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C1CKI0

- DNLJ_STRZP

UniProt

C1CKI0 - DNLJ_STRZP

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Protein
DNA ligase
Gene
ligA, SPP_1122
Organism
Streptococcus pneumoniae (strain P1031)
Status
Reviewed - 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 By similarity.UniRule annotation

Catalytic activityi

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Magnesium or manganese By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei107 – 1071NAD By similarity
Active sitei109 – 1091N6-AMP-lysine intermediate By similarity
Binding sitei130 – 1301NAD By similarity
Binding sitei164 – 1641NAD By similarity
Binding sitei278 – 2781NAD By similarity
Binding sitei302 – 3021NAD By similarity
Metal bindingi395 – 3951Zinc By similarity
Metal bindingi398 – 3981Zinc By similarity
Metal bindingi413 – 4131Zinc By similarity
Metal bindingi418 – 4181Zinc By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi29 – 335NAD By similarity
Nucleotide bindingi78 – 792NAD By similarity

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. DNA ligase (NAD+) activity Source: UniProtKB-HAMAP
  3. metal ion binding Source: UniProtKB-KW
Complete GO annotation...

GO - Biological processi

  1. DNA repair Source: UniProtKB-KW
  2. DNA replication Source: UniProtKB-KW
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

BioCyciSPNE488223:GHE7-1100-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase (EC:6.5.1.2)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]
Gene namesi
Name:ligA
Ordered Locus Names:SPP_1122
OrganismiStreptococcus pneumoniae (strain P1031)
Taxonomic identifieri488223 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
ProteomesiUP000002202: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 652652DNA ligaseUniRule annotation
PRO_0000380487Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi488223.SPP_1122.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 64
Helixi38 – 458
Helixi47 – 493
Helixi55 – 584
Beta strandi68 – 714
Helixi85 – 9511
Turni96 – 983
Beta strandi104 – 1107
Beta strandi112 – 1209
Beta strandi123 – 1297
Beta strandi133 – 1386
Helixi140 – 1434
Beta strandi159 – 1668
Helixi169 – 18113
Helixi190 – 1989
Beta strandi199 – 2024
Helixi203 – 2086
Beta strandi212 – 22110
Beta strandi223 – 2264
Helixi227 – 23711
Beta strandi246 – 2505
Helixi251 – 26414
Helixi265 – 2673
Beta strandi268 – 2703
Beta strandi272 – 2798
Helixi282 – 2887
Beta strandi292 – 30211

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GLWX-ray2.00A/B1-305[»]
ProteinModelPortaliC1CKI0.
SMRiC1CKI0. Positions 2-304.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini577 – 65276BRCT
Add
BLAST

Sequence similaritiesi

Contains 1 BRCT domain.

Phylogenomic databases

eggNOGiCOG0272.
HOGENOMiHOG000218458.
KOiK01972.
OMAiSCGAKLA.
OrthoDBiEOG6TTVM9.

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.
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

MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV    50
LADSPTHRVG GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA 100
HPTYICELKI DGLSISLTYE KGILVAGVTR GDGSIGENIT ENLKRVKDIP 150
LTLPEELDIT VRGECYMPRA SFDQVNQARQ ENGEPEFANP RNAAAGTLRQ 200
LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV VNPKRILAEN 250
IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA 300
YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD 350
YIAEKDIRKD DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS 400
DLLHFEDEVA LRCINPRCPA QIMEGLIHFA SRDAMNITGL GPSIVEKLFA 450
ANLVKDVADI YRLQEEDFLL LEGVKEKSAA KLYQAIQASK ENSAEKLLFG 500
LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG VIAKSLQTYF 550
ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE 600
AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE 650
SL 652
Length:652
Mass (Da):72,276
Last modified:May 26, 2009 - v1
Checksum:iC2220D1F3504D47B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000920 Genomic DNA. Translation: ACO21382.1.
RefSeqiYP_002738268.1. NC_012467.1.

Genome annotation databases

EnsemblBacteriaiACO21382; ACO21382; SPP_1122.
GeneIDi7682167.
KEGGispp:SPP_1122.
PATRICi32459541. VBIStrPne91701_1167.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000920 Genomic DNA. Translation: ACO21382.1 .
RefSeqi YP_002738268.1. NC_012467.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4GLW X-ray 2.00 A/B 1-305 [» ]
ProteinModelPortali C1CKI0.
SMRi C1CKI0. Positions 2-304.
ModBasei Search...

Protein-protein interaction databases

STRINGi 488223.SPP_1122.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACO21382 ; ACO21382 ; SPP_1122 .
GeneIDi 7682167.
KEGGi spp:SPP_1122.
PATRICi 32459541. VBIStrPne91701_1167.

Phylogenomic databases

eggNOGi COG0272.
HOGENOMi HOG000218458.
KOi K01972.
OMAi SCGAKLA.
OrthoDBi EOG6TTVM9.

Enzyme and pathway databases

BioCyci SPNE488223:GHE7-1100-MONOMER.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPi MF_01588. DNA_ligase_A.
InterProi IPR001357. 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 ]
Pfami PF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view ]
PIRSFi PIRSF001604. LigA. 1 hit.
SMARTi SM00292. BRCT. 1 hit.
SM00278. HhH1. 2 hits.
SM00532. LIGANc. 1 hit.
[Graphical view ]
SUPFAMi SSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsi TIGR00575. dnlj. 1 hit.
PROSITEi PS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

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: May 14, 2014
This is version 41 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, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3
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