DNA ligase - Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

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Q9HHC4 (DNLI_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 91. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA ligase
EC=6.5.1.1

Alternative name(s):
Lig(Tk)
Polydeoxyribonucleotide synthase [ATP]

Gene names

Name:	lig
Ordered Locus Names:	TK2140

Organism

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]

Taxonomic identifier

69014 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›

Protein attributes

Sequence length	559 AA.
Sequence status	Complete.
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-Rule MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_00407
Cofactor	Magnesium. Binds 1 lipoyl cofactor covalently By similarity.
Subunit structure	Monomer.
Miscellaneous	Can also use NAD, but less efficiently than ATP. HAMAP-Rule MF_00407
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.
Biophysicochemical properties	pH dependence: Optimum pH is 8.0. HAMAP-Rule MF_00407 Temperature dependence: Still active at 100 degrees Celsius. Thermostable.
Sequence caution	The sequence BAB15949.1 differs from that shown. Reason: Erroneous initiation. The sequence BAD86329.1 differs from that shown. Reason: Erroneous initiation.

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 Reference 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: 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-Rule MF_00407

PRO_0000059615

Sites

Active site

249

N6-AMP-lysine intermediate By similarity

Binding site

247

ATP By similarity

Binding site

254

ATP By similarity

Binding site

269

ATP By similarity

Binding site

299

ATP By similarity

Binding site

339

ATP By similarity

Binding site

414

ATP By similarity

Binding site

420

ATP By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q9HHC4 [UniParc].

Last modified June 20, 2001. Version 2.
Checksum: 91AB32542E03D20D
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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

« Hide

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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: ATCC BAA-918 / JCM 12380 / 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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB042527 Genomic DNA. Translation: BAB15949.1. Different initiation. AP006878 Genomic DNA. Translation: BAD86329.1. Different initiation.
RefSeq	YP_184553.1. NC_006624.1.
3D structure databases
ProteinModelPortal	Q9HHC4.
SMR	Q9HHC4. Positions 1-558.
ModBase	Search...
Protein-protein interaction databases
STRING	69014.TK2140.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAD86329; BAD86329; TK2140.
GeneID	3235455.
KEGG	tko:TK2140.
Phylogenomic databases
eggNOG	COG1793.
HOGENOM	HOG000036008.
KO	K10747.
ProtClustDB	PRK01109.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
HAMAP	MF_00407. DNA_ligase.
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. [Graphical view]
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. 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:	May 1, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents