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Protein

DNA ligase

Gene

ligA

Organism
Staphylococcus aureus
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.

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 sitei110 – 1101NADUniRule annotation
Active sitei112 – 1121N6-AMP-lysine intermediateUniRule annotation
Binding sitei133 – 1331NADUniRule annotation
Binding sitei167 – 1671NADUniRule annotation
Binding sitei283 – 2831NADUniRule annotation
Binding sitei307 – 3071NADUniRule annotation
Metal bindingi401 – 4011ZincUniRule annotation
Metal bindingi404 – 4041ZincUniRule annotation
Metal bindingi419 – 4191ZincUniRule annotation
Metal bindingi424 – 4241ZincUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi32 – 365NADUniRule annotation
Nucleotide bindingi81 – 822NADUniRule annotation

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

ChEMBLiCHEMBL2163181.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 667667DNA ligasePRO_0000161762Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL1965.

Chemistry

BindingDBiQ9AIU7.

Structurei

Secondary structure

1
667
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 2319Combined sources
Helixi32 – 4817Combined sources
Helixi50 – 523Combined sources
Helixi58 – 625Combined sources
Beta strandi72 – 743Combined sources
Beta strandi83 – 853Combined sources
Helixi88 – 10114Combined sources
Beta strandi107 – 1137Combined sources
Beta strandi115 – 1239Combined sources
Beta strandi126 – 1327Combined sources
Beta strandi136 – 1416Combined sources
Helixi143 – 1464Combined sources
Beta strandi162 – 1698Combined sources
Helixi172 – 18211Combined sources
Turni183 – 1864Combined sources
Helixi193 – 2019Combined sources
Helixi206 – 2116Combined sources
Beta strandi215 – 2228Combined sources
Helixi232 – 24211Combined sources
Beta strandi251 – 2555Combined sources
Helixi256 – 26914Combined sources
Helixi270 – 2723Combined sources
Beta strandi273 – 2753Combined sources
Beta strandi277 – 28610Combined sources
Helixi287 – 2937Combined sources
Beta strandi297 – 3004Combined sources
Beta strandi303 – 3075Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-575, 586-658.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9AIU7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini586 – 66782BRCTUniRule annotationAdd
BLAST

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

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A.
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_LOSC01000004.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF234833 Genomic DNA. Translation: AAK15020.1.
RefSeqiWP_000774565.1. NZ_LOSC01000004.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-575, 586-658.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL1965.

Chemistry

BindingDBiQ9AIU7.
ChEMBLiCHEMBL2163181.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.

Enzyme and pathway databases

BRENDAi6.5.1.2. 3352.

Miscellaneous databases

EvolutionaryTraceiQ9AIU7.

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.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
    Strain: NT64.

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: March 16, 2016
This is version 83 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.