LIGD_MYCTU
ID LIGD_MYCTU Reviewed; 759 AA.
AC P9WNV3; L0T5C5; O05865; P71571;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=Multifunctional non-homologous end joining DNA repair protein LigD;
DE Short=NHEJ DNA repair protein D;
DE AltName: Full=Mt-Lig;
DE AltName: Full=NHEJ DNA polymerase;
DE Includes:
DE RecName: Full=DNA repair polymerase;
DE Short=Pol;
DE AltName: Full=Polymerase/primase;
DE Includes:
DE RecName: Full=3'-phosphoesterase;
DE Short=3'-ribonuclease/3'-phosphatase;
DE Short=PE;
DE Includes:
DE RecName: Full=DNA ligase;
DE Short=Lig;
DE EC=6.5.1.1 {ECO:0000269|PubMed:12215643, ECO:0000269|PubMed:16023671, ECO:0000269|PubMed:16476729};
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP];
GN Name=ligD; OrderedLocusNames=Rv0938; ORFNames=MTCY08D9.01c, MTCY10D7.36c;
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 AS A LIGASE, CATALYTIC ACTIVITY, ACTIVITY REGULATION, INTERACTION
RP WITH MKU, SUBUNIT, DNA-BINDING, ACTIVE SITE, AND MUTAGENESIS OF LYS-481.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=12215643; DOI=10.1126/science.1074584;
RA Weller G.R., Kysela B., Roy R., Tonkin L.M., Scanlan E., Della M.,
RA Devine S.K., Day J.P., Wilkinson A., d'Adda di Fagagna F., Devine K.M.,
RA Bowater R.P., Jeggo P.A., Jackson S.P., Doherty A.J.;
RT "Identification of a DNA nonhomologous end-joining complex in bacteria.";
RL Science 297:1686-1689(2002).
RN [3]
RP FUNCTION, COFACTOR, SUBUNIT, DOMAIN, AND DISRUPTION PHENOTYPE.
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 [4]
RP FUNCTION IN DNA REPAIR, COFACTOR, SUBUNIT, AND MUTAGENESIS OF
RP 137-ASP--ASP-139 AND HIS-373.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=15499016; DOI=10.1126/science.1099824;
RA Della M., Palmbos P.L., Tseng H.M., Tonkin L.M., Daley J.M., Topper L.M.,
RA Pitcher R.S., Tomkinson A.E., Wilson T.E., Doherty A.J.;
RT "Mycobacterial Ku and ligase proteins constitute a two-component NHEJ
RT repair machine.";
RL Science 306:683-685(2004).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, INTERACTION WITH MKU,
RP SUBUNIT, COFACTOR, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF 137-ASP--ASP-139
RP AND LYS-481.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=16023671; DOI=10.1016/j.jmb.2005.06.038;
RA Pitcher R.S., Tonkin L.M., Green A.J., Doherty A.J.;
RT "Domain structure of a NHEJ DNA repair ligase from Mycobacterium
RT tuberculosis.";
RL J. Mol. Biol. 351:531-544(2005).
RN [6]
RP FUNCTION, INTERACTION WITH KU, AND DOMAIN.
RX PubMed=15778718; DOI=10.1038/nsmb915;
RA Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S.,
RA Glickman M.S.;
RT "Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity
RT repair system driven by Ku, ligase D and ligase C.";
RL Nat. Struct. Mol. Biol. 12:304-312(2005).
RN [7]
RP FUNCTION, AND PROBABLE INTERACTION WITH VIRAL KU.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=16949369; DOI=10.1016/j.molcel.2006.07.009;
RA Pitcher R.S., Tonkin L.M., Daley J.M., Palmbos P.L., Green A.J.,
RA Velting T.L., Brzostek A., Korycka-Machala M., Cresawn S., Dziadek J.,
RA Hatfull G.F., Wilson T.E., Doherty A.J.;
RT "Mycobacteriophage exploit NHEJ to facilitate genome circularization.";
RL Mol. Cell 23:743-748(2006).
RN [8]
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 [9]
RP INTERACTION WITH SIR2, AND SUBUNIT.
