DNA ligase - Pyrococcus abyssi

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Reviewed, UniProtKB/Swiss-Prot Q9V185 (DNLI_PYRAB)

Last modified June 16, 2009. Version 65. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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 [Complete proteome] [HAMAP]

Taxonomic identifier

29292 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

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Protein attributes

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

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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	Divalent metal cations By similarity.
Subunit structure	Monomer By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.
biophysicochemical properties	Temperature dependence: Thermostable. HAMAP MF_00407

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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 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...

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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_0000059612

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

Natural variations

Natural variant

100

K → R in strain: ST 549. HAMAP MF_00407

Natural variant

292

T → A in strain: ST 549. HAMAP MF_00407

Natural variant

367

T → A in strain: ST 549. HAMAP MF_00407

Natural variant

408

V → I in strain: ST 549. HAMAP MF_00407

Natural variant

484

K → R in strain: ST 549. HAMAP MF_00407

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9V185-1 [UniParc].

Last modified May 1, 2000. 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

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and expression of a new thermostable DNA ligase from the hyperthermophilic Pyrococcus abyssi sp. ST 549." Rolland J.L., Dietrich J. Submitted (JUN-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ST 549.
[2]	"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: 12622808] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: GE5 / Orsay.

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Cross-references

Sequence databases
	AJ006532 Genomic DNA. Translation: CAC20743.1. AJ248284 Genomic DNA. Translation: CAB49465.1.
PIR	B75173.
RefSeq	NP_126234.1.
3D structure databases
SMR	Q9V185. Positions 1-559.
ModBase	Search...
Genome annotation databases
GeneID	1495445.
GenomeReviews	Gene locus PYRAB05430 in contig AL096836_GR.
KEGG	pab:PAB2002.
NMPDR	fig\|272844.1.peg.569.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q9V185.
OMA	Q9V185. SNLHLGA.
Enzyme and pathway databases
BioCyc	PABY272844:PAB2002-MON.
BRENDA	6.5.1.1. 262861.
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...

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Entry information

Entry name

DNLI_PYRAB

Accession

Primary (citable) accession number: Q9V185
Secondary accession number(s): Q9HH10

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 21, 2001
Last sequence update:	May 1, 2000
Last modified:	June 16, 2009
This is version 65 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)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Natural variations

Sequences

References

Cross-references

Sequence databases

3D structure databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents