniParc]. Last modified October 23, 2007. Version 1. Checksum: 4EBA47E0D5A89E59	FASTA	669	75,237
	10 20 30 40 50 60 MMDKETAKHR AEELRRTIDQ YSYEYYTLDE PSVPDSEYDR LMQELIAIEE EHPELRTPDS 70 80 90 100 110 120 PTQRVGGAVL ESFQKVQHGT PMLSLGNAFN DDDLRDFDRR VRQAVGDGVA YNVELKIDGL 130 140 150 160 170 180 AVSLRYEDGY FVRGATRGDG TTGEDITENL KTIRNIPLKM KRNLSIEVRG EAYMPKQSFE 190 200 210 220 230 240 ALNEERLKHE EEPFANPRNA AAGSLRQLDP KIAAKRNLDI FVYSIAELDE MGVETQSQGL 250 260 270 280 290 300 DFLDELGFKT NQERKKCATI DEVIEMIEEL QAKRADLPYE IDGIVIKVDS LDQQEELGYT 310 320 330 340 350 360 AKSPRWAIAY KFPAEEVVTK LLDIELNVGR TGVITPTAVL EPVKVAGTTV SRASLHNEDL 370 380 390 400 410 420 IKEKDIRILD KVVVKKAGDI IPEVVNVLIE QRTGEEKEFN MPTGCPECES ELVRIEGEVA 430 440 450 460 470 480 LRCINPECPA QIREGLIHFV SRNAMNIDGL GERVITQLFR EHLVRNVADL YKLTKEQVIR 490 500 510 520 530 540 LERMGEKSTD NLISSIQKSK ENSLERLLFG LGIRFIGSKA AKTLAMHFES LENLKQVTEE 550 560 570 580 590 600 ELLAVDEIGE KMADAVITYF RKEEMLELLN ELEELGVNTL YKGPKKVKAE DSDSYFAGKT 610 620 630 640 650 660 IVLTGKLEEL SRNEAKAQIE ALGGKLTGSV SKKTDLLIAG EAAGSKLTKA QELNIEVWNE AQLLGELKK

References

[1]

"Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42." Chen X.H., Koumoutsi A., Scholz R., Eisenreich A., Schneider K., Heinemeyer I., Morgenstern B., Voss B., Hess W.R., Reva O., Junge H., Voigt B., Jungblut P.R., Vater J., Suessmuth R., Liesegang H., Strittmatter A., Gottschalk G., Borriss R. Nat. Biotechnol. 25:1007-1014(2007) [PubMed: 17704766] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000560 Genomic DNA. Translation: ABS73087.1.
RefSeq	YP_001420318.1.
3D structure databases
SMR	A7Z261. Positions 2-315, 579-668.
ModBase	Search...
Protein-protein interaction databases
STRING	A7Z261.
Genome annotation databases
GeneID	5461227.
GenomeReviews	Gene locus RBAM_007020 in contig CP000560_GR.
KEGG	bay:RBAM_007020.
Organism-specific databases
CMR	Search...
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. IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif. IPR012340. NA-bd_OB-fold. IPR016027. NA-bd_OB-fold-like. IPR002078. RNA_pol_sigma_54_int. 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...

Entry information

Entry name

DNLJ_BACA2

Accession

Primary (citable) accession number: A7Z261

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 23, 2007
Last modified:	February 9, 2010
This is version 20 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)