DNLJ_METEP
ID DNLJ_METEP Reviewed; 814 AA.
AC A9VWA4;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-FEB-2008, sequence version 1.
DT 03-AUG-2022, entry version 89.
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=Mext_4642;
OS Methylorubrum extorquens (strain PA1) (Methylobacterium extorquens).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Methylobacteriaceae; Methylorubrum.
OX NCBI_TaxID=419610;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PA1;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C.,
RA Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E.,
RA Marx C., Richardson P.;
RT "Complete sequence of Methylobacterium extorquens PA1.";
RL Submitted (DEC-2007) 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: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; CP000908; ABY33010.1; -; Genomic_DNA.
DR RefSeq; WP_012255700.1; NC_010172.1.
DR AlphaFoldDB; A9VWA4; -.
DR SMR; A9VWA4; -.
DR STRING; 419610.Mext_4642; -.
DR PRIDE; A9VWA4; -.
DR EnsemblBacteria; ABY33010; ABY33010; Mext_4642.
DR KEGG; mex:Mext_4642; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_5; -.
DR OMA; GRDQLDI; -.
DR BioCyc; MEXT419610:MEXT_RS23320-MON; -.
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; 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; 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 3: Inferred from homology;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Zinc.
FT CHAIN 1..814
FT /note="DNA ligase"
FT /id="PRO_0000380415"
FT DOMAIN 735..814
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 525..548
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 131
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 46..50
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 95..96
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 129
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 152
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 189
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 305
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 329
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 434
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 437
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 458
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 464
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 814 AA; 87940 MW; 3090B2837F21CDA2 CRC64;
MPSTPLSAAV EALSEDAAQA RHAELSRAIE RANQLYYNED APELTDAEYD ALRQELEAIE
ARFPALTGTT EASAGVGAKP SEKFAKVRHA VPMLSLGNAF ADEDVDEFVA RVRRFLNLPA
EESVAFTAEP KIDGLSLSLR YEAGRLVTAA TRGDGEVGEN VTANALTVDD IPETLSGENI
PEVLEVRGEV YLSHEDFAAI NARQEAAGKP LFANPRNAAA GSLRQLDPAI TASRPLRFFA
YAWGEVSEPF TDTQSAVLER FRGWGLPVNP RTKLCRSAEE MIAHYRTIEA ERAGLGYDID
GVVYKVDDLG FQRRLGFVSR APRWALAHKF AAQEAITELL AIDINVGRTG SLNPLARLKP
VTVGGVVVSN ATLHNEGYVQ GVGADGEPIR EGRDIRVGDT VIVVRAGDVI PKVRDVVIEK
RPADAVPYVF PDTCPACGSR AVRELNPRTK KLDAIRRCTG GLICPAQGVE RLKHFVSRNG
FDLEGFGQTY IEVLFEAGLV KQPADLFRLE FEPLKAAIVA RRETLSAQRR SEGEPAPKKP
TKKKGEEEDK AIKNLLASLD ARRTIPLNRF LFALGIPQIG ESTAKALAKR FPDMPSLMAA
LEAATREQAG RDWLELSALP RIGPGTRDRL FETLDPLPGE AMQDLSLGAR LRGRLTPSQR
EAVLAHYGSE EKVDAALERA ASQRPGDAYR LFADDGEIGP VATDSLIQFF SEPHNDAAVR
ALLEEVGTEP LATTTSAAAF AGKTVVFTGS LEKMTRSEAK ATAERLGAKV SGSVSAKTDL
VVAGPGAGSK LKDAEKHGVK VVSEDDWLAM LAEA
