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A0QUP1 (DNLI_MYCS2) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 64. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase B

EC=6.5.1.1
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]
Gene names
Name:ligB
Ordered Locus Names:MSMEG_2277, MSMEI_2220
OrganismMycobacterium smegmatis (strain ATCC 700084 / mc(2)155) [Reference proteome] [HAMAP]
Taxonomic identifier246196 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

Protein attributes

Sequence length509 AA.
Sequence statusComplete.
Protein existenceInferred 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. Ref.5

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

Disruption phenotype

Not essential for growth, no effect on NHEJ. In quadruple ligB-ligC1-ligC2-ligD deletions NHEJ on blunt and 5'-overhangs is 0.22 and 0.12% of wild-type respectively; only 4-fold decrease in 3'-overhang NHEJ. Ref.4 Ref.5

Sequence similarities

Belongs to the ATP-dependent DNA ligase family.

Sequence caution

The sequence AFP38690.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 509509DNA ligase B HAMAP-Rule MF_00407
PRO_0000365227

Sites

Active site2141N6-AMP-lysine intermediate By similarity
Binding site2121ATP By similarity
Binding site2191ATP By similarity
Binding site2341ATP By similarity
Binding site2631ATP By similarity
Binding site2991ATP By similarity
Binding site3711ATP By similarity
Binding site3771ATP By similarity

Sequences

Sequence LengthMass (Da)Tools
A0QUP1 [UniParc].

Last modified January 9, 2007. Version 1.
Checksum: E5C3AADF5B8F311C

FASTA50954,594
        10         20         30         40         50         60 
MLADVAAAST EVAASSARLV KIERIATLLA RSAAEDDTQA VAVIVSWLSG ELPQRQIGVG 

        70         80         90        100        110        120 
WAALRTLPPP AATPSLTVDD VDDRLSTIKA VAGKGSQATR AGLVHELFSA ATDPEQKFLR 

       130        140        150        160        170        180 
HLLSGELRQG ALAGVMADAV AKAAGLPAAE IRRAAMLAGN LPAVAAAAVT GGRAALADFR 

       190        200        210        220        230        240 
LRVGRPVGPM LAQTATSVDD ALQRLGGTAV LEAKLDGARV QIHRSGCDVS IYTRSLDDVT 

       250        260        270        280        290        300 
HRLPEVVEAT LALPATELIA DAEAIALRPD GRPHLFQVTA ARFGRKDPGD LGPLSVFFFD 

       310        320        330        340        350        360 
LLHVDGRDLL DLPTEERFGA LDALVRQDQR VDRLVTTDTV AAQEFLERTL AAGHEGVMAK 

       370        380        390        400        410        420 
SPHAAYEAGR RGAGWLKVKP VHTLDLVVLA VEWGSGRRQG KLSNIHLGAR DPDSSGFVML 

       430        440        450        460        470        480 
GKTFKGMTDA MLEWQTQRFL ELADGPTDGY VVHLRPEQVV EIAFDGVQRS SRYPAGMALR 

       490        500 
FVRVLRYRDD KSPAEADTVE TVRRFYERD 

« Hide

References

« Hide 'large scale' references
[1]Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C., Fraser C.M.
Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700084 / mc(2)155.
[2]"Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700084 / mc(2)155.
[3]"Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700084 / mc(2)155.
[4]"Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C."
Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S., Glickman M.S.
Nat. Struct. Mol. Biol. 12:304-312(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
Strain: ATCC 700084 / mc(2)155.
[5]"The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends."
Aniukwu J., Glickman M.S., Shuman S.
Genes Dev. 22:512-527(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE.
Strain: ATCC 700084 / mc(2)155.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000480 Genomic DNA. Translation: ABK74122.1.
CP001663 Genomic DNA. Translation: AFP38690.1. Different initiation.
RefSeqYP_006566985.1. NC_018289.1.
YP_886629.1. NC_008596.1.

3D structure databases

ProteinModelPortalA0QUP1.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING246196.MSMEG_2277.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABK74122; ABK74122; MSMEG_2277.
AFP38690; AFP38690; MSMEI_2220.
GeneID13428737.
4536201.
KEGGmsg:MSMEI_2220.
msm:MSMEG_2277.
PATRIC18076976. VBIMycSme59918_2242.

Phylogenomic databases

eggNOGCOG1793.
HOGENOMHOG000036008.
KOK01971.
OMAGRPRPFQ.
OrthoDBEOG6Q8HXT.
ProtClustDBPRK03180.

Enzyme and pathway databases

BioCycMSME246196:GJ4Y-2277-MONOMER.

Family and domain databases

Gene3D1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPMF_00407. DNA_ligase.
InterProIPR022865. 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]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDNLI_MYCS2
AccessionPrimary (citable) accession number: A0QUP1
Secondary accession number(s): I7FAW2
Entry history
Integrated into UniProtKB/Swiss-Prot: March 3, 2009
Last sequence update: January 9, 2007
Last modified: March 19, 2014
This is version 64 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