DNLJ_MYCTU
ID DNLJ_MYCTU Reviewed; 691 AA.
AC P9WNV1; L0TBA8; O53261; P63973;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=DNA ligase A {ECO:0000255|HAMAP-Rule:MF_01588};
DE Short=LigA;
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}; Synonyms=lig;
GN OrderedLocusNames=Rv3014c; ORFNames=MTV012.28c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION, COFACTOR, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=14985346; DOI=10.1074/jbc.m401841200;
RA Gong C., Martins A., Bongiorno P., Glickman M., Shuman S.;
RT "Biochemical and genetic analysis of the four DNA ligases of
RT mycobacteria.";
RL J. Biol. Chem. 279:20594-20606(2004).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS) OF 1-328 IN COMPLEX WITH AMP,
RP CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=15901723; DOI=10.1074/jbc.m503780200;
RA Srivastava S.K., Tripathi R.P., Ramachandran R.;
RT "NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis.
RT Crystal structure of the adenylation domain and identification of novel
RT inhibitors.";
RL J. Biol. Chem. 280:30273-30281(2005).
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, ECO:0000269|PubMed:14985346}.
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, ECO:0000269|PubMed:15901723};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:14985346, ECO:0000269|PubMed:15901723};
CC -!- ACTIVITY REGULATION: Inhibited by pyridochromanone.
CC {ECO:0000269|PubMed:14985346}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.3 uM for NAD(+) {ECO:0000269|PubMed:14985346};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:14985346,
CC ECO:0000269|PubMed:15901723}.
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; AL123456; CCP45820.1; -; Genomic_DNA.
DR PIR; A70857; A70857.
DR RefSeq; NP_217530.1; NC_000962.3.
DR RefSeq; WP_003415263.1; NZ_NVQJ01000041.1.
DR PDB; 1ZAU; X-ray; 3.15 A; A=1-328.
DR PDB; 3SGI; X-ray; 3.50 A; A=2-605.
DR PDB; 6KDU; X-ray; 2.20 A; A=8-328.
DR PDB; 6KJM; X-ray; 2.20 A; A=1-328.
DR PDB; 6KKV; X-ray; 2.56 A; A=8-328.
DR PDB; 6KRH; X-ray; 2.60 A; A=8-328.
DR PDB; 6KSC; X-ray; 2.40 A; A=8-328.
DR PDB; 6KSD; X-ray; 2.50 A; A=8-328.
DR PDB; 6LW8; X-ray; 2.40 A; A=1-328.
DR PDB; 7K72; X-ray; 2.05 A; A/B/C/D=1-328.
DR PDBsum; 1ZAU; -.
DR PDBsum; 3SGI; -.
DR PDBsum; 6KDU; -.
DR PDBsum; 6KJM; -.
DR PDBsum; 6KKV; -.
DR PDBsum; 6KRH; -.
DR PDBsum; 6KSC; -.
DR PDBsum; 6KSD; -.
DR PDBsum; 6LW8; -.
DR PDBsum; 7K72; -.
DR AlphaFoldDB; P9WNV1; -.
DR SASBDB; P9WNV1; -.
DR SMR; P9WNV1; -.
DR STRING; 83332.Rv3014c; -.
DR BindingDB; P9WNV1; -.
DR ChEMBL; CHEMBL2259249; -.
DR PaxDb; P9WNV1; -.
DR GeneID; 887354; -.
DR KEGG; mtu:Rv3014c; -.
DR TubercuList; Rv3014c; -.
DR eggNOG; COG0272; Bacteria.
DR OMA; HDVEHEI; -.
DR PhylomeDB; P9WNV1; -.
DR BRENDA; 6.5.1.2; 3445.
DR SABIO-RK; P9WNV1; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; HDA:MTBBASE.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0003911; F:DNA ligase (NAD+) activity; IDA:MTBBASE.
DR GO; GO:0000287; F:magnesium ion binding; IDA:MTBBASE.
DR GO; GO:0006288; P:base-excision repair, DNA ligation; IBA:GO_Central.
DR GO; GO:0006266; P:DNA ligation; IDA:MTBBASE.
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 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA replication; Ligase; Magnesium;
KW Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..691
FT /note="DNA ligase A"
FT /id="PRO_0000161752"
FT DOMAIN 607..691
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 123
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 41..45
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 91..92
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000305|PubMed:15901723"
FT BINDING 121
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 144
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000305|PubMed:15901723"
FT BINDING 184
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000305|PubMed:15901723"
FT BINDING 300
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000305|PubMed:15901723"
FT BINDING 324
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
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 BINDING 421
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 443
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT HELIX 10..32
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 41..57
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 59..61
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:7K72"
FT TURN 72..75
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 77..79
FT /evidence="ECO:0007829|PDB:3SGI"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:6KSD"
FT HELIX 98..112
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 118..124
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 126..134
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 154..158
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 160..162
FT /evidence="ECO:0007829|PDB:1ZAU"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 177..186
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 189..201
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 210..218
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 223..227
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 232..243
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 249..258
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 268..272
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 273..286
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 287..289
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 290..292
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 294..301
FT /evidence="ECO:0007829|PDB:7K72"
FT HELIX 304..310
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 314..324
FT /evidence="ECO:0007829|PDB:7K72"
FT STRAND 328..333
FT /evidence="ECO:0007829|PDB:3SGI"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:3SGI"
FT STRAND 350..352
FT /evidence="ECO:0007829|PDB:3SGI"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:3SGI"
FT TURN 371..377
FT /evidence="ECO:0007829|PDB:3SGI"
FT STRAND 384..388
FT /evidence="ECO:0007829|PDB:3SGI"
FT STRAND 391..394
FT /evidence="ECO:0007829|PDB:3SGI"
SQ SEQUENCE 691 AA; 75289 MW; 94AD5AEDCD065567 CRC64;
MSSPDADQTA PEVLRQWQAL AEEVREHQFR YYVRDAPIIS DAEFDELLRR LEALEEQHPE
LRTPDSPTQL VGGAGFATDF EPVDHLERML SLDNAFTADE LAAWAGRIHA EVGDAAHYLC
ELKIDGVALS LVYREGRLTR ASTRGDGRTG EDVTLNARTI ADVPERLTPG DDYPVPEVLE
VRGEVFFRLD DFQALNASLV EEGKAPFANP RNSAAGSLRQ KDPAVTARRR LRMICHGLGH
VEGFRPATLH QAYLALRAWG LPVSEHTTLA TDLAGVRERI DYWGEHRHEV DHEIDGVVVK
VDEVALQRRL GSTSRAPRWA IAYKYPPEEA QTKLLDIRVN VGRTGRITPF AFMTPVKVAG
STVGQATLHN ASEIKRKGVL IGDTVVIRKA GDVIPEVLGP VVELRDGSER EFIMPTTCPE
CGSPLAPEKE GDADIRCPNA RGCPGQLRER VFHVASRNGL DIEVLGYEAG VALLQAKVIA
DEGELFALTE RDLLRTDLFR TKAGELSANG KRLLVNLDKA KAAPLWRVLV ALSIRHVGPT
AARALATEFG SLDAIAAAST DQLAAVEGVG PTIAAAVTEW FAVDWHREIV DKWRAAGVRM
VDERDESVPR TLAGLTIVVT GSLTGFSRDD AKEAIVARGG KAAGSVSKKT NYVVAGDSPG
SKYDKAVELG VPILDEDGFR RLLADGPASR T
