Reviewed, UniProtKB/Swiss-Prot A5FWJ5 (DNLJ_ACICJ)

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:	Acry_0757

Organism

Acidiphilium cryptum (strain JF-5) [Complete proteome] [HAMAP]

Taxonomic identifier

349163 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodospirillales › Acetobacteraceae › Acidiphilium

Protein attributes

Sequence length	682 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 – 682	682	DNA ligase HAMAP MF_01588		PRO_0000313528
Regions
	Domain	601 – 682	82	BRCT
	Nucleotide binding	42 – 46	5	NAD By similarity
	Nucleotide binding	88 – 89	2	NAD By similarity
Sites
	Active site	123	1	N6-AMP-lysine intermediate By similarity
	Metal binding	409	1	Zinc By similarity
	Metal binding	412	1	Zinc By similarity
	Metal binding	427	1	Zinc By similarity
	Metal binding	433	1	Zinc By similarity
	Binding site	121	1	NAD By similarity
	Binding site	144	1	NAD By similarity
	Binding site	180	1	NAD By similarity
	Binding site	291	1	NAD By similarity
	Binding site	315	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	A5FWJ5-1 [UniParc]. Last modified June 12, 2007. Version 1. Checksum: 1A2105E6C0E93630	FASTA	682	73,603
	10 20 30 40 50 60 MTSPASGVPE PADPKARLAE LVERLAAADA AYYRDDAPIM DDAAYDALRR EAESLRAAHP 70 80 90 100 110 120 DLAAALDQVG AAPSGAFGKV RHRLPMLSLD NVFEPADFVE FCASIRRFLG LGAAPLAFVA 130 140 150 160 170 180 EPKIDGLSIS LTYENRRFVR GATRGDGTEG EDVTENLRTL RELPATLPDD APDFIEIRGE 190 200 210 220 230 240 VYMTKTDFIT LNQGQARQFA NPRNAAAGSL RQLDPAVTAS RRLSLFAYAR GAASQAVGET 250 260 270 280 290 300 HWDYLAILRR WGFPVNPLAE RVSEAGAEPF QRSIGERRAG LDYDIDGVVY KIDDLALQER 310 320 330 340 350 360 LGFAGRAPRW AVAWKFPAER ALTTLLGIDI QVGRTGALTP RARLDPVNVG GVLVSHATLH 370 380 390 400 410 420 NEDEIARKDV RIGDTVELQR AGDVIPQILR ALPERRPADS VPFVFPDHCP VCGALAIRPA 430 440 450 460 470 480 GEVVRRCTGG LSCPAQVVER LIHFCSRLAF DIEGMGEKTV QEFHGLGWLE SPADIFTLRD 490 500 510 520 530 540 REAAIAALEG WGEVSARKLI AAIDARRRIS LARFIYALGI RRIGEQNAKL LARHYSSYAV 550 560 570 580 590 600 WRRQMEEAGV IGSDARLELG SISGIGPSIA EELAGFFAEP HNRDLLDRLV PMLTIEDEVA 610 620 630 640 650 660 AAGGALAGKT IVFTGTLESL TRPEAKARAE ALGARVTESV SKKTDFVVVG ADAGSKAAKA 670 680 ASLGVTVLSE AEFRSLAGLP PG

References

[1]

"Complete sequence of chromosome of Acidiphilium cryptum JF-5." 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., Sims D., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M. , Hauser L., Kyrpides N., Kim E., Magnuson T., Richardson P. Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000697 Genomic DNA. Translation: ABQ29977.1.
RefSeq	YP_001233896.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	A5FWJ5.
Genome annotation databases
GeneID	5160952.
GenomeReviews	Gene locus Acry_0757 in contig CP000697_GR.
KEGG	acr:Acry_0757.
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. IPR005220. DUF388_OB-fold. IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif. IPR004149. Znf_DNAligase_C4. [Graphical view]
Gene3D	G3DSA:2.40.50.200. DNA_ligase_OB. 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.
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. 1 hit. PS01056. DNA_LIGASE_N2. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ_ACICJ

Accession

Primary (citable) accession number: A5FWJ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	June 12, 2007
Last modified:	November 3, 2009
This is version 22 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)