Reviewed, UniProtKB/Swiss-Prot A1VDM7 (DNLJ2_DESVV)

Names and origin

Protein names

Recommended name:
    DNA ligase 2
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+] 2

Gene names

Name:	ligA2
Ordered Locus Names:	Dvul_1526

Organism

Desulfovibrio vulgaris subsp. vulgaris (strain DP4) [Complete proteome] [HAMAP]

Taxonomic identifier

391774 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	797 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 – 797	797	DNA ligase 2 HAMAP MF_01588		PRO_0000313221
Regions
	Domain	634 – 723	90	BRCT
	Nucleotide binding	67 – 71	5	NAD By similarity
	Nucleotide binding	116 – 117	2	NAD By similarity
Sites
	Active site	149	1	N6-AMP-lysine intermediate By similarity
	Metal binding	445	1	Zinc By similarity
	Metal binding	448	1	Zinc By similarity
	Metal binding	463	1	Zinc By similarity
	Metal binding	468	1	Zinc By similarity
	Binding site	147	1	NAD By similarity
	Binding site	170	1	NAD By similarity
	Binding site	207	1	NAD By similarity
	Binding site	327	1	NAD By similarity
	Binding site	351	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1VDM7-1 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: 5CE4C16336CF2228	FASTA	797	86,516
	10 20 30 40 50 60 MTEVKKGRVV DDAPVNDAPE NDAAEVTSPA RHDAIPEEAR QRAAQLRADL ERHNRLYYEL 70 80 90 100 110 120 DTPEISDAEY DVLYRELVGL ERRWPALRDE ASPTQRVGGE VLEGLEKQAH TLRMYSLDNA 130 140 150 160 170 180 FSRDEWGAFM QRMYNALPDA PSAFWCDPKM DGLALEVIYE NGVFTSALTR GNGEVGEVVT 190 200 210 220 230 240 AAMRTVRNLP LALRGDDVPR RIEVRGEVVI AKADFEQLNA RQSAAGGKLF ANPRNAAAGS 250 260 270 280 290 300 VRQLDTTVTA GRPLQFLAYG VGQVVLEGGT APWTTHSGLM ARLREWGFDT PPEGRLCASP 310 320 330 340 350 360 DEVWAYYEAL GARRESLAIE IDGVVAKLDD TEAQEALGFT ARAPRWALAL KFPAMQARTR 370 380 390 400 410 420 LDDIRVQVGR TGVLTPVAIL EPVRVGGVEV SRATLHNEDE IRAKGLMLGD MVLVQRAGDV 430 440 450 460 470 480 IPEVVRPLVE ERTGDERPFV FPENCPECDS PVVRPQGEVA HRCVNVMCPA VRRQSIIHFV 490 500 510 520 530 540 SKAGLDVRGV GERWVQQLVD GGHVTSPVGL FSLTKLDLMR FERMGPTSAA NFVTALDAAR 550 560 570 580 590 600 TGATLVRLIC ALGIRHVGEQ TARTLAANFT DLDALREADA ETLQQLPDIG PEVAGSIRTF 610 620 630 640 650 660 FANEGNLELL ERLRAIGLWP KRQDAPPAPE GADAIVRPLQ GLKVLFTGSL TRVGRTEAED 670 680 690 700 710 720 MARAAGANIA SSVTKSLDLL VVGGKPGSKL EKARKLGIRV MEEADFFAML ESAEMPAEGS 730 740 750 760 770 780 DAAEVPAPSV EDVDAKEVPS RDVAHVRIVH DGTASDPGGD SRSVAEDAPA RSTEGDAVST 790 AEGEDVPRGR AEQLKLF

References

[1]

"Complete sequence of chromosome 1 of Desulfovibrio vulgaris subsp. vulgaris DP4." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N. , Lykidis A., Walker C., Richardson P. Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000527 Genomic DNA. Translation: ABM28543.1.
RefSeq	YP_966970.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	A1VDM7.
Genome annotation databases
GeneID	4664583.
GenomeReviews	Gene locus Dvul_1526 in contig CP000527_GR.
KEGG	dvl:Dvul_1526.
NMPDR	fig|391774.5.peg.1538.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	RFAIAYK.
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. 3 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. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ2_DESVV

Accession

Primary (citable) accession number: A1VDM7

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	February 6, 2007
Last modified:	November 3, 2009
This is version 24 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)