Reviewed, UniProtKB/Swiss-Prot A8MLJ8 (DNLJ_ALKOO)

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:	Clos_0550

Organism

Alkaliphilus oremlandii (strain OhILAs) (Clostridium oremlandii (strain OhILAs)) [Complete proteome] [HAMAP]

Taxonomic identifier

350688 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Alkaliphilus

Protein attributes

Sequence length	661 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 – 661	661	DNA ligase HAMAP MF_01588		PRO_0000340325
Regions
	Domain	578 – 661	84	BRCT
	Nucleotide binding	31 – 35	5	NAD By similarity
	Nucleotide binding	79 – 80	2	NAD By similarity
Sites
	Active site	114	1	N6-AMP-lysine intermediate By similarity
	Metal binding	398	1	Zinc By similarity
	Metal binding	401	1	Zinc By similarity
	Metal binding	414	1	Zinc By similarity
	Metal binding	420	1	Zinc By similarity
	Binding site	112	1	NAD By similarity
	Binding site	135	1	NAD By similarity
	Binding site	169	1	NAD By similarity
	Binding site	281	1	NAD By similarity
	Binding site	305	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A8MLJ8-1 [UniParc]. Last modified December 4, 2007. Version 1. Checksum: 99E55927D5CE668B	FASTA	661	74,559
	10 20 30 40 50 60 MGSMERLRQL VDILNEYSYQ YYVLDEPVVS DKEYDQLYDE LVLLEKELNT VLEDSPTIRV 70 80 90 100 110 120 GGDVLKNFKA HNHLAPLWSL DKCKTPEELI SWDLRVRRLL EGSGVPIEYV MEYKFDGLTL 130 140 150 160 170 180 NLTYNNGQLV QAATRGNGTT GEGILEQVKT IKTIPLTIPH KGRIEVQGEG LMGLSVLAAY 190 200 210 220 230 240 NKTALEPLKN PRNAAAGALR NLDPKVTAKR KLSAFCYNVG FYEGIDFNTH MEILAFLKAN 250 260 270 280 290 300 KFPVSNYTKK FHTIHQVIEE IETIGEQVKS LDFLTDGLVI KVNHMEARRL LGYTQKFPRW 310 320 330 340 350 360 AMAFKFEAEE MTTELKDVIW QVGRTGKLTP AAVLEPIDIG GVTVSRATLN NWEDIQRKKV 370 380 390 400 410 420 KIGCRVWIRR SNDVIPEIMG SIEETLEGAM DIEKPQHCPA CHSEVVERGA HIFCPNSLSC 430 440 450 460 470 480 KPQLVSRIVH YASRDAMDIV GFSEKTAEQL FEELNLRDLA DLYEIKYEDL IKLPRFGDKK 490 500 510 520 530 540 ARNLLEAIEN SKNCKLDSFV YALGIPNVGR KTATDLAKHY KSFQAIQEAE FQELITLPDV 550 560 570 580 590 600 GDIVAQSIID FFEDEEIKKS VNRLINEGIR PLFKEVEQQE NIFLGKTVVV TGTLEKYGRK 610 620 630 640 650 660 EIKELLEKLG AKVTGSVSKN TDFLLAGEAA GSKLEKAMEI IASGVETSLR IISEAEFEAM L

References

[1]

"Complete genome of Alkaliphilus oremlandii OhILAs." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M. , Hauser L., Kyrpides N., Mikhailova N., Stolz J.F., Dawson A., Fisher E., Crable B., Perera E., Lisak J., Ranganathan M., Basu P., Richardson P. Submitted (OCT-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000853 Genomic DNA. Translation: ABW18112.1.
RefSeq	YP_001512108.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	5678256.
GenomeReviews	Gene locus Clos_0550 in contig CP000853_GR.
KEGG	aoe:Clos_0550.
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. False negative. PS01056. DNA_LIGASE_N2. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ_ALKOO

Accession

Primary (citable) accession number: A8MLJ8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	December 4, 2007
Last modified:	November 3, 2009
This is version 15 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)