Reviewed, UniProtKB/Swiss-Prot O59288 (DNLI_PYRHO)

Names and origin

Protein names

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

Gene names

Name:	lig
Ordered Locus Names:	PH1622

Organism

Pyrococcus horikoshii [Complete proteome] [HAMAP]

Taxonomic identifier

53953 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	559 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP MF_00407
Cofactor	Magnesium By similarity.
Subunit structure	Monomer By similarity.
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 Magnesium 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 magnesium 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 – 559	559	Probable thermostable DNA ligase HAMAP MF_00407		PRO_0000059614
Sites
	Active site	249	1	N6-AMP-lysine intermediate By similarity
	Binding site	247	1	ATP By similarity
	Binding site	254	1	ATP By similarity
	Binding site	269	1	ATP By similarity
	Binding site	299	1	ATP By similarity
	Binding site	339	1	ATP By similarity
	Binding site	414	1	ATP By similarity
	Binding site	420	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	O59288-1 [UniParc]. Last modified August 1, 1998. Version 1. Checksum: D1E85172B1D72188	FASTA	559	63,623
	10 20 30 40 50 60 MKYIELAQLY QKLEKTTMKL IKTRLVADFL KRVPEDHLDF IPYLILGDVF PEWDERELGV 70 80 90 100 110 120 GEKLLIKAVS MATGVDPKEI ENSVKDTGDL GESIALAIKR RKQKSFFSQP LTIKRVYQTL 130 140 150 160 170 180 VKIAETTGEG SQEKKMKYLA NLFMDAEPLE AKYLARTVLG TMRTGVAEGL LRDAIALAFH 190 200 210 220 230 240 VKVELVERAY MLTSDFGFVA KIAKAEGNEG LEKVTIQLGK PIKPMLAQQA ANIKEALLEM 250 260 270 280 290 300 GGEAEFEIKY DGARVQVHKD GEKVIIYSRR LENVTRAIPE IVEAIKEAIE PEKVIVEGEL 310 320 330 340 350 360 VAIGEEGRPL PFQYVLRRFR RKHNIEEMMK KIPLELNLFD VLYVDGKSFV DTKFIERRKK 370 380 390 400 410 420 LEEIVKPNGK IKVAENLITK NAEEAEKFYK RALEMGHEGL MAKRLDAVYE PGNRGKKWLK 430 440 450 460 470 480 IKPTMENLDL VIIGAEWGEG RRAHLFGSFI LGAYDPETGE FLEVGKVGSG FTDDDLVEFT 490 500 510 520 530 540 KMLKPLIVKE EGKRVVIQPK IVIEVTYQEI QKSPKYRSGF ALRFPRYVAL RDDKGPEDAD 550 TIERIAQLYE LQERIKGKV

References

[1]

"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3." Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H. DNA Res. 5:55-76(1998) [PubMed: 9679194] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: OT3.

Cross-references

Sequence databases
EMBLGenBankDDBJ	BA000001 Genomic DNA. Translation: BAA30734.1.
PIR	F71041.
RefSeq	NP_143476.1.
3D structure databases
SMR	O59288. Positions 1-559.
ModBase	Search...
Genome annotation databases
GeneID	1442475.
GenomeReviews	Gene locus PH1622 in contig BA000001_GR.
KEGG	pho:PH1622.
NMPDR	fig|70601.1.peg.1589.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	O59288.
OMA	O59288. SNLHLGA.
Enzyme and pathway databases
BRENDA	6.5.1.1. 74679.
Family and domain databases
HAMAP	MF_00407. [Tree]
InterPro	IPR000977. DNA_ligase. IPR012309. DNA_ligase_A_C. IPR012310. DNA_ligase_A_M. IPR012308. DNA_ligase_A_N. 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. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI_PYRHO

Accession

Primary (citable) accession number: O59288

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	August 1, 1998
Last modified:	June 16, 2009
This is version 63 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)