Reviewed, UniProtKB/Swiss-Prot A9CIB3 (DNLJ_AGRT5)

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:	Atu2082
ORF Names:	AGR_C_3775

Organism

Agrobacterium tumefaciens (strain C58 / ATCC 33970) [Complete proteome] [HAMAP]

Taxonomic identifier

176299 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Agrobacterium

Protein attributes

Sequence length	724 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 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 – 724	724	DNA ligase HAMAP MF_01588		PRO_0000313106
Regions
	Domain	646 – 724	79	BRCT
	Nucleotide binding	44 – 48	5	NAD By similarity
	Nucleotide binding	93 – 94	2	NAD By similarity
Sites
	Active site	129	1	N6-AMP-lysine intermediate By similarity
	Metal binding	437	1	Zinc By similarity
	Metal binding	440	1	Zinc By similarity
	Metal binding	461	1	Zinc By similarity
	Metal binding	467	1	Zinc By similarity
	Binding site	127	1	NAD By similarity
	Binding site	150	1	NAD By similarity
	Binding site	186	1	NAD By similarity
	Binding site	307	1	NAD By similarity
	Binding site	331	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A9CIB3-1 [UniParc]. Last modified January 15, 2008. Version 1. Checksum: A54BF20FD962377D	FASTA	724	79,392
	10 20 30 40 50 60 MSKDQIPVEN LTELEASSEL AFLAAELARH DALYHGKDAP EISDADYDAL KRRNDAIEAA 70 80 90 100 110 120 FPALVRADSP SKKVGFTPLP TFAPIVHARP MLSLDNTFSE EDLRDFVSSV YRFLGHLPDD 130 140 150 160 170 180 SIAFTAEPKI DGLSMSIRYE NRKLKTAATR GDGTTGENVT ANIRTIKEIP NELPADAPDV 190 200 210 220 230 240 VEVRGEVYMA KSDFLALNAQ MEADGKQTYV NPRNTASGSL RQLDANVTAK RKLRFFAYAL 250 260 270 280 290 300 GEVSNGGQPA RIADTQYGIV EKFREWGFPV NPLMKRFTSA QQLLEHYNEI GVARPDLDYD 310 320 330 340 350 360 IDGVVYKVDR LDLQERLGFR SRSPRWATAH KFPAEQAFTT VENIEIQVGR TGALTPVARL 370 380 390 400 410 420 TPITVGGVVV TNATLHNADY IEGIGNSGER IRPEDHDIRI GDTVIVQRAG DVIPQVLDVL 430 440 450 460 470 480 LEKRAAGAAK YVFPEKCPVC GSHAVRERNE KTGKLDSVTR CTGGFVCRAQ AVEHLKHFVS 490 500 510 520 530 540 RNAFDIEGLG TKQIDFFFES DDPALSIKTA PDIFTLKARQ EASHLTKLEN IDGFGKVSVK 550 560 570 580 590 600 KLFDAIDARR AIDLHRLIFA LGIRHVGETT AKLLARSYGT YEHFEKAMKA AADPASDAWA 610 620 630 640 650 660 ELNSIDGIGE VVARAIIEFY KEPRNLDVID RLIRELQPKE AEKPSTEGSP VAGKTVVFTG 670 680 690 700 710 720 SLEKFTRDEA KARAESLGAK VAGSVSKKTD ILVAGPGAGS KLAKATELGV QTMDEDEWLA LIGG

References

[1]

"The genome of the natural genetic engineer Agrobacterium tumefaciens C58." Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K., Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y., Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P., Clendenning J. , Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R., Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G., Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y., Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S., Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F., Gordon M.P., Olson M.V., Nester E.W. Science 294:2317-2323(2001) [PubMed: 11743193] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

[2]

"Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58." Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C. , Allinger M., Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C., Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S. Science 294:2323-2328(2001) [PubMed: 11743194] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE007869 Genomic DNA. Translation: AAK87832.1.
PIR	AC2832. G97609.
RefSeq	NP_355047.1.
3D structure databases
SMR	A9CIB3. Positions 16-635, 643-723.
ModBase	Search...
Protein-protein interaction databases
STRING	A9CIB3.
Genome annotation databases
GeneID	1134120.
GenomeReviews	Gene locus Atu2082 in contig AE007869_GR.
KEGG	atu:Atu2082.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	IKHFASR.
PhylomeDB	A9CIB3.
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. 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_AGRT5

Accession

Primary (citable) accession number: A9CIB3

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	January 15, 2008
Last modified:	February 9, 2010
This is version 19 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)