Reviewed, UniProtKB/Swiss-Prot Q9HHC4 (DNLI_PYRKO)

Names and origin

Protein names

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

Gene names

Name:	lig
Ordered Locus Names:	TK2140

Organism

Pyrococcus kodakaraensis (Thermococcus kodakaraensis) [Complete proteome] [HAMAP]

Taxonomic identifier

69014 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus

Protein attributes

Sequence length	559 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. HAMAP MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP MF_00407
Cofactor	Magnesium. HAMAP MF_00407 Binds 1 lipoyl cofactor covalently By similarity.
Subunit structure	Monomer. HAMAP MF_00407
Miscellaneous	Can also use NAD, but less efficiently than ATP. HAMAP MF_00407
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.
biophysicochemical properties	pH dependence: Optimum pH is 8.0. HAMAP MF_00407 Temperature dependence: Still active at 100 degrees Celsius. Thermostable.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Ligand	ATP-binding Metal-binding NAD Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Direct protein sequencing
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 – 559	559	DNA ligase HAMAP MF_00407		PRO_0000059615
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)
	Q9HHC4-1 [UniParc]. Last modified June 20, 2001. Version 2. Checksum: 91AB32542E03D20D	FASTA	559	63,749
	10 20 30 40 50 60 MRYSELADLY RRLEKTTLKT LKTKFVADFL KKTPDELLEI VPYLILGKVF PDWDERELGV 70 80 90 100 110 120 GEKLLIKAVS MATGVPEKEI EDSVRDTGDL GESVALAIKK KKQKSFFSQP LTIKRVYDTF 130 140 150 160 170 180 VKIAEAQGEG SQDRKMKYLA NLFMDAEPEE GKYLARTVLG TMRTGVAEGI LRDAIAEAFR 190 200 210 220 230 240 VKPELVERAY MLTSDFGYVA KIAKLEGNEG LSKVRIQIGK PIRPMLAQNA ASVKDALIEM 250 260 270 280 290 300 GGEAAFEIKY DGARVQVHKD GDKVIVYSRR LENVTRSIPE VIEAIKAALK PEKAIVEGEL 310 320 330 340 350 360 VAVGENGRPR PFQYVLRRFR RKYNIDEMIE KIPLELNLFD VMFVDGESLI ETKFIDRRNK 370 380 390 400 410 420 LEEIVKESEK IKLAEQLITK KVEEAEAFYR RALELGHEGL MAKRLDSIYE PGNRGKKWLK 430 440 450 460 470 480 IKPTMENLDL VIIGAEWGEG RRAHLLGSFL VAAYDPHSGE FLPVGKVGSG FTDEDLVEFT 490 500 510 520 530 540 KMLKPYIVRQ EGKFVEIEPK FVIEVTYQEI QKSPKYKSGF ALRFPRYVAL REDKSPEEAD 550 TIERVAELYE LQERFKAKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity." Nakatani M., Ezaki S., Atomi H., Imanaka T. J. Bacteriol. 182:6424-6433(2000) [PubMed: 11053387] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: KOD1.
[2]	"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Genome Res. 15:352-363(2005) [PubMed: 15710748] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: KOD1.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AB042527 Genomic DNA. Translation: BAB15949.1. Different initiation. AP006878 Genomic DNA. Translation: BAD86329.1. Different initiation.
RefSeq	YP_184553.1.
3D structure databases
SMR	Q9HHC4. Positions 1-558.
ModBase	Search...
Genome annotation databases
GeneID	3235455.
GenomeReviews	Gene locus TK2140 in contig AP006878_GR.
KEGG	tko:TK2140.
NMPDR	fig|69014.3.peg.2141.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q9HHC4.
Enzyme and pathway databases
BioCyc	TKOD69014:TK2140-MON.
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_PYRKO

Accession

Primary (citable) accession number: Q9HHC4
Secondary accession number(s): Q5JHF2

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 20, 2001
Last sequence update:	June 20, 2001
Last modified:	March 24, 2009
This is version 61 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)