RX PubMed=21637345; DOI=10.1371/journal.pone.0020045;
RA Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X., Sui L.,
RA Bi L.J., Zhang X.E.;
RT "A Sir2-like protein participates in mycobacterial NHEJ.";
RL PLoS ONE 6:E20045-E20045(2011).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 452-759 IN COMPLEX WITH DIVALENT
RP CATION, CATALYTIC ACTIVITY FOR LIGASE, ACTIVE SITE, AND MUTAGENESIS OF
RP LYS-481; ASP-483; GLU-530; GLU-613; LYS-635 AND LYS-637.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=16476729; DOI=10.1074/jbc.m513550200;
RA Akey D., Martins A., Aniukwu J., Glickman M.S., Shuman S., Berger J.M.;
RT "Crystal structure and nonhomologous end-joining function of the ligase
RT component of Mycobacterium DNA ligase D.";
RL J. Biol. Chem. 281:13412-13423(2006).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 1-300 OF APOENZYME AND IN COMPLEX
RP WITH MANGANESE AND SUBSTRATE, FUNCTION, COFACTOR, AND DNA-BINDING.
RX PubMed=17174332; DOI=10.1016/j.jmb.2006.10.046;
RA Pitcher R.S., Brissett N.C., Picher A.J., Andrade P., Juarez R.,
RA Thompson D., Fox G.C., Blanco L., Doherty A.J.;
RT "Structure and function of a mycobacterial NHEJ DNA repair polymerase.";
RL J. Mol. Biol. 366:391-405(2007).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 1-300 IN COMPLEX WITH DNA,
RP FUNCTION, SUBUNIT, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF LYS-16 AND
RP 83-HIS--SER-85.
RX PubMed=17947582; DOI=10.1126/science.1145112;
RA Brissett N.C., Pitcher R.S., Juarez R., Picher A.J., Green A.J.,
RA Dafforn T.R., Fox G.C., Blanco L., Doherty A.J.;
RT "Structure of a NHEJ polymerase-mediated DNA synaptic complex.";
RL Science 318:456-459(2007).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS) OF 1-300 IN PRETERNARY COMPLEX WITH
RP DNA, SUBSTRATE AND MANGANESE, COFACTOR, DNA-BINDING, AND MUTAGENESIS OF
RP ARG-220.
RX PubMed=21255731; DOI=10.1016/j.molcel.2010.12.026;
RA Brissett N.C., Martin M.J., Pitcher R.S., Bianchi J., Juarez R.,
RA Green A.J., Fox G.C., Blanco L., Doherty A.J.;
RT "Structure of a preternary complex involving a prokaryotic NHEJ DNA
RT polymerase.";
RL Mol. Cell 41:221-231(2011).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 1-300 IN COMPLEX WITH DNA,
RP REACTION MECHANISM, DNA-BINDING, AND MUTAGENESIS OF ARG-53; PHE-63; PHE-64;
RP 83-HIS--SER-85; LYS-217; GLN-230 AND LYS-235.
RX PubMed=24239356; DOI=10.1016/j.celrep.2013.10.016;
RA Brissett N.C., Martin M.J., Bartlett E.J., Bianchi J., Blanco L.,
RA Doherty A.J.;
RT "Molecular basis for DNA double-strand break annealing and primer extension
RT by an NHEJ DNA polymerase.";
RL Cell Rep. 5:1108-1120(2013).
CC -!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) repair
CC enzyme which repairs DNA double-strand breaks (DSB) with reduced
CC fidelity. Recognizes, processes and reseals DSBs, including repairs on
CC incompatible DSB which require 3'-resection, gap filling and ligation.
CC Anneals the 3' overhanging strands from opposing breaks to form a
CC gapped intermediate, which then can be extended in trans by using the
CC termini as primers for extension of the annealed break. Binds to the
CC recessed 5'-phosphate moiety of the downstream DNA strand forming a
CC stable synaptic complex even when the 3'-protruding ends of the
CC template DNA strands are not complementary. Has numerous activities;
CC gap filling copies the template strand, and prefers a 5'-phosphate in
CC the gap and rNTPS (PubMed:17174332, PubMed:17947582), DNA-directed DNA
CC or RNA polymerase on 5'-overhangs, terminal transferase (extending
CC ssDNA or blunt dsDNA in a non-templated fashion, preferentially with
CC rNTPs), DNA-dependent RNA primase (synthesizes short RNAs on unprimed
CC closed ssDNA) and 3'- to 5'-exonuclease on ssDNA (PubMed:15499016).
