DNLJ_THEFI
ID DNLJ_THEFI Reviewed; 670 AA.
AC Q9ZHI0; Q9ZFY4;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 119.
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};
DE AltName: Full=Tfi DNA ligase;
GN Name=ligA {ECO:0000255|HAMAP-Rule:MF_01588};
OS Thermus filiformis.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=276;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9749531;
RA Kim H.K., Kwon S.-T.;
RT "Cloning, nucleotide sequence, and expression of the DNA ligase-encoding
RT gene from Thermus filiformis.";
RL Mol. Cells 8:438-443(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 50-586.
RC STRAIN=Tok6A1;
RX PubMed=9889274; DOI=10.1093/nar/27.3.788;
RA Tong J., Cao W., Barany F.;
RT "Biochemical properties of a high fidelity DNA ligase from Thermus species
RT AK16D.";
RL Nucleic Acids Res. 27:788-794(1999).
RN [3]
RP FUNCTION, ACTIVE SITE, COFACTOR, INTERACTION WITH DNA, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15268945; DOI=10.1111/j.1574-6968.2004.tb09685.x;
RA Jeon H.J., Shin H.-J., Choi J.J., Hoe H.-S., Kim H.-K., Suh S.W.,
RA Kwon S.-T.;
RT "Mutational analyses of the thermostable NAD+-dependent DNA ligase from
RT Thermus filiformis.";
RL FEMS Microbiol. Lett. 237:111-118(2004).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEXES WITH AMP AND ZINC IONS,
RP AND ACTIVE SITE.
RX PubMed=10698952; DOI=10.1093/emboj/19.5.1119;
RA Lee J.Y., Chang C., Song H.K., Moon J., Yang J.K., Kim H.-K., Kwon S.-T.,
RA Suh S.W.;
RT "Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and
RT functional implications.";
RL EMBO J. 19:1119-1129(2000).
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:15268945}.
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:0000269|PubMed:15268945};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 70 degrees Celsius.
CC {ECO:0000269|PubMed:15268945};
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; AF061572; AAC68862.1; -; Genomic_DNA.
DR EMBL; AF092866; AAD13192.1; -; Genomic_DNA.
DR PDB; 1DGS; X-ray; 2.90 A; A/B=1-670.
DR PDB; 1V9P; X-ray; 2.90 A; A/B=1-584.
DR PDBsum; 1DGS; -.
DR PDBsum; 1V9P; -.
DR AlphaFoldDB; Q9ZHI0; -.
DR SMR; Q9ZHI0; -.
DR STRING; 276.THFILI_03970; -.
DR BRENDA; 6.5.1.2; 6336.
DR EvolutionaryTrace; Q9ZHI0; -.
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 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; SM00278; HhH1; 4.
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; Zinc.
FT CHAIN 1..670
FT /note="DNA ligase"
FT /id="PRO_0000161769"
FT DOMAIN 586..670
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 118
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:10698952, ECO:0000269|PubMed:15268945"
FT BINDING 34..38
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 84..85
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 116..119
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305|PubMed:10698952"
FT BINDING 139
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 174
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 226
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 291
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 315
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000305|PubMed:10698952"
FT BINDING 409
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:10698952"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:10698952"
FT BINDING 425
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:10698952"
FT BINDING 430
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:10698952"
FT CONFLICT 104..111
FT /note="ALGRKRPF -> LAEAPS (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 125
FT /note="Missing (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 133..139
FT /note="LVFGATR -> WSTGS (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 232
FT /note="L -> LGL (in Ref. 1)"
FT /evidence="ECO:0000305"
FT CONFLICT 257
FT /note="G -> C (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 274
FT /note="F -> G (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 290
FT /note="V -> L (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 296
FT /note="A -> T (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 299
FT /note="R -> G (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 399
FT /note="E -> K (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 408
FT /note="T -> A (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT CONFLICT 545
FT /note="L -> I (in Ref. 1; AAC68862)"
FT /evidence="ECO:0000305"
FT HELIX 3..25
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 38..47
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 91..100
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 112..117
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 132..137
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 141..147
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 167..176
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 179..192
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 200..208
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 213..218
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 222..224
FT /evidence="ECO:0007829|PDB:1DGS"
FT TURN 230..233
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 240..249
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 258..262
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 263..276
FT /evidence="ECO:0007829|PDB:1DGS"
FT TURN 277..280
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 281..283
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 287..294
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 296..300
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 308..315
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 321..332
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 336..349
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 352..358
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 362..367
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 371..373
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:1DGS"
FT TURN 382..384
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 385..391
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 393..395
FT /evidence="ECO:0007829|PDB:1DGS"
FT TURN 410..412
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 417..419
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 431..433
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 434..442
FT /evidence="ECO:0007829|PDB:1DGS"
FT TURN 444..447
FT /evidence="ECO:0007829|PDB:1V9P"
FT HELIX 454..462
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 469..475
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 478..481
FT /evidence="ECO:0007829|PDB:1DGS"
FT STRAND 488..490
FT /evidence="ECO:0007829|PDB:1V9P"
FT HELIX 491..500
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 501..503
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 506..512
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 520..528
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 533..536
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 541..545
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 552..563
FT /evidence="ECO:0007829|PDB:1DGS"
FT HELIX 565..576
FT /evidence="ECO:0007829|PDB:1DGS"
SQ SEQUENCE 670 AA; 76594 MW; 21F0FCAF9B9515FA CRC64;
MTREEARRRI NELRDLIRYH NYRYYVLADP EISDAEYDRL LRELKELEER FPEFKSPDSP
TEQVGARPLE PTFRPVRHPT RMYSLDNAFT YEEVLAFEER LERALGRKRP FLYTVEHKVD
GLSVNLYYEE GVLVFGATRG DGEVGEEVTQ NLLTIPTIPR RLKGVPDRLE VRGEVYMPIE
AFLRLNEELE ERGEKVFKNP RNAAAGSLRQ KDPRVTAKRG LRATFYALGL GLEESGLKSQ
YELLLWLKEK GFPVEHGYEK ALGAEGVEEV YRRFLAQRHA LPFEADGVVV KLDDLALWRE
LGYTARAPRF ALAYKFPAEE KETRLLDVVF QVGRTGRVTP VGVLEPVFIE GSEVSRVTLH
NESYIEELDI RIGDWVLVHK AGGVIPEVLR VLKERRTGEE RPIRWPETCP ECGHRLVKEG
KVHRCPNPLC PAKRFEAIRH YASRKAMDIE GLGEKLIERL LEKGLVRDVA DLYHLRKEDL
LGLERMGEKS AQNLLRQIEE SKHRGLERLL YALGLPGVGE VLARNLARRF GTMDRLLEAS
LEELLEVEEV GELTARAILE TLKDPAFRDL VRRLKEAGVS MESKEEVSDL LSGLTFVLTG
ELSRPREEVK ALLQRLGAKV TDSVSRKTSY LVVGENPGSK LEKARALGVA VLTEEEFWRF
LKEKGAPVPA
