Reviewed, UniProtKB/Swiss-Prot Q1II25 (DNLI_ACIBL)

Names and origin

Protein names

Recommended name:
    Probable DNA ligase
    EC=6.5.1.1
Alternative name(s):
    Polydeoxyribonucleotide synthase [ATP]

Gene names

Name:	lig
Ordered Locus Names:	Acid345_4475

Organism

Acidobacteria bacterium (strain Ellin345) [Complete proteome] [HAMAP]

Taxonomic identifier

204669 [NCBI]

Taxonomic lineage

Bacteria › Acidobacteria › Candidatus Koribacter

Protein attributes

Sequence length	576 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair By similarity. HAMAP MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP MF_00407
Cofactor	Divalent metal cations By similarity. HAMAP MF_00407
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Ligand	ATP-binding Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: HAMAP DNA repair Inferred from electronic annotation. Source: HAMAP DNA replication Inferred from electronic annotation. Source: HAMAP cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: HAMAP metal 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 – 576	576	Probable DNA ligase HAMAP MF_00407		PRO_0000365215
Sites
	Active site	237	1	N6-AMP-lysine intermediate By similarity
	Binding site	235	1	ATP By similarity
	Binding site	242	1	ATP By similarity
	Binding site	257	1	ATP By similarity
	Binding site	285	1	ATP By similarity
	Binding site	324	1	ATP By similarity
	Binding site	422	1	ATP By similarity
	Binding site	428	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q1II25-1 [UniParc]. Last modified June 13, 2006. Version 1. Checksum: 69C4D0AC018B7BB8	FASTA	576	63,771
	10 20 30 40 50 60 MQLLAQTCEA IAATSKKTEK IAIVATYLQS RTVPEAALST LFLSGRTFAA HEERTLQVGG 70 80 90 100 110 120 SILWRVVGEL SGASEAKMTA AYKRHGDLGD ATLGVLRGVA PEESTLTLKE VDYMFQQIAA 130 140 150 160 170 180 VSGPAAKSRL IVTLLARATA PEAKYLVKFI TGELRIGLKE SQVEEAIAKA YGRELAEVRR 190 200 210 220 230 240 ANMLVGDIGE TLVLAAHDKL ATARMRLFHP MGFMLATPAE SANEAFAEFE HAIVEDKYDG 250 260 270 280 290 300 IRAQAHISRD KVRIFSRTLD DITDSFPELI PALKAIEHEV ILDGEILAWR CGQALAFSEL 310 320 330 340 350 360 QKRLGRKNVS AAMQREVPVS YVTFDLLYAK GQLVIDRPLQ ERAAMLDGIF SEGAPRLVNV 370 380 390 400 410 420 DPHGQASLMF AEVTPEQRVL RAPQARADSP EELDRLFAAA QERGNEGLMI KDIHSAYAVG 430 440 450 460 470 480 RRGKSWLKLK RELAMLDVVV TAVELGHGKR AGILSDYTFA VRGGEELLNI GKAYSGLTDK 490 500 510 520 530 540 EIAEMDEWFR AHTLVDHGFV REVEPKIVIE VAFNAVMKSD RHASGFALRF PRILRIRDDK 550 560 570 GGEEIDTLER AEEIYRSQFH QRTRRIHRGD TKAQSS

References

[1]

"Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils." Ward N.L., Challacombe J.F., Janssen P.H., Henrissat B., Coutinho P.M., Wu M., Xie G., Haft D.H., Sait M., Badger J., Barabote R.D., Bradley B., Brettin T.S., Brinkac L.M., Bruce D., Creasy T., Daugherty S.C., Davidsen T.M. , DeBoy R.T., Detter J.C., Dodson R.J., Durkin A.S., Ganapathy A., Gwinn-Giglio M., Han C.S., Khouri H., Kiss H., Kothari S.P., Madupu R., Nelson K.E., Nelson W.C., Paulsen I., Penn K., Ren Q., Rosovitz M.J., Selengut J.D., Shrivastava S., Sullivan S.A., Tapia R., Thompson L.S., Watkins K.L., Yang Q., Yu C., Zafar N., Zhou L., Kuske C.R. Appl. Environ. Microbiol. 75:2046-2056(2009) [PubMed: 19201974] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000360 Genomic DNA. Translation: ABF43475.1.
RefSeq	YP_593549.1.
3D structure databases
SMR	Q1II25. Positions 3-559.
ModBase	Search...
Protein-protein interaction databases
STRING	Q1II25.
Genome annotation databases
GeneID	4070958.
GenomeReviews	Gene locus Acid345_4475 in contig CP000360_GR.
KEGG	aba:Acid345_4475.
NMPDR	fig|204669.6.peg.4453.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1793.
HOGENOM	HBG570821.
OMA	GRPRPFQ.
PhylomeDB	Q1II25.
Enzyme and pathway databases
BioCyc	ABAC204669:ACID345_4475-MONOMER.
Family and domain databases
HAMAP	MF_00407. DNA_ligase. [Tree]
InterPro	IPR000977. DNA_ligase. IPR012309. DNA_ligase_A_C. IPR012310. DNA_ligase_A_M. IPR016059. DNA_ligase_CS. IPR012340. NA-bd_OB-fold. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. [Graphical view]
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. False negative. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI_ACIBL

Accession

Primary (citable) accession number: Q1II25

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 3, 2009
Last sequence update:	June 13, 2006
Last modified:	February 9, 2010
This is version 37 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)