CC Isolated Pol domain (and presumably the holoenzyme) is able to form
CC complexes between 2 noncompatible protruding 3'-ends DNA ends via
CC microhomologous DNA strands, in a end-bridging function to which it
CC adds a templated nucleotide (PubMed:17947582). Minimal primer length is
CC 2 nucleotides (PubMed:21255731). {ECO:0000269|PubMed:15499016,
CC ECO:0000269|PubMed:17174332, ECO:0000269|PubMed:17947582,
CC ECO:0000269|PubMed:21255731}.
CC -!- FUNCTION: The preference of the polymerase domain for rNTPs over dNTPs
CC may be advantageous in dormant cells, where the dNTP pool is limiting.
CC -!- FUNCTION: In conjunction with endogenous or Mycobacterium phage Omega
CC Ku (AC Q853W0) can reconstitute NHEJ in Saccharomyces cerevisiae.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC diphosphate.; EC=6.5.1.1; Evidence={ECO:0000269|PubMed:12215643,
CC ECO:0000269|PubMed:16023671, ECO:0000269|PubMed:16476729};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000305|PubMed:14985346, ECO:0000305|PubMed:15499016,
CC ECO:0000305|PubMed:16023671, ECO:0000305|PubMed:17174332,
CC ECO:0000305|PubMed:21255731};
CC Note=Binds 4 Mn(2+); 2 Mn(2+) for polymerase/primase activity, 1 each
CC for 3-phosphoesterase and ligase. {ECO:0000305|PubMed:14985346,
CC ECO:0000305|PubMed:15499016, ECO:0000305|PubMed:16023671,
CC ECO:0000305|PubMed:17174332, ECO:0000305|PubMed:21255731};
CC -!- ACTIVITY REGULATION: The polymerase, exonuclease and ligase activities
CC are stimulated by Ku. Polymerase activity is inhibited by EDTA.
CC {ECO:0000269|PubMed:12215643, ECO:0000269|PubMed:16023671}.
CC -!- SUBUNIT: Monomer. Component of the NHEJ repair enzyme with mKu.
CC Interacts with Ku in the absence of DSB via the Pol domain. In
CC structures of the Pol domain with template DNA 2 Pol domains are bound
CC to microhomologous DNA complexes to form an end-bridging complex.
CC Probably interacts with Mycobacterium phage Omega and Corndog Ku
CC homologs (AC Q853W0, AC Q856K7). Interacts with Sir2; may form a
CC trimeric complex with LigD during NHEJ. {ECO:0000269|PubMed:12215643,
CC ECO:0000269|PubMed:14985346, ECO:0000269|PubMed:15499016,
CC ECO:0000269|PubMed:15778718, ECO:0000269|PubMed:16023671,
CC ECO:0000269|PubMed:16476729, ECO:0000269|PubMed:17174332,
CC ECO:0000269|PubMed:17947582, ECO:0000269|PubMed:21637345,
CC ECO:0000269|PubMed:24239356}.
CC -!- DOMAIN: The N-terminal Mn(2+)-dependent polymerase/primase domain (Pol)
CC functions as an independent domain, binds DNA, is sufficient for DNA-
CC directed and non-DNA-directed DNA synthesis (PubMed:15778718) and
CC interacts with Ku (PubMed:16023671). {ECO:0000269|PubMed:15778718,
CC ECO:0000269|PubMed:16023671}.
CC -!- DOMAIN: The central 3'-phosphoesterase domain (PE) has exonuclease
CC activity probably constituted of 3'-ribonuclease and 3'-phosphatase
CC activity (PubMed:15499016). It does not function as an independent
CC domain (PubMed:16023671). {ECO:0000269|PubMed:15499016,
CC ECO:0000269|PubMed:16023671}.
CC -!- DOMAIN: The C-terminal ligase domain (Lig) binds dsDNA and functions as
CC an independent domain (PubMed:14985346, PubMed:16023671).
