Reviewed, UniProtKB/Swiss-Prot Q5YVN7 (DNLJ1_NOCFA)

Names and origin

Protein names

Recommended name:
    DNA ligase 1
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+] 1

Gene names

Name:	ligA1
Ordered Locus Names:	NFA_29070

Organism

Nocardia farcinica [Complete proteome] [HAMAP]

Taxonomic identifier

37329 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Nocardia

Protein attributes

Sequence length	663 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 – 663	663	DNA ligase 1 HAMAP MF_01588		PRO_0000313342
Regions
	Domain	574 – 663	90	BRCT
	Nucleotide binding	30 – 34	5	NAD By similarity
	Nucleotide binding	78 – 79	2	NAD By similarity
Sites
	Active site	105	1	N6-AMP-lysine intermediate By similarity
	Metal binding	389	1	Zinc By similarity
	Metal binding	392	1	Zinc By similarity
	Metal binding	407	1	Zinc By similarity
	Metal binding	412	1	Zinc By similarity
	Binding site	126	1	NAD By similarity
	Binding site	161	1	NAD By similarity
	Binding site	294	1	NAD By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5YVN7-1 [UniParc]. Last modified November 23, 2004. Version 1. Checksum: 42F1C43410049ED0	FASTA	663	70,584
	10 20 30 40 50 60 MDAGERIREL ADRIVELRTA YYEGAPLVAD AEYDAVEDEL RALIAAHPEL APDPNPLDQV 70 80 90 100 110 120 GAPAVLHAPV RHSRPMLSLE KATTPEQVAA FFERFPGQPV VVMPKLDGLS LALVYEDGRL 130 140 150 160 170 180 VRAVTRGDGT TGDDVTMLVR ALVDGVPEQI DVPGRVEVRG EAVMLRSTFL AYNAAHPDKP 190 200 210 220 230 240 LINPRNAAAG TLRAKDPATV AERRLRFFGF DLDTAEGGAA ADLGEGLRAL GIAGAAMRMC 250 260 270 280 290 300 ADAEQAQAAI TDIERGRNDL DYDIDGAVLR LADRDAYAAA GTRSNSPRGA LAFKFAAEEK 310 320 330 340 350 360 TTVLEAVTWD VGKTGKIVPV ARLEPVFVGG TTVTKATLAN QQVIRARDIK VGDTVLVRRA 370 380 390 400 410 420 GDVIPFVAGV LDASKRTGAE VEIVPPTECP SCGQPVTEQG NSRELFCTNA SCPAQTVRRL 430 440 450 460 470 480 IHWASRAAAD IDAIGGVWIE RLAEAGILEN PSDFYTLTKE RLLEFDRIGE VSATRMIESI 490 500 510 520 530 540 DRSRDVGLRR ALIGLAIPMA SEGTAARLAR AGFASLEEVA DAGEERLVAV EDIGPKVAAS 550 560 570 580 590 600 LVEHLTRLRP ELERLRERGV SLDVREEDLP PVVAAGAPLA GKTVVVTGAI SDPRSGEKVA 610 620 630 640 650 660 RPTFQRLCEK AGATAASSVS ANTDLLITGA GVGESKLAKA EKLGVEIVDQ ATIWAQLIEA KLV

References

[1]

"The complete genomic sequence of Nocardia farcinica IFM 10152." Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K., Shiba T., Hattori M. Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004) [PubMed: 15466710] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: IFM 10152.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AP006618 Genomic DNA. Translation: BAD57754.1.
RefSeq	YP_119118.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	3107592.
GenomeReviews	Gene locus NFA_29070 in contig AP006618_GR.
KEGG	nfa:nfa29070.
NMPDR	fig|247156.1.peg.2848.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q5YVN7.
OMA	HRWQIAF.
Enzyme and pathway databases
BioCyc	NFAR247156:NFA29070-MON.
BRENDA	6.5.1.2. 290697.
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. [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. 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. 2 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

DNLJ1_NOCFA

Accession

Primary (citable) accession number: Q5YVN7

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	November 23, 2004
Last modified:	November 3, 2009
This is version 42 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)