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Protein

DNA ligase

Gene

ligA

Organism
Staphylococcus aureus
Status
Reviewed-Annotation score: Annotation score: 4 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.

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 sitei110NADUniRule annotation1
Active sitei112N6-AMP-lysine intermediateUniRule annotation1
Binding sitei133NADUniRule annotation1
Binding sitei167NADUniRule annotation1
Binding sitei283NADUniRule annotation1
Binding sitei307NADUniRule annotation1
Metal bindingi401ZincUniRule annotation1
Metal bindingi404ZincUniRule annotation1
Metal bindingi419ZincUniRule annotation1
Metal bindingi424ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi32 – 36NADUniRule annotation5
Nucleotide bindingi81 – 82NADUniRule 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. 3352.

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
OrganismiStaphylococcus aureus
Taxonomic identifieri1280 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL2163181.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001617621 – 667DNA ligaseAdd BLAST667

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL1965.

Chemistry databases

BindingDBiQ9AIU7.

Structurei

Secondary structure

1667
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 23Combined sources19
Helixi32 – 48Combined sources17
Helixi50 – 52Combined sources3
Helixi58 – 62Combined sources5
Beta strandi72 – 74Combined sources3
Beta strandi83 – 85Combined sources3
Helixi88 – 101Combined sources14
Beta strandi107 – 113Combined sources7
Beta strandi115 – 123Combined sources9
Beta strandi126 – 132Combined sources7
Beta strandi136 – 141Combined sources6
Helixi143 – 146Combined sources4
Beta strandi162 – 169Combined sources8
Helixi172 – 182Combined sources11
Turni183 – 186Combined sources4
Helixi193 – 201Combined sources9
Helixi206 – 211Combined sources6
Beta strandi215 – 222Combined sources8
Helixi232 – 242Combined sources11
Beta strandi251 – 255Combined sources5
Helixi256 – 269Combined sources14
Helixi270 – 272Combined sources3
Beta strandi273 – 275Combined sources3
Beta strandi277 – 286Combined sources10
Helixi287 – 293Combined sources7
Beta strandi297 – 300Combined sources4
Beta strandi303 – 307Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JSLX-ray1.80A/B1-312[»]
3JSNX-ray1.90A1-312[»]
4CC5X-ray1.88A1-312[»]
4CC6X-ray2.01A1-312[»]
5FPOX-ray1.83A1-312[»]
5FPRX-ray2.00A1-312[»]
ProteinModelPortaliQ9AIU7.
SMRiQ9AIU7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9AIU7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini586 – 667BRCTUniRule annotationAdd BLAST82

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.

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.

Q9AIU7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADLSSRVNE LHDLLNQYSY EYYVEDNPSV PDSEYDKLLH ELIKIEEEHP
60 70 80 90 100
EYKTVDSPTV RVGGEAQASF NKVNHDTPML SLGNAFNEDD LRKFDQRIRE
110 120 130 140 150
QIGNVEYMCE LKIDGLAVSL KYVDGYFVQG LTRGDGTTGE DITENLKTIH
160 170 180 190 200
AIPLKMKEPL NVEVRGEAYM PRRSFLRLNE EKEKNDEQLF ANPRNAAAGS
210 220 230 240 250
LRQLDSKLTA KRKLSVFIYS VNDFTDFNAR SQSEALDELD KLGFTTNKNR
260 270 280 290 300
ARVNNIDGVL EYIEKWTSQR ESLPYDIDGI VIKVNDLDQQ DEMGFTQKSP
310 320 330 340 350
RWAIAYKFPA EEVVTKLLDI ELSIGRTGVV TPTAILEPVK VAGTTVSRAS
360 370 380 390 400
LHNEDLIHDR DIRIGDSVVV KKAGDIIPEV VRSIPERRPE DAVTYHMPTH
410 420 430 440 450
CPSCGHELVR IEGEVALRCI NPKCQAQLVE GLIHFVSRQA MNIDGLGTKI
460 470 480 490 500
IQQLYQSELI KDVADIFYLT EEDLLPLDRM GQKKVDNLLA AIQQAKDNSL
510 520 530 540 550
ENLLFGLGIR HLGVKASQVL AEKYETIDRL LTVTEAELVE IHDIGDKVAQ
560 570 580 590 600
SVVTYLENED IRALIQKLKD KHVNMIYKGI KTSDIEGHPE FSGKTIVLTG
610 620 630 640 650
KLHQMTRNEA SKWLASQGAK VTSSVTKNTD VVIAGEDAGS KLTKAQSLGI
660
EIWTEQQFVD KQNELNS
Length:667
Mass (Da):75,081
Last modified:June 1, 2001 - v1
Checksum:iF599F7BC8AB59D67
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF234833 Genomic DNA. Translation: AAK15020.1.
RefSeqiWP_000774565.1. NZ_MAQU01000039.1.

Genome annotation databases

GeneIDi28380449.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF234833 Genomic DNA. Translation: AAK15020.1.
RefSeqiWP_000774565.1. NZ_MAQU01000039.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JSLX-ray1.80A/B1-312[»]
3JSNX-ray1.90A1-312[»]
4CC5X-ray1.88A1-312[»]
4CC6X-ray2.01A1-312[»]
5FPOX-ray1.83A1-312[»]
5FPRX-ray2.00A1-312[»]
ProteinModelPortaliQ9AIU7.
SMRiQ9AIU7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL1965.

Chemistry databases

BindingDBiQ9AIU7.
ChEMBLiCHEMBL2163181.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi28380449.

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.

Enzyme and pathway databases

BRENDAi6.5.1.2. 3352.

Miscellaneous databases

EvolutionaryTraceiQ9AIU7.

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_STAAU
AccessioniPrimary (citable) accession number: Q9AIU7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: June 1, 2001
Last modified: November 30, 2016
This is version 86 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.