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Protein

DNA ligase

Gene

ligA

Organism
Streptococcus pneumoniae (strain P1031)
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 sitei107NADUniRule annotation1
Active sitei109N6-AMP-lysine intermediateUniRule annotation1
Binding sitei130NADUniRule annotation1
Binding sitei164NADUniRule annotation1
Binding sitei278NADUniRule annotation1
Binding sitei302NADUniRule annotation1
Metal bindingi395ZincUniRule annotation1
Metal bindingi398ZincUniRule annotation1
Metal bindingi413ZincUniRule annotation1
Metal bindingi418ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi29 – 33NADUniRule annotation5
Nucleotide bindingi78 – 79NADUniRule 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

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
Ordered Locus Names:SPP_1122
OrganismiStreptococcus pneumoniae (strain P1031)
Taxonomic identifieri488223 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003804871 – 652DNA ligaseAdd BLAST652

Structurei

Secondary structure

1652
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 6Combined sources4
Helixi8 – 12Combined sources5
Helixi38 – 45Combined sources8
Helixi47 – 49Combined sources3
Helixi55 – 58Combined sources4
Beta strandi68 – 71Combined sources4
Helixi85 – 95Combined sources11
Turni96 – 98Combined sources3
Beta strandi104 – 110Combined sources7
Beta strandi112 – 120Combined sources9
Beta strandi123 – 129Combined sources7
Beta strandi133 – 138Combined sources6
Helixi140 – 143Combined sources4
Beta strandi159 – 166Combined sources8
Helixi169 – 181Combined sources13
Helixi190 – 198Combined sources9
Beta strandi199 – 202Combined sources4
Helixi203 – 208Combined sources6
Beta strandi212 – 221Combined sources10
Beta strandi223 – 226Combined sources4
Helixi227 – 237Combined sources11
Beta strandi246 – 250Combined sources5
Helixi251 – 264Combined sources14
Helixi265 – 267Combined sources3
Beta strandi268 – 270Combined sources3
Beta strandi272 – 279Combined sources8
Helixi282 – 288Combined sources7
Beta strandi292 – 302Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GLWX-ray2.00A/B1-305[»]
ProteinModelPortaliC1CKI0.
SMRiC1CKI0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini577 – 652BRCTUniRule annotationAdd BLAST76

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000218458.
KOiK01972.
OMAiFTAKSPR.

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. 2 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.

C1CKI0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV
60 70 80 90 100
LADSPTHRVG GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA
110 120 130 140 150
HPTYICELKI DGLSISLTYE KGILVAGVTR GDGSIGENIT ENLKRVKDIP
160 170 180 190 200
LTLPEELDIT VRGECYMPRA SFDQVNQARQ ENGEPEFANP RNAAAGTLRQ
210 220 230 240 250
LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV VNPKRILAEN
260 270 280 290 300
IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA
310 320 330 340 350
YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD
360 370 380 390 400
YIAEKDIRKD DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS
410 420 430 440 450
DLLHFEDEVA LRCINPRCPA QIMEGLIHFA SRDAMNITGL GPSIVEKLFA
460 470 480 490 500
ANLVKDVADI YRLQEEDFLL LEGVKEKSAA KLYQAIQASK ENSAEKLLFG
510 520 530 540 550
LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG VIAKSLQTYF
560 570 580 590 600
ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE
610 620 630 640 650
AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE

SL
Length:652
Mass (Da):72,276
Last modified:May 26, 2009 - v1
Checksum:iC2220D1F3504D47B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000920 Genomic DNA. Translation: ACO21382.1.
RefSeqiWP_001042590.1. NC_012467.1.

Genome annotation databases

EnsemblBacteriaiACO21382; ACO21382; SPP_1122.
KEGGispp:SPP_1122.
PATRICi32459541. VBIStrPne91701_1167.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000920 Genomic DNA. Translation: ACO21382.1.
RefSeqiWP_001042590.1. NC_012467.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GLWX-ray2.00A/B1-305[»]
ProteinModelPortaliC1CKI0.
SMRiC1CKI0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACO21382; ACO21382; SPP_1122.
KEGGispp:SPP_1122.
PATRICi32459541. VBIStrPne91701_1167.

Phylogenomic databases

HOGENOMiHOG000218458.
KOiK01972.
OMAiFTAKSPR.

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. 2 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_STRZP
AccessioniPrimary (citable) accession number: C1CKI0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 2009
Last modified: November 30, 2016
This is version 58 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.