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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)DescriptionActionsGraphical viewLength
Binding sitei112NADUniRule annotation1
Active sitei114N6-AMP-lysine intermediateUniRule annotation1 Publication1
Binding sitei135NADUniRule annotation1
Binding sitei169NADUniRule annotation1
Binding sitei285NADUniRule annotation1
Binding sitei309NADUniRule annotation1
Metal bindingi403ZincUniRule annotation1
Metal bindingi406ZincUniRule annotation1
Metal bindingi421ZincUniRule annotation1
Metal bindingi426ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi34 – 38NADUniRule annotation5
Nucleotide bindingi83 – 84NADUniRule annotation2

GO - Molecular functioni

GO - Biological processi

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001617371 – 670DNA ligaseAdd BLAST670

Proteomic databases

PRIDEiO87703.

Structurei

Secondary structure

1670
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 25Combined sources23
Helixi35 – 50Combined sources16
Helixi52 – 54Combined sources3
Helixi60 – 63Combined sources4
Helixi92 – 104Combined sources13
Beta strandi109 – 125Combined sources17
Beta strandi128 – 134Combined sources7
Beta strandi141 – 143Combined sources3
Helixi145 – 149Combined sources5
Beta strandi164 – 171Combined sources8
Helixi174 – 186Combined sources13
Helixi195 – 204Combined sources10
Helixi208 – 213Combined sources6
Beta strandi217 – 223Combined sources7
Turni224 – 230Combined sources7
Helixi234 – 243Combined sources10
Beta strandi253 – 257Combined sources5
Helixi258 – 271Combined sources14
Beta strandi279 – 286Combined sources8
Helixi289 – 295Combined sources7
Beta strandi299 – 301Combined sources3
Beta strandi305 – 309Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO87703.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini589 – 670BRCTUniRule annotationAdd BLAST82

Sequence similaritiesi

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

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
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.
[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.
RefSeqiWP_033016671.1. NZ_LUCR01000196.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ011676 Genomic DNA. Translation: CAA09732.1.
RefSeqiWP_033016671.1. NZ_LUCR01000196.1.

3D structure databases

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

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
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.
[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...

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: November 30, 2016
This is version 102 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

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.