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Q1RK40 (DNLJ_RICBR) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 44. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
DNA ligase
EC=6.5.1.2
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD+]
Gene names
Name:ligA
Synonyms:lig
Ordered Locus Names:RBE_0193
OrganismRickettsia bellii (strain RML369-C) [Complete proteome] [HAMAP]
Taxonomic identifier336407 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rickettsiales › Rickettsiaceae › Rickettsieae › Rickettsia

Protein attributes

Sequence length689 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA By similarity. HAMAP MF_01588

Catalytic activity

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588

Cofactor

Magnesium or manganese By similarity. HAMAP MF_01588

Sequence similarities

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.

Contains 1 BRCT domain.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
DNA replication
   LigandMagnesium
Manganese
Metal-binding
NAD
Zinc
   Molecular functionLigase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

DNA replication

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentintracellular

Inferred from electronic annotation. Source: InterPro

   Molecular functionDNA ligase (NAD+) activity

Inferred from electronic annotation. Source: EC

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 689689DNA ligase HAMAP MF_01588
PRO_0000280945

Regions

Domain610 – 68980BRCT
Nucleotide binding40 – 445NAD By similarity
Nucleotide binding89 – 902NAD By similarity

Sites

Active site1231N6-AMP-lysine intermediate By similarity
Metal binding4131Zinc By similarity
Metal binding4161Zinc By similarity
Metal binding4311Zinc By similarity
Metal binding4371Zinc By similarity
Binding site1211NAD By similarity
Binding site1441NAD By similarity
Binding site1791NAD By similarity
Binding site2951NAD By similarity
Binding site3191NAD By similarity

Sequences

Sequence LengthMass (Da)Tools
Q1RK40 [UniParc].

Last modified May 16, 2006. Version 1.
Checksum: D0083E2FDE617158

FASTA68977,643
        10         20         30         40         50         60 
MQNIEKINEE EAKKLLIELA DKIAQYNHAY YIEDKPLVSD AEYDQLFNTN LKLEQKFPHL 

        70         80         90        100        110        120 
ILENSPSKKI GAKVENKFAK VTHQVPMLSL SNVFDEEDVK DFLDRIKSFL RLDQFSPIFC 

       130        140        150        160        170        180 
EPKIDGLSFA ATYKNGILTT GATRGDGYIG EDITANIKTI KDFPHKINNA PELLEVRGEI 

       190        200        210        220        230        240 
YIEKNDFTSL NQEQEQQGKD KFANPRNAAA GSLRQLDPSV TAKRPLKYFV YAIGSAKEEL 

       250        260        270        280        290        300 
ANSQDQLLAK FKELGFNVNE IGKLANSEEE IFSFYEYLKT NRKNLPYEID GVVYKLNDFA 

       310        320        330        340        350        360 
LQDRMGFIAR SPRFATAHKF PAIIGQTKLL SITVQVGRTG TLTPVAELEP IEIGGVIVSR 

       370        380        390        400        410        420 
ATLHNYQEIA RKDVRVGDYV FLQRAGDVIP QITGVDLAKR SADATTFDPP LFCPSCNSKL 

       430        440        450        460        470        480 
HYVPEDIIIR CDNGLNCPAQ NYERIRHFVS KNAMDIEGLG RKQVEFLIDK GLISNPYDIF 

       490        500        510        520        530        540 
FLKEKNEASL TKLENMDGWG KKSVENLFNN IEKSKNVSLP RFIYALGIRH IGEQNAKLLT 

       550        560        570        580        590        600 
REFGSYENFI AQMELLKEND PEIYQKLNNL DGIGDKMLVD IIDFFDVKEN IELIKNLSEV 

       610        620        630        640        650        660 
LNIEDYKETR EQSSLTGKIV VFTGSMPTLS RAEAKATAEK LGAKVAASVS SNTDLVIAGE 

       670        680 
DAGSKLKKAK ELGIKIIDEA EWLTLVRDI

« Hide

References

[1]"Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens."
Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C., Fournier P.-E., Claverie J.-M., Raoult D.
PLoS Genet. 2:733-744(2006) [PubMed: 16703114] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: RML369-C.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000087 Genomic DNA. Translation: ABE04274.1.
RefSeqYP_537363.1. NC_007940.1.

3D structure databases

ProteinModelPortalQ1RK40.
ModBaseSearch...

Protein-protein interaction databases

STRINGQ1RK40.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID3995337.
GenomeReviewsGene locus RBE_0193 in contig CP000087_GR.
KEGGrbe:RBE_0193.
PATRIC17881681. VBIRicBel102610_0221.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0272.
HOGENOMHBG620317.
OMAENVRTIR.
ProtClustDBPRK07956.

Enzyme and pathway databases

BioCycRBEL336407:RBE_0193-MONOMER.

Family and domain databases

HAMAPMF_01588. DNA_ligase_A.
[Tree]
InterProIPR001357. BRCT.
IPR018239. DNA_ligase_AS.
IPR004150. DNA_ligase_OB.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR012340. NA-bd_OB-fold.
IPR016027. NA-bd_OB-fold-like.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
Gene3DG3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
KOK01972.
PfamPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
SMARTSM00292. BRCT. 1 hit.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMSSF52113. BRCT. 1 hit.
SSF50249. Nucleic_acid_OB. 1 hit.
SSF47781. RuvA_2_like. 1 hit.
TIGRFAMsTIGR00575. Dnlj. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDNLJ_RICBR
AccessionPrimary (citable) accession number: Q1RK40
Entry history
Integrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: May 16, 2006
Last modified: January 25, 2012
This is version 44 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Rickettsia bellii strain RML369-C

Rickettsia bellii (strain RML369-C): entries and gene names

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents