DNA ligase - Pyrococcus abyssi (strain GE5 / Orsay)

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P0CL75 (DNLI_PYRAB) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 19. 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):
Polydeoxyribonucleotide synthase [ATP]

Gene names

Name:	lig
Ordered Locus Names:	PYRAB05430
ORF Names:	PAB2002

Organism

Pyrococcus abyssi (strain GE5 / Orsay) [Complete proteome] [HAMAP]

Taxonomic identifier

272844 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus ›

Protein attributes

Sequence length	559 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-Rule MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_00407
Cofactor	Divalent metal cations By similarity. HAMAP-Rule MF_00407
Subunit structure	Monomer By similarity. HAMAP-Rule 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: 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_0000407282

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

P0CL75 [UniParc].

Last modified April 5, 2011. Version 1.
Checksum: 64CDBA1BBD188433
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FASTA

559

63,553

        10         20         30         40         50         60 
MRYIELAQLY QKLEKTTMKL IKTRLVADFL KKVPEDHLEF IPYLILGDVF PEWDERELGV 

        70         80         90        100        110        120 
GEKLLIKAVS MATGIDSKEI ENSVKDTGDL GESIALAVKK RKQKSFFSQP LTIKRVYQTL 

       130        140        150        160        170        180 
VKVAETTGEG SQDKKMKYLA NLFMDAEPIE AKYIARTVLG TMRTGVAEGL LRDAISLAFN 

       190        200        210        220        230        240 
VKVELVERAY MLTSDFGFVA KIAKTEGNDG LAKVTIQIGK PIKPMLAQQA ANIKEALLEM 

       250        260        270        280        290        300 
GGEAEFEIKY DGARVQVHKD GEKVTIYSRR LENVTRAIPE IVEAIKEALK PTKAIVEGEL 

       310        320        330        340        350        360 
VAIGEDGRPL PFQYVLRRFR RKYNIEEMME KIPLELNLFD VLYVDGVSLI DTKFMERRKK 

       370        380        390        400        410        420 
LEEIVETNGK VKIAENLITK NVEEAEQFYK RALEMGHEGL MAKRLDAVYE PGNRGKKWLK 

       430        440        450        460        470        480 
IKPTMENLDL VIIGAEWGEG RRAHLLGSFI LGAYDPETGE FLEVGKVGSG FTDDDLVEFT 

       490        500        510        520        530        540 
KMLKPLIIKE EGKRVWIQPK VVIEVTYQEI QKSPKYRSGF ALRFPRYVAL REDKGPEDAD 

       550 
TIERIAQLYE LQERMKGKV

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi." Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J., Weissenbach J., Zivanovic Y., Forterre P. Mol. Microbiol. 47:1495-1512(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: GE5 / Orsay.
[2]	"Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638." Gao J., Wang J. Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract] Cited for: GENOME REANNOTATION. Strain: GE5 / Orsay.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ248284 Genomic DNA. Translation: CAB49465.1. HE613800 Genomic DNA. Translation: CCE69932.1.
PIR	B75173.
RefSeq	NP_126234.1. NC_000868.1.
3D structure databases
ProteinModelPortal	P0CL75.
SMR	P0CL75. Positions 1-559.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	CAB49465; CAB49465; PAB2002.
GeneID	1495445.
KEGG	pab:PAB2002.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HOG000036008.
KO	K10747.
OMA	ARVQVHK.
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_PYRAB

Accession

Primary (citable) accession number: P0CL75
Secondary accession number(s): G8ZGQ3, Q9HH10, Q9V185

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 5, 2011
Last sequence update:	April 5, 2011
Last modified:	May 1, 2013
This is version 19 of the entry and version 1 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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents