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Protein

DNA ligase B

Gene

ligB

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Reviewed-Annotation score: 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 annotation1 Publication

Catalytic activityi

ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei212ATPUniRule annotation1
Active sitei214N6-AMP-lysine intermediateUniRule annotation1
Binding sitei219ATPUniRule annotation1
Binding sitei234ATPUniRule annotation1
Binding sitei263ATPUniRule annotation1
Binding sitei299ATPUniRule annotation1
Binding sitei371ATPUniRule annotation1
Binding sitei377ATPUniRule annotation1

GO - Molecular functioni

GO - Biological processi

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, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase B (EC:6.5.1.1UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]UniRule annotation
Gene namesi
Name:ligB
Ordered Locus Names:MSMEG_2277, MSMEI_2220
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
Proteomesi
  • UP000006158 Componenti: Chromosome
  • UP000000757 Componenti: 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)DescriptionActionsGraphical viewLength
ChainiPRO_00003652271 – 509DNA ligase BAdd BLAST509

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

eggNOGiENOG4107RYT. Bacteria.
COG1793. LUCA.
HOGENOMiHOG000036008.
KOiK10747.
OMAiRKHNIEE.
OrthoDBiPOG091H0BGA.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
HAMAPiMF_00407. DNA_ligase. 1 hit.
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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK74122.1.
CP001663 Genomic DNA. Translation: AFP38690.1. Different initiation.
RefSeqiWP_011728274.1. NC_008596.1.
WP_014877353.1. NZ_CP009494.1.
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:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK74122.1.
CP001663 Genomic DNA. Translation: AFP38690.1. Different initiation.
RefSeqiWP_011728274.1. NC_008596.1.
WP_014877353.1. NZ_CP009494.1.
YP_886629.1. NC_008596.1.

3D structure databases

ProteinModelPortaliA0QUP1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_2277.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4107RYT. Bacteria.
COG1793. LUCA.
HOGENOMiHOG000036008.
KOiK10747.
OMAiRKHNIEE.
OrthoDBiPOG091H0BGA.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
HAMAPiMF_00407. DNA_ligase. 1 hit.
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]
ProtoNetiSearch...

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: November 30, 2016
This is version 89 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.