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C1CKI0 (DNLJ_STRZP) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 40. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase

EC=6.5.1.2
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]
Gene names
Name:ligA
Ordered Locus Names:SPP_1122
OrganismStreptococcus pneumoniae (strain P1031) [Complete proteome] [HAMAP]
Taxonomic identifier488223 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

Protein attributes

Sequence length652 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 By similarity. HAMAP-Rule MF_01588

Catalytic activity

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_01588

Cofactor

Magnesium or manganese By similarity. HAMAP-Rule MF_01588

Sequence similarities

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.

Contains 1 BRCT domain.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
DNA replication
   LigandMagnesium
Manganese
Metal-binding
NAD
Zinc
   Molecular functionLigase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

DNA replication

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

DNA ligase (NAD+) activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 652652DNA ligase HAMAP-Rule MF_01588
PRO_0000380487

Regions

Domain577 – 65276BRCT
Nucleotide binding29 – 335NAD By similarity
Nucleotide binding78 – 792NAD By similarity

Sites

Active site1091N6-AMP-lysine intermediate By similarity
Metal binding3951Zinc By similarity
Metal binding3981Zinc By similarity
Metal binding4131Zinc By similarity
Metal binding4181Zinc By similarity
Binding site1071NAD By similarity
Binding site1301NAD By similarity
Binding site1641NAD By similarity
Binding site2781NAD By similarity
Binding site3021NAD By similarity

Secondary structure

................................................ 652
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
C1CKI0 [UniParc].

Last modified May 26, 2009. Version 1.
Checksum: C2220D1F3504D47B

FASTA65272,276
        10         20         30         40         50         60 
MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV LADSPTHRVG 

        70         80         90        100        110        120 
GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA HPTYICELKI DGLSISLTYE 

       130        140        150        160        170        180 
KGILVAGVTR GDGSIGENIT ENLKRVKDIP LTLPEELDIT VRGECYMPRA SFDQVNQARQ 

       190        200        210        220        230        240 
ENGEPEFANP RNAAAGTLRQ LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV 

       250        260        270        280        290        300 
VNPKRILAEN IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA 

       310        320        330        340        350        360 
YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD YIAEKDIRKD 

       370        380        390        400        410        420 
DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS DLLHFEDEVA LRCINPRCPA 

       430        440        450        460        470        480 
QIMEGLIHFA SRDAMNITGL GPSIVEKLFA ANLVKDVADI YRLQEEDFLL LEGVKEKSAA 

       490        500        510        520        530        540 
KLYQAIQASK ENSAEKLLFG LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG 

       550        560        570        580        590        600 
VIAKSLQTYF ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE 

       610        620        630        640        650 
AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE SL 

« Hide

References

[1]"Complete genome sequence of Streptococcus pneumoniae strain P1031."
Hotopp J.D., Censini S., Masignani V., Covacci A., Tettelin H.
Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: P1031.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000920 Genomic DNA. Translation: ACO21382.1.
RefSeqYP_002738268.1. NC_012467.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4GLWX-ray2.00A/B1-305[»]
ProteinModelPortalC1CKI0.
SMRC1CKI0. Positions 2-304.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING488223.SPP_1122.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACO21382; ACO21382; SPP_1122.
GeneID7682167.
KEGGspp:SPP_1122.
PATRIC32459541. VBIStrPne91701_1167.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0272.
HOGENOMHOG000218458.
KOK01972.
OMAFTAKSPR.
OrthoDBEOG6TTVM9.
ProtClustDBPRK07956.

Enzyme and pathway databases

BioCycSPNE488223:GHE7-1100-MONOMER.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPMF_01588. DNA_ligase_A.
InterProIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR004150. DNA_ligase_OB.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
SMARTSM00292. BRCT. 1 hit.
SM00278. HhH1. 2 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsTIGR00575. dnlj. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDNLJ_STRZP
AccessionPrimary (citable) accession number: C1CKI0
Entry history
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 2009
Last modified: April 16, 2014
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references