DNLJ_STRZP
ID DNLJ_STRZP Reviewed; 652 AA.
AC C1CKI0;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 1.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_01588};
DE EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000255|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000255|HAMAP-Rule:MF_01588}; OrderedLocusNames=SPP_1122;
OS Streptococcus pneumoniae (strain P1031).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=488223;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=P1031;
RX PubMed=21034474; DOI=10.1186/gb-2010-11-10-r107;
RA Donati C., Hiller N.L., Tettelin H., Muzzi A., Croucher N.J.,
RA Angiuoli S.V., Oggioni M., Dunning Hotopp J.C., Hu F.Z., Riley D.R.,
RA Covacci A., Mitchell T.J., Bentley S.D., Kilian M., Ehrlich G.D.,
RA Rappuoli R., Moxon E.R., Masignani V.;
RT "Structure and dynamics of the pan-genome of Streptococcus pneumoniae and
RT closely related species.";
RL Genome Biol. 11:R107.1-R107.19(2010).
CC -!- FUNCTION: DNA ligase that catalyzes the formation of phosphodiester
CC linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-
CC stranded DNA using NAD as a coenzyme and as the energy source for the
CC reaction. It is essential for DNA replication and repair of damaged
CC DNA. {ECO:0000255|HAMAP-Rule:MF_01588}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-
CC nicotinamide D-nucleotide.; EC=6.5.1.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01588};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01588}.
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DR EMBL; CP000920; ACO21382.1; -; Genomic_DNA.
DR RefSeq; WP_001042590.1; NC_012467.1.
DR PDB; 4GLW; X-ray; 2.00 A; A/B=1-305.
DR PDBsum; 4GLW; -.
DR AlphaFoldDB; C1CKI0; -.
DR SMR; C1CKI0; -.
DR KEGG; spp:SPP_1122; -.
DR HOGENOM; CLU_007764_2_1_9; -.
DR OMA; HDVEHEI; -.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003911; F:DNA ligase (NAD+) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR CDD; cd00114; LIGANc; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 1.
DR HAMAP; MF_01588; DNA_ligase_A; 1.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR041663; DisA/LigA_HHH.
DR InterPro; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
DR InterPro; IPR001679; DNAligase.
DR InterPro; IPR013839; DNAligase_adenylation.
DR InterPro; IPR013840; DNAligase_N.
DR InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004150; NAD_DNA_ligase_OB.
DR InterPro; IPR010994; RuvA_2-like.
DR InterPro; IPR004149; Znf_DNAligase_C4.
DR Pfam; PF00533; BRCT; 1.
DR Pfam; PF01653; DNA_ligase_aden; 1.
DR Pfam; PF03120; DNA_ligase_OB; 1.
DR Pfam; PF03119; DNA_ligase_ZBD; 1.
DR Pfam; PF12826; HHH_2; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 2.
DR SMART; SM00532; LIGANc; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR TIGRFAMs; TIGR00575; dnlj; 1.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS01055; DNA_LIGASE_N1; 1.
DR PROSITE; PS01056; DNA_LIGASE_N2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA replication; Ligase; Magnesium;
KW Manganese; Metal-binding; NAD; Zinc.
FT CHAIN 1..652
FT /note="DNA ligase"
FT /id="PRO_0000380487"
FT DOMAIN 577..652
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 109
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 29..33
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 78..79
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 107
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 130
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 164
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 278
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 302
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 395
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 398
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 413
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 418
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT HELIX 3..6
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 8..12
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 38..45
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 55..58
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 85..95
FT /evidence="ECO:0007829|PDB:4GLW"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 104..110
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 112..120
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 123..129
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 159..166
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 169..181
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 190..198
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 199..202
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 203..208
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 212..221
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 223..226
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 227..237
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 246..250
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 251..264
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 268..270
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 272..279
FT /evidence="ECO:0007829|PDB:4GLW"
FT HELIX 282..288
FT /evidence="ECO:0007829|PDB:4GLW"
FT STRAND 292..302
FT /evidence="ECO:0007829|PDB:4GLW"
SQ SEQUENCE 652 AA; 72276 MW; C2220D1F3504D47B CRC64;
MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV LADSPTHRVG
GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA HPTYICELKI DGLSISLTYE
KGILVAGVTR GDGSIGENIT ENLKRVKDIP LTLPEELDIT VRGECYMPRA SFDQVNQARQ
ENGEPEFANP RNAAAGTLRQ LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV
VNPKRILAEN IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA
YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD YIAEKDIRKD
DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS DLLHFEDEVA LRCINPRCPA
QIMEGLIHFA SRDAMNITGL GPSIVEKLFA ANLVKDVADI YRLQEEDFLL LEGVKEKSAA
KLYQAIQASK ENSAEKLLFG LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG
VIAKSLQTYF ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE
AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE SL