CC {ECO:0000269|PubMed:14985346, ECO:0000269|PubMed:16023671}.
CC -!- DISRUPTION PHENOTYPE: Not essential for growth, 80% reduction in NHEJ
CC (in strain Erdman). {ECO:0000269|PubMed:14985346}.
CC -!- MISCELLANEOUS: LigD has variable architecture; domain order can be
CC permutated, domains can be independently encoded, while some bacteria
CC lack the 3'-phosphoesterase domain entirely.
CC -!- MISCELLANEOUS: It is not clear whether there is a 5- to 3'-exonuclease
CC activity associated with the enzyme.
CC -!- SIMILARITY: In the N-terminal section; belongs to the LigD polymerase
CC family. {ECO:0000305}.
CC -!- SIMILARITY: In the central section; belongs to the LigD 3'-
CC phosphoesterase family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the ATP-dependent DNA
CC ligase family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL123456; CCP43686.1; -; Genomic_DNA.
DR PIR; B70585; B70585.
DR RefSeq; NP_215453.1; NC_000962.3.
DR RefSeq; WP_003911307.1; NZ_NVQJ01000001.1.
DR PDB; 1VS0; X-ray; 2.40 A; A/B=452-759.
DR PDB; 2IRU; X-ray; 1.65 A; A/B=1-300.
DR PDB; 2IRX; X-ray; 1.80 A; A=1-300.
DR PDB; 2IRY; X-ray; 1.78 A; A/B=1-300.
DR PDB; 2R9L; X-ray; 2.40 A; A/B=1-300.
DR PDB; 3PKY; X-ray; 3.10 A; A/B=1-300.
DR PDB; 4MKY; X-ray; 2.40 A; A/B/C/D=1-300.
DR PDBsum; 1VS0; -.
DR PDBsum; 2IRU; -.
DR PDBsum; 2IRX; -.
DR PDBsum; 2IRY; -.
DR PDBsum; 2R9L; -.
DR PDBsum; 3PKY; -.
DR PDBsum; 4MKY; -.
DR AlphaFoldDB; P9WNV3; -.
DR SMR; P9WNV3; -.
DR STRING; 83332.Rv0938; -.
DR PaxDb; P9WNV3; -.
DR PRIDE; P9WNV3; -.
DR DNASU; 885561; -.
DR GeneID; 885561; -.
DR KEGG; mtu:Rv0938; -.
DR TubercuList; Rv0938; -.
DR eggNOG; COG1793; Bacteria.
DR eggNOG; COG3285; Bacteria.
DR OMA; QWLAHRM; -.
DR PhylomeDB; P9WNV3; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0005524; F:ATP binding; IDA:MTBBASE.
DR GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IDA:UniProtKB.
DR GO; GO:0003909; F:DNA ligase activity; IDA:UniProtKB.
DR GO; GO:0003896; F:DNA primase activity; IDA:MTBBASE.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IDA:MTBBASE.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:MTBBASE.
DR GO; GO:0000287; F:magnesium ion binding; IDA:MTBBASE.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IDA:UniProtKB.
DR GO; GO:0004652; F:polynucleotide adenylyltransferase activity; IDA:MTBBASE.
DR GO; GO:0032553; F:ribonucleotide binding; IDA:UniProtKB.
DR GO; GO:0008310; F:single-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:MTBBASE.
DR GO; GO:0006266; P:DNA ligation; IDA:UniProtKB.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006269; P:DNA replication, synthesis of RNA primer; IDA:MTBBASE.
DR GO; GO:0006302; P:double-strand break repair; IDA:UniProtKB.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:UniProtKB.
DR CDD; cd04863; MtLigD_Pol_like; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR014146; LigD_ligase_dom.
DR InterPro; IPR014144; LigD_PE_domain.
DR InterPro; IPR014145; LigD_pol_dom.
DR InterPro; IPR033649; MtLigD_Pol-like.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF13298; LigD_N; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR TIGRFAMs; TIGR02777; LigD_PE_dom; 1.
DR TIGRFAMs; TIGR02778; ligD_pol; 1.
