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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei107 – 1071NADUniRule annotation
Active sitei109 – 1091N6-AMP-lysine intermediateUniRule annotation
Binding sitei130 – 1301NADUniRule annotation
Binding sitei164 – 1641NADUniRule annotation
Binding sitei278 – 2781NADUniRule annotation
Binding sitei302 – 3021NADUniRule annotation
Metal bindingi395 – 3951ZincUniRule annotation
Metal bindingi398 – 3981ZincUniRule annotation
Metal bindingi413 – 4131ZincUniRule annotation
Metal bindingi418 – 4181ZincUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi29 – 335NADUniRule annotation
Nucleotide bindingi78 – 792NADUniRule 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

BioCyciSPNE488223:GHE7-1100-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:SPP_1122
OrganismiStreptococcus pneumoniae (strain P1031)
Taxonomic identifieri488223 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 652652DNA ligasePRO_0000380487Add
BLAST

Structurei

Secondary structure

1
652
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 64Combined sources
Helixi8 – 125Combined sources
Helixi38 – 458Combined sources
Helixi47 – 493Combined sources
Helixi55 – 584Combined sources
Beta strandi68 – 714Combined sources
Helixi85 – 9511Combined sources
Turni96 – 983Combined sources
Beta strandi104 – 1107Combined sources
Beta strandi112 – 1209Combined sources
Beta strandi123 – 1297Combined sources
Beta strandi133 – 1386Combined sources
Helixi140 – 1434Combined sources
Beta strandi159 – 1668Combined sources
Helixi169 – 18113Combined sources
Helixi190 – 1989Combined sources
Beta strandi199 – 2024Combined sources
Helixi203 – 2086Combined sources
Beta strandi212 – 22110Combined sources
Beta strandi223 – 2264Combined sources
Helixi227 – 23711Combined sources
Beta strandi246 – 2505Combined sources
Helixi251 – 26414Combined sources
Helixi265 – 2673Combined sources
Beta strandi268 – 2703Combined sources
Beta strandi272 – 2798Combined sources
Helixi282 – 2887Combined sources
Beta strandi292 – 30211Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GLWX-ray2.00A/B1-305[»]
ProteinModelPortaliC1CKI0.
SMRiC1CKI0. Positions 2-304.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini577 – 65276BRCTUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0272.
HOGENOMiHOG000218458.
KOiK01972.
OMAiKFPRWAI.
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

        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.
YP_002738268.1. 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.
YP_002738268.1. NC_012467.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GLWX-ray2.00A/B1-305[»]
ProteinModelPortaliC1CKI0.
SMRiC1CKI0. Positions 2-304.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0272.
HOGENOMiHOG000218458.
KOiK01972.
OMAiKFPRWAI.
OrthoDBiEOG6TTVM9.

Enzyme and pathway databases

BioCyciSPNE488223:GHE7-1100-MONOMER.

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]
ProtoNetiSearch...

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: June 24, 2015
This is version 48 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

External Data

Dasty 3

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 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.