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A0QUP1

- DNLI_MYCS2

UniProt

A0QUP1 - DNLI_MYCS2

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Protein

DNA ligase B

Gene

ligB

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi

Functioni

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.UniRule annotation

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Divalent metal cations.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei212 – 2121ATPUniRule annotation
Active sitei214 – 2141N6-AMP-lysine intermediateUniRule annotation
Binding sitei219 – 2191ATPUniRule annotation
Binding sitei234 – 2341ATPUniRule annotation
Binding sitei263 – 2631ATPUniRule annotation
Binding sitei299 – 2991ATPUniRule annotation
Binding sitei371 – 3711ATPUniRule annotation
Binding sitei377 – 3771ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: InterPro
  3. DNA ligase (ATP) activity Source: UniProtKB-HAMAP
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. DNA biosynthetic process Source: InterPro
  4. DNA ligation involved in DNA repair Source: InterPro
  5. DNA recombination Source: UniProtKB-HAMAP
  6. DNA replication Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-2277-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase BUniRule annotation (EC:6.5.1.1UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]UniRule annotation
Gene namesi
Name:ligBUniRule annotation
Ordered Locus Names:MSMEG_2277, MSMEI_2220
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000000757: Chromosome, UP000006158: Chromosome

Pathology & Biotechi

Disruption phenotypei

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.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 509509DNA ligase BPRO_0000365227Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi246196.MSMEG_2277.

Structurei

3D structure databases

ProteinModelPortaliA0QUP1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK01971.
OMAiKTENNIS.
OrthoDBiEOG6Q8HXT.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPiMF_00407. DNA_ligase.
InterProiIPR022865. 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]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A0QUP1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLADVAAAST EVAASSARLV KIERIATLLA RSAAEDDTQA VAVIVSWLSG
60 70 80 90 100
ELPQRQIGVG WAALRTLPPP AATPSLTVDD VDDRLSTIKA VAGKGSQATR
110 120 130 140 150
AGLVHELFSA ATDPEQKFLR HLLSGELRQG ALAGVMADAV AKAAGLPAAE
160 170 180 190 200
IRRAAMLAGN LPAVAAAAVT GGRAALADFR LRVGRPVGPM LAQTATSVDD
210 220 230 240 250
ALQRLGGTAV LEAKLDGARV QIHRSGCDVS IYTRSLDDVT HRLPEVVEAT
260 270 280 290 300
LALPATELIA DAEAIALRPD GRPHLFQVTA ARFGRKDPGD LGPLSVFFFD
310 320 330 340 350
LLHVDGRDLL DLPTEERFGA LDALVRQDQR VDRLVTTDTV AAQEFLERTL
360 370 380 390 400
AAGHEGVMAK SPHAAYEAGR RGAGWLKVKP VHTLDLVVLA VEWGSGRRQG
410 420 430 440 450
KLSNIHLGAR DPDSSGFVML GKTFKGMTDA MLEWQTQRFL ELADGPTDGY
460 470 480 490 500
VVHLRPEQVV EIAFDGVQRS SRYPAGMALR FVRVLRYRDD KSPAEADTVE

TVRRFYERD
Length:509
Mass (Da):54,594
Last modified:January 9, 2007 - v1
Checksum:iE5C3AADF5B8F311C
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000480 Genomic DNA. Translation: ABK74122.1.
CP001663 Genomic DNA. Translation: AFP38690.1. Different initiation.
RefSeqiWP_011728274.1. NC_008596.1.
YP_006566985.1. NC_018289.1.
YP_886629.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK74122; ABK74122; MSMEG_2277.
AFP38690; AFP38690; MSMEI_2220.
GeneIDi4536201.
KEGGimsg:MSMEI_2220.
msm:MSMEG_2277.
PATRICi18076976. VBIMycSme59918_2242.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000480 Genomic DNA. Translation: ABK74122.1 .
CP001663 Genomic DNA. Translation: AFP38690.1 . Different initiation.
RefSeqi WP_011728274.1. NC_008596.1.
YP_006566985.1. NC_018289.1.
YP_886629.1. NC_008596.1.

3D structure databases

ProteinModelPortali A0QUP1.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 246196.MSMEG_2277.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABK74122 ; ABK74122 ; MSMEG_2277 .
AFP38690 ; AFP38690 ; MSMEI_2220 .
GeneIDi 4536201.
KEGGi msg:MSMEI_2220.
msm:MSMEG_2277.
PATRICi 18076976. VBIMycSme59918_2242.

Phylogenomic databases

eggNOGi COG1793.
HOGENOMi HOG000036008.
KOi K01971.
OMAi KTENNIS.
OrthoDBi EOG6Q8HXT.

Enzyme and pathway databases

BioCyci MSME246196:GJ4Y-2277-MONOMER.

Family and domain databases

Gene3Di 1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPi MF_00407. DNA_ligase.
InterProi 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 ]
Pfami PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view ]
SUPFAMi SSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsi TIGR00574. dnl1. 1 hit.
PROSITEi PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiDNLI_MYCS2
AccessioniPrimary (citable) accession number: A0QUP1
Secondary accession number(s): I7FAW2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 3, 2009
Last sequence update: January 9, 2007
Last modified: October 29, 2014
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3