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Protein

DNA ligase

Gene

ligA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei112 – 1121NADUniRule annotation
Active sitei114 – 1141N6-AMP-lysine intermediate
Binding sitei135 – 1351NADUniRule annotation
Binding sitei169 – 1691NADUniRule annotation
Binding sitei285 – 2851NADUniRule annotation
Binding sitei309 – 3091NADUniRule annotation
Metal bindingi403 – 4031ZincUniRule annotation
Metal bindingi406 – 4061ZincUniRule annotation
Metal bindingi421 – 4211ZincUniRule annotation
Metal bindingi426 – 4261ZincUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi34 – 385NADUniRule annotation
Nucleotide bindingi83 – 842NADUniRule annotation

GO - Molecular functioni

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

GO - Biological processi

  1. DNA repair Source: UniProtKB-KW
  2. DNA replication Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD, Zinc

Enzyme and pathway databases

BRENDAi6.5.1.2. 623.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.2UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]UniRule annotation
Gene namesi
Name:ligAUniRule annotation
Synonyms:lig
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 670670DNA ligasePRO_0000161737Add
BLAST

Proteomic databases

PRIDEiO87703.

Structurei

Secondary structure

1
670
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 2523Combined sources
Helixi35 – 5016Combined sources
Helixi52 – 543Combined sources
Helixi60 – 634Combined sources
Helixi92 – 10413Combined sources
Beta strandi109 – 12517Combined sources
Beta strandi128 – 1347Combined sources
Beta strandi141 – 1433Combined sources
Helixi145 – 1495Combined sources
Beta strandi164 – 1718Combined sources
Helixi174 – 18613Combined sources
Helixi195 – 20410Combined sources
Helixi208 – 2136Combined sources
Beta strandi217 – 2237Combined sources
Turni224 – 2307Combined sources
Helixi234 – 24310Combined sources
Beta strandi253 – 2575Combined sources
Helixi258 – 27114Combined sources
Beta strandi279 – 2868Combined sources
Helixi289 – 2957Combined sources
Beta strandi299 – 3013Combined sources
Beta strandi305 – 3095Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B04X-ray2.80A/B1-318[»]
ProteinModelPortaliO87703.
SMRiO87703. Positions 1-313.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO87703.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini589 – 67082BRCTUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.UniRule annotation
Contains 1 BRCT domain.UniRule annotation

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR000445. HhH_motif.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
PF00633. HHH. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00278. HhH1. 3 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O87703-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDRQQAERRA AELRELLNRY GYEYYVLDRP SVPDAEYDRL MQELIAIEEQ
60 70 80 90 100
YPELKTSDSP TQRIGGPPLE AFRKVAHRVP MMSLANAFGE GDLRDFDRRV
110 120 130 140 150
RQEVGEAAYV CELKIDGLAV SVRYEDGYFV QGATRGDGTT GEDITENLKT
160 170 180 190 200
IRSLPLRLKE PVSLEARGEA FMPKASFLRL NEERKARGEE LFANPRNAAA
210 220 230 240 250
GSLRQLDPKV AASRQLDLFV YGLADAEALG IASHSEALDY LQALGFKVNP
260 270 280 290 300
ERRRCANIDE VIAFVSEWHD KRPQLPYEID GIVIKVDSFA QQRALGATAK
310 320 330 340 350
SPRWAIAYKF PAEEVVTTLI GIEVNVGRTG VVTPTAILEP VRVAGTTVQR
360 370 380 390 400
ATLHNEDFIR EKDIRIGDAV IIKKAGDIIP EVVGVVVDRR DGDETPFAMP
410 420 430 440 450
THCPECESEL VRLEGEVALR CLNPNCPAQL RERLIHFASR AAMNIEGLGE
460 470 480 490 500
KVVTQLFNAG LVRDVADLYC LTKEQLVGLE RMGEKSAANL LAAIEASKQN
510 520 530 540 550
SLERLLFGLG IRYVGAKAAQ LLAEHFETME RLERATKEEL MAVPEIGEKM
560 570 580 590 600
ADAITAFFAQ PEATELLQEL RAYGVNMAYK GPKRSAEAPA DSAFAGKTVV
610 620 630 640 650
LTGKLASMSR NEAKEQIERL GGRVTGSVSR STDLVIAGED AGSKLEKAQQ
660 670
LGIEIWDESR FLQEINRGKR
Length:670
Mass (Da):74,231
Last modified:November 1, 1998 - v1
Checksum:iB52462314CF9ACF5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ011676 Genomic DNA. Translation: CAA09732.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ011676 Genomic DNA. Translation: CAA09732.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B04X-ray2.80A/B1-318[»]
ProteinModelPortaliO87703.
SMRiO87703. Positions 1-313.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiO87703.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi6.5.1.2. 623.

Miscellaneous databases

EvolutionaryTraceiO87703.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR000445. HhH_motif.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
PF00633. HHH. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00278. HhH1. 3 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Nucleotide sequence, heterologous expression and novel purification of DNA ligase from Bacillus stearothermophilus."
    Brannigan J.A., Ashford S.R., Doherty A.J., Timson D.J., Wigley D.B.
    Biochim. Biophys. Acta 1432:413-418(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924.
  2. "Structure of the adenylation domain of an NAD+-dependent DNA ligase."
    Singleton M.R., Hakansson K., Timson D.J., Wigley D.B.
    Structure 7:35-42(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-318.

Entry informationi

Entry nameiDNLJ_GEOSE
AccessioniPrimary (citable) accession number: O87703
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1998
Last modified: April 1, 2015
This is version 93 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

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.