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C1B1S4 (DNLJ_RHOOB) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 21. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | 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
Ordered Locus Names:ROP_65220
OrganismRhodococcus opacus (strain B4) [Complete proteome] [HAMAP]
Taxonomic identifier632772 [NCBI]
Taxonomic lineageBacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Rhodococcus

Protein attributes

Sequence length697 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 binding

Inferred from electronic annotation. Source: InterPro

DNA 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 – 697697DNA ligase HAMAP MF_01588
PRO_0000380456

Regions

Domain609 – 69789BRCT
Nucleotide binding44 – 485NAD By similarity
Nucleotide binding93 – 942NAD By similarity

Sites

Active site1251N6-AMP-lysine intermediate By similarity
Metal binding4201Zinc By similarity
Metal binding4231Zinc By similarity
Metal binding4391Zinc By similarity
Metal binding4451Zinc By similarity
Binding site1231NAD By similarity
Binding site1461NAD By similarity
Binding site1861NAD By similarity
Binding site3021NAD By similarity
Binding site3261NAD By similarity

Sequences

Sequence LengthMass (Da)Tools
C1B1S4 [UniParc].

Last modified May 26, 2009. Version 1.
Checksum: B0DBF295CEAFDF67

FASTA69775,697
        10         20         30         40         50         60 
MVSESTEAPT PAPGSVREHW NELAEDVRQH QFRYYVRDAP IISDGEFDAL LGELNDLENQ 

        70         80         90        100        110        120 
YPDLRTPDSP TQLVGGGFAT DFASADHLER MLSLDNVFAT DELRTWISRV EQETGPDLHY 

       130        140        150        160        170        180 
LCEVKIDGVA LNLVYENGRL VRAATRGDGR TGEEVTLNAR TIDDIPEKLT GTDKYPIPAL 

       190        200        210        220        230        240 
LEVRGEVFFR LEDFAALNAA LVEEGKAPFA NPRNSAAGSL RQKNPAVTAR RRLGMICHGL 

       250        260        270        280        290        300 
GRSEGFEPAS QYDAYTALAA WGLPVSTHTV RVTGADAVVD RVQYWGEHRH DVEHEIDGLV 

       310        320        330        340        350        360 
VKVDETSLQR RLGSTSRAPR WAIAYKYPPE EATTKLLDIR VNVGRTGRVT PFAYMEPVTV 

       370        380        390        400        410        420 
AGSTVSLATL HNGSEVKRKG VLIGDTVVLR KAGDVIPEVL GPVVDARTGD EYEFVMPANC 

       430        440        450        460        470        480 
PECDTPLAPA KEGDADIRCP NQQYCPAQLR ERVFHVAGRG AFDIEVLGYE AATSLLEAKA 

       490        500        510        520        530        540 
IGDEGDLFSL TEDDLLKTTL FRTKAGGLSA NGRRLLDNLD SAKDKPLWRV LVALSIRHVG 

       550        560        570        580        590        600 
PTAARALAGE FGSLDRIRES SVEELAAVDG VGGTIAAAVA EWFGVDWHRQ IVDKWSAAGV 

       610        620        630        640        650        660 
RMEDERDESI PRNLEGLSIV VTGSLETFSR DQAKEAILVR GGKAAGSVSK KTAFVVAGES 

       670        680        690 
PGSKHDKAVE LGVPVLDEDG FRRLLEGGPD AVTDSGV

« Hide

References

[1]"Comparison of the complete genome sequences of Rhodococcus erythropolis PR4 and Rhodococcus opacus B4."
Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S., Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.
Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: B4.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AP011115 Genomic DNA. Translation: BAH54769.1.
RefSeqYP_002783714.1. NC_012522.1.

3D structure databases

ProteinModelPortalC1B1S4.
ModBaseSearch...

Protein-protein interaction databases

STRINGC1B1S4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID7745262.
GenomeReviewsGene locus ROP_65220 in contig AP011115_GR.
KEGGrop:ROP_65220.
PATRIC23230471. VBIRhoOpa21106_6602.

Organism-specific databases

CMRSearch...

Phylogenomic databases

OMAENVRTIR.
ProtClustDBPRK07956.

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.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
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.
SM00278. HhH1. 2 hits.
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_RHOOB
AccessionPrimary (citable) accession number: C1B1S4
Entry history
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 2009
Last modified: January 25, 2012
This is version 21 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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