Q3IPX0 (DNLI_NATPD) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA ligase
EC=6.5.1.1

Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]

Gene names

Name:	lig
Ordered Locus Names:	NP3474A

Organism

Natronomonas pharaonis (strain DSM 2160 / ATCC 35678) [Complete proteome] [HAMAP]

Taxonomic identifier

348780 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Halobacteria › Halobacteriales › Halobacteriaceae › Natronomonas

Protein attributes

Sequence length	548 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 ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: EC 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 – 548	548	DNA ligase HAMAP MF_00407		PRO_1000049874
Sites
	Active site	254	1	N6-AMP-lysine intermediate By similarity
	Binding site	252	1	ATP By similarity
	Binding site	259	1	ATP By similarity
	Binding site	274	1	ATP By similarity
	Binding site	303	1	ATP By similarity
	Binding site	343	1	ATP By similarity
	Binding site	414	1	ATP By similarity
	Binding site	420	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q3IPX0 [UniParc]. Last modified November 8, 2005. Version 1. Checksum: 621F22FEEA73D814	FASTA	548	58,865
	10 20 30 40 50 60 MEFAEFAARA AEIESEPADL ETVDLVATLC ADAGDDLGTV ARFVQGRVFP AHDSTKLDIG 70 80 90 100 110 120 PSLCYEALAK AAGPNVDSDD IERRLAEVGE IGAVAESLDL GGQQGLAAFG GGTDREALTV 130 140 150 160 170 180 SGVEETLQAL AAAAGDGSTD AKRDRLFDLF NRAEPTEARF LARLVLGEMR VGVGEGTVRD 190 200 210 220 230 240 AIAAAFEVPE PDVERALQVA NDCGLVAETA RDDGAAGLDD IGLVVGRPVK AMLAQAGTAV 250 260 270 280 290 300 EALDEWGTAA VETKYDGARV QVHYDGDSAR LFSRNLEEVT EPLPEVVEFV EQSLSVPAIL 310 320 330 340 350 360 DGEVVAVDDD GTPRPFQEIL RRFRRKHDVA AAREDVSVEL YAFDCLHVDG EDLLDTPLSE 370 380 390 400 410 420 RHDRLESLLA DGVSPLSYAD DADEVADIEA DALDAGHEGI MLKNPDSTYT PGSRGKNWLK 430 440 450 460 470 480 RKPDVETLDL VVTGAEWGEG RRANLLGTFV VSARADDGYE PVGKVATGIT DEELERLHER 490 500 510 520 530 540 LQPHVRTEDG TDVDIEPAVV FEVGYEEIQQ SPTYGSGYAL RFPRFVGVRE DKSPSDADSL ERIDRLTS

References

[1]

"Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis." Falb M., Pfeiffer F., Palm P., Rodewald K., Hickmann V., Tittor J., Oesterhelt D. Genome Res. 15:1336-1343(2005) [PubMed: 16169924] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: DSM 2160 / ATCC 35678.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CR936257 Genomic DNA. Translation: CAI49828.1.
RefSeq	YP_327383.1. NC_007426.1.
3D structure databases
HSSP	HSSP built from PDB template 1VS0 based on UniProtKB P71571.
ProteinModelPortal	Q3IPX0.
ModBase	Search...
Protein-protein interaction databases
STRING	Q3IPX0.
Proteomic databases
PRIDE	Q3IPX0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3702886.
GenomeReviews	Gene locus NP3474A in contig CR936257_GR.
KEGG	nph:NP3474A.
NMPDR	fig|348780.3.peg.1913.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	arNOG04596.
HOGENOM	HBG570821.
OMA	GRPRPFQ.
PhylomeDB	Q3IPX0.
ProtClustDB	CLSK511253.
Enzyme and pathway databases
BioCyc	NPHA348780:NP3474A-MONOMER.
Family and domain databases
HAMAP	MF_00407. DNA_ligase. [Tree]
InterPro	IPR022865. DNA_ligae_ATP-dep_bac/arc. IPR000977. DNA_ligase_ATP-dep. IPR012309. DNA_ligase_ATP-dep_C. IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR012308. DNA_ligase_ATP-dep_N. IPR012340. NA-bd_OB-fold. IPR016027. NA-bd_OB-fold-like. [Graphical view]
Gene3D	G3DSA:1.10.3260.10. DNA_ligase_ATP-dep_N. 1 hit. G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
KO	K10747.
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
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_NATPD

Accession

Primary (citable) accession number: Q3IPX0

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	November 8, 2005
Last modified:	November 16, 2011
This is version 52 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program