DR TIGRFAMs; TIGR02779; NHEJ_ligase_lig; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA damage; DNA recombination; DNA repair;
KW DNA-binding; DNA-directed DNA polymerase; Exonuclease;
KW Host-virus interaction; Hydrolase; Ligase; Manganese; Metal-binding;
KW Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW Nucleotidyltransferase; Reference proteome; Transferase.
FT CHAIN 1..759
FT /note="Multifunctional non-homologous end joining DNA
FT repair protein LigD"
FT /id="PRO_0000059627"
FT DNA_BIND 13..16
FT /note="Interaction with target DNA"
FT DNA_BIND 26
FT /note="Interaction with target DNA"
FT DNA_BIND 53..55
FT /note="Interaction with target DNA"
FT DNA_BIND 63..67
FT /note="Interaction with target DNA"
FT DNA_BIND 71
FT /note="Interaction with target DNA"
FT DNA_BIND 83..88
FT /note="Interaction with target DNA"
FT DNA_BIND 104
FT /note="Interaction with target DNA"
FT DNA_BIND 137
FT /note="Interaction with target DNA"
FT DNA_BIND 215..220
FT /note="Interaction with target DNA"
FT DNA_BIND 227..235
FT /note="Interaction with target DNA"
FT REGION 1..411
FT /note="Not required for ligase activity"
FT REGION 9..261
FT /note="DNA repair polymerase domain (Pol); interacts with
FT Ku"
FT REGION 297..446
FT /note="3-phosphoesterase domain (PE)"
FT REGION 460..757
FT /note="Ligase domain (Lig)"
FT REGION 740..759
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 743..759
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 481
FT /note="N6-AMP-lysine intermediate; for ligase activity"
FT /evidence="ECO:0000269|PubMed:12215643,
FT ECO:0000269|PubMed:16476729"
FT BINDING 52
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 111
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 137..139
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 137
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 137
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 139
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 139
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 172..178
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 227
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 230
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 236
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 244
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000269|PubMed:17174332"
FT BINDING 331
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /ligand_note="catalytic; for 3'-phosphoesterase activity"
FT /evidence="ECO:0000250"
FT BINDING 337
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /ligand_note="catalytic; for 3'-phosphoesterase activity"
FT /evidence="ECO:0000250"
FT BINDING 339
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /ligand_note="catalytic; for 3'-phosphoesterase activity"
FT /evidence="ECO:0000250"
FT BINDING 483
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000305|PubMed:17174332"
FT BINDING 613
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000305|PubMed:17174332"
FT SITE 373
FT /note="Transition state stabilizer; for 3'-phosphoesterase
FT activity"
FT /evidence="ECO:0000250"
FT MUTAGEN 16
FT /note="K->A: Loss of DNA-binding, no polymerase activity,
FT no effect of gap-filling (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:17947582"
FT MUTAGEN 53
FT /note="R->A: On substrate with 5'-phosphate, 1 base pair
FT (bp) complementarity and 1 nucleotide (nt) gap, greatly
FT reduced DNA-binding and gap-filling. Barely detectable
FT activity on substrate with high complementarity and 3'-
FT overhang (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:24239356"
FT MUTAGEN 63
FT /note="F->A: On substrate with 5'-phosphate, 1 bp
FT complementarity and 1 nt gap, greatly reduced DNA-binding
FT and gap-filling. No activity on substrate with high
FT complementarity and 3'-overhang (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:24239356"
FT MUTAGEN 64
FT /note="F->A: On substrate with 5'-phosphate, 1 bp
FT complementarity and 1 nt gap, greatly reduced DNA-binding
FT and gap-filling. Barely detectable activity on substrate
FT with high complementarity and 3'-overhang (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:24239356"
FT MUTAGEN 83..85
FT /note="HRS->AAA: Binds DNA, no formation of DNA end-
FT bridging complex, no polymerase activity. Significantly
FT decreased ability to fill in 2 nt gaps (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:17947582,
FT ECO:0000269|PubMed:24239356"
FT MUTAGEN 137..139
FT /note="DLD->ALA: Loss of polymerase activities, no DNA
FT repair (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:15499016,
FT ECO:0000269|PubMed:16023671"
FT MUTAGEN 217
FT /note="K->A: Better than wild-type DNA-binding and filling
FT on single nt gaps, impaired gap filling on more complicated
FT templates (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:24239356"
FT MUTAGEN 220
FT /note="R->A: Binds DNA, no gap-filling (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:21255731"
FT MUTAGEN 230
FT /note="Q->A: Wild-type filling on single nt gaps, impaired
FT gap filling on more complicated templates (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:24239356"
FT MUTAGEN 235
FT /note="K->A: Wild-type filling on single nt gaps, impaired
FT gap filling on more complicated templates (in Pol domain)."
