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Database: UniProt
Entry: H6QI60_RICMA
LinkDB: H6QI60_RICMA
Original site: H6QI60_RICMA 
ID   H6QI60_RICMA            Unreviewed;       689 AA.
AC   H6QI60;
DT   18-APR-2012, integrated into UniProtKB/TrEMBL.
DT   18-APR-2012, sequence version 1.
DT   24-JAN-2024, entry version 63.
DE   RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE            EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE   AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
GN   Name=ligA {ECO:0000256|HAMAP-Rule:MF_01588,
GN   ECO:0000313|EMBL:AFB31360.1};
GN   ORFNames=RMB_02430 {ECO:0000313|EMBL:AFB31360.1};
OS   Rickettsia massiliae str. AZT80.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Rickettsiales;
OC   Rickettsiaceae; Rickettsieae; Rickettsia; spotted fever group.
OX   NCBI_TaxID=1105112 {ECO:0000313|EMBL:AFB31360.1, ECO:0000313|Proteomes:UP000007999};
RN   [1] {ECO:0000313|Proteomes:UP000007999}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AZT80 (RMB) {ECO:0000313|Proteomes:UP000007999};
RA   Johnson S.L., Munk A.C., Han S., Bruce D.C., Dasch G.A.;
RT   "Complete genome sequence of Rickettsia parkeri strain Portsmouth.";
RL   Submitted (FEB-2012) to the EMBL/GenBank/DDBJ databases.
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:0000256|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;
CC         Evidence={ECO:0000256|ARBA:ARBA00034005, ECO:0000256|HAMAP-
CC         Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC   -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC       subfamily. {ECO:0000256|HAMAP-Rule:MF_01588}.
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DR   EMBL; CP003319; AFB31360.1; -; Genomic_DNA.
DR   RefSeq; WP_014365478.1; NC_016931.1.
DR   AlphaFoldDB; H6QI60; -.
DR   KEGG; rmi:RMB_02430; -.
DR   HOGENOM; CLU_007764_2_1_5; -.
DR   Proteomes; UP000007999; Chromosome.
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; cd17748; BRCT_DNA_ligase_like; 1.
DR   CDD; cd00114; LIGANc; 1.
DR   Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 2.
DR   Gene3D; 3.40.50.10190; BRCT domain; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 1.10.287.610; Helix hairpin bin; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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; IPR001679; DNA_ligase.
DR   InterPro; IPR018239; DNA_ligase_AS.
DR   InterPro; IPR033136; DNA_ligase_CS.
DR   InterPro; IPR013839; DNAligase_adenylation.
DR   InterPro; IPR013840; DNAligase_N.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR004150; NAD_DNA_ligase_OB.
DR   InterPro; IPR010994; RuvA_2-like.
DR   NCBIfam; TIGR00575; dnlj; 1.
DR   PANTHER; PTHR23389; CHROMOSOME TRANSMISSION FIDELITY FACTOR 18; 1.
DR   PANTHER; PTHR23389:SF9; DNA LIGASE; 1.
DR   Pfam; PF00533; BRCT; 1.
DR   Pfam; PF01653; DNA_ligase_aden; 1.
DR   Pfam; PF03120; DNA_ligase_OB; 1.
DR   Pfam; PF12826; HHH_2; 1.
DR   PIRSF; PIRSF001604; LigA; 1.
DR   SMART; SM00292; BRCT; 1.
DR   SMART; SM00532; LIGANc; 1.
DR   SUPFAM; SSF52113; BRCT domain; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   SUPFAM; SSF47781; RuvA domain 2-like; 1.
DR   PROSITE; PS50172; BRCT; 1.
DR   PROSITE; PS01055; DNA_LIGASE_N1; 1.
DR   PROSITE; PS01056; DNA_LIGASE_N2; 1.
PE   3: Inferred from homology;
KW   DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT   DOMAIN          610..683
FT                   /note="BRCT"
FT                   /evidence="ECO:0000259|PROSITE:PS50172"
FT   ACT_SITE        123
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         40..44
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         89..90
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         121
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         144
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         179
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         295
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         319
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         413
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         416
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         431
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         437
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   689 AA;  77585 MW;  CB2886416B74D622 CRC64;
     MQNIDLISEK EAQKLLEELA DKIAAYNHAY YIEDNPLVSD SEYDQLFNTN LKLEQKFPHL
     ILENSPSKKV GAKIANKFAK VTHQVPMLSL SNAFDEQDVR DFVDRIKNFL RLNEFAPIFC
     EPKIDGLSFS AVYKNGVLTT GATRGDGYVG EDITANIKTI KNFPHKIDNV PEFLEVRGEI
     YIEKQDFLNL NKEQEEQGKD KFANPRNAAA GSLRQLDASI TAKRPLKYFV YSGGVTEQNL
     ASSQDQLLTK LKECGFNINE ISKLASSEEE LFAFYEYLKT NREDLPYEID GVVYKLNDFA
     LQNRMGFIAR SPRFATAHKF PAIIGQTQLL SITVQVGRTG TLTPVAELEP IEIGGVTVSR
     ATLHNFQEIA RKDVRIKDYV FLQRAGDVIP KIMGVDFDKR PNDTATFDTP LFCLSCNSKL
     HYMPEDIIIR CDNGLNCPAQ NYERIRHFVS KNAMDIEGLG RKQVEFLIDK GLISNPLDIF
     FLKEKNDSSL AKLENMDGWG KKSVANLFKN IEKSKNVSLP RFIYALGIRH IGEQNAKLLA
     REVGSYNNFI AQMELLSTNE PDIYQKLNNL EGIGDKILVD IIDFFDVKEN IELIKKLGEI
     LNIEDYKETR EQSSLTDKIV VFTGSLPTIS RAEAKATAEK LGAKVTAGVS SNTDLVVAGV
     DAGSKLKKAK ELNIKIIDEE EWLTLIKNV
//
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