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Protein

DNA ligase

Gene

ligA

Organism
Peptoclostridium difficile (strain 630) (Clostridium difficile)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 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 bindingi31 – 35NADUniRule annotation5
Nucleotide bindingi80 – 81NADUniRule 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

BioCyciPDIF272563:G12WB-3476-MONOMER.

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:CD630_33090
OrganismiPeptoclostridium difficile (strain 630) (Clostridium difficile)
Taxonomic identifieri272563 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaeClostridioides
Proteomesi
  • UP000001978 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003131971 – 674DNA ligaseAdd BLAST674

Interactioni

Protein-protein interaction databases

STRINGi272563.CD3309.

Structurei

3D structure databases

ProteinModelPortaliQ180F3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini584 – 673BRCTUniRule annotationAdd BLAST90

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.
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.
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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q180F3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVKDEINKL IETINYHNER YYNQDSPEIS DYEYDKLMKE LISLEEEHPE
60 70 80 90 100
LKRIDSPTNR VGGKPLDKFN QIVHKTPMLS LSNAFSEQDL RDFDKRVQEY
110 120 130 140 150
VGENVEYVVE FKIDGLSVGL TYNNGEFEKG ATRGDGVVGE DISQNLMTVK
160 170 180 190 200
SIPLKINDKK ELIVRGEVYI SKDNFRKVNE QQEEQEQPLF ANPRNLAAGS
210 220 230 240 250
LRQLDPKLTA KRPLDIFVFN MENIEEYDLE SHSESLEYLE KLGFSVSQSY
260 270 280 290 300
KVCKSIDEVI EHIEYWTDNR GNLDYEIDGM VIKVNNIKQR DEMGYTAKSP
310 320 330 340 350
RWAIAYKFPA EKKKTKIVDI IVEVGRTGTI TPSAILEPVR LAGTTVSRAT
360 370 380 390 400
LHNEDYIREK DIKINDTVLV QKAGDIIPQV LEVIKEERTG DEIDFKMPEK
410 420 430 440 450
CPVCSEPTIR LEGEAAVKCI NMSCPAQIRR GIIHFVSRDA MNIDGLGESI
460 470 480 490 500
ITLLLNEKII QDVSDLYYIK KEDVVDLERM GEKSADNLIN SIEKSKENDL
510 520 530 540 550
WRLINGLGIK FIGVKAAKIL AYNFKDLDEV ISATSEQLEE LEEFGSIMAN
560 570 580 590 600
SVVEFFKEDK NMNVINKLKN VGVNTKSLDN TGEKVEKIFE GMKIVLTGTL
610 620 630 640 650
PTLKRNDAKE MIEKRGGKAT SSVSKSTTFV LAGEEAGSKL TKANDLGIKV
660 670
IDEERFLELL KLSSKDEVKA VLES
Length:674
Mass (Da):76,416
Last modified:September 21, 2011 - v2
Checksum:i122C0080A510C20A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM180355 Genomic DNA. Translation: CAJ70206.2.
RefSeqiWP_011861898.1. NZ_CP010905.1.
YP_001089825.2. NC_009089.1.

Genome annotation databases

EnsemblBacteriaiCAJ70206; CAJ70206; CD630_33090.
GeneIDi4912919.
KEGGicdf:CD630_33090.
pdc:CDIF630_03610.
PATRICi19445159. VBICloDif38397_3463.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM180355 Genomic DNA. Translation: CAJ70206.2.
RefSeqiWP_011861898.1. NZ_CP010905.1.
YP_001089825.2. NC_009089.1.

3D structure databases

ProteinModelPortaliQ180F3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272563.CD3309.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAJ70206; CAJ70206; CD630_33090.
GeneIDi4912919.
KEGGicdf:CD630_33090.
pdc:CDIF630_03610.
PATRICi19445159. VBICloDif38397_3463.

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
HOGENOMiHOG000218458.
KOiK01972.
OMAiFTAKSPR.

Enzyme and pathway databases

BioCyciPDIF272563:G12WB-3476-MONOMER.

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.
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.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNLJ_PEPD6
AccessioniPrimary (citable) accession number: Q180F3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: September 21, 2011
Last modified: November 30, 2016
This is version 75 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.