FT /evidence="ECO:0000269|PubMed:24239356"
FT MUTAGEN 373
FT /note="H->A: Loss of exonuclease, no DNA repair."
FT /evidence="ECO:0000269|PubMed:15499016"
FT MUTAGEN 481
FT /note="K->A: Loss of adenyltransferase activity, no N6-AMP-
FT lysine formation and loss of ligase activity. No effect on
FT phosphodiester bond formation on pre-adenylated nicked DNA,
FT or on DNA polymerase."
FT /evidence="ECO:0000269|PubMed:12215643,
FT ECO:0000269|PubMed:16023671, ECO:0000269|PubMed:16476729"
FT MUTAGEN 483
FT /note="D->A: No ligase of singly nicked dsDNA activity, no
FT N6-AMP-lysine intermediate formed, decreased phosphodiester
FT bond formation on pre-adenylated nicked DNA, no effect on
FT DNA polymerase."
FT /evidence="ECO:0000269|PubMed:16476729"
FT MUTAGEN 530
FT /note="E->A: No ligase of singly nicked dsDNA activity, no
FT N6-AMP-lysine intermediate formed, no phosphodiester bond
FT formation on pre-adenylated nicked DNA, no effect on DNA
FT polymerase."
FT /evidence="ECO:0000269|PubMed:16476729"
FT MUTAGEN 613
FT /note="E->A: No ligase of singly nicked dsDNA activity, no
FT N6-AMP-lysine intermediate formed, decreased phosphodiester
FT bond formation on pre-adenylated nicked DNA, no effect on
FT DNA polymerase."
FT /evidence="ECO:0000269|PubMed:16476729"
FT MUTAGEN 635
FT /note="K->A: 20% ligase activity for singly nicked dsDNA,
FT normal N6-AMP-lysine intermediate formed, no effect on
FT phosphodiester bond formation, no effect on DNA
FT polymerase."
FT /evidence="ECO:0000269|PubMed:16476729"
FT MUTAGEN 637
FT /note="K->A: No ligase of singly nicked dsDNA activity, 25%
FT N6-AMP-lysine intermediate formed, decreased phosphodiester
FT bond formation, no effect on DNA polymerase."
FT /evidence="ECO:0000269|PubMed:16476729"
FT STRAND 17..19
FT /evidence="ECO:0007829|PDB:4MKY"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 26..44
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 88..92
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 109..112
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:2IRU"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 126..140
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 146..161
FT /evidence="ECO:0007829|PDB:2IRU"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 168..171
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 177..187
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 189..206
FT /evidence="ECO:0007829|PDB:2IRU"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 211..214
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 217..219
FT /evidence="ECO:0007829|PDB:2IRU"
FT TURN 220..222
FT /evidence="ECO:0007829|PDB:4MKY"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:2IRU"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 257..260
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 270..280
FT /evidence="ECO:0007829|PDB:2IRU"
FT TURN 283..287
FT /evidence="ECO:0007829|PDB:2IRU"
FT HELIX 455..457
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 462..465
FT /evidence="ECO:0007829|PDB:1VS0"
FT TURN 473..475
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 476..481
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 484..492
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 495..500
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 507..509
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 511..513
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 514..519
FT /evidence="ECO:0007829|PDB:1VS0"
FT TURN 520..522
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 524..532
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 542..546
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 555..564
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 574..587
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 600..609
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 614..619
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 629..650
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 662..669
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 672..679
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 685..695
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 696..698
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 704..707
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 711..714
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 717..720
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 725..731
FT /evidence="ECO:0007829|PDB:1VS0"
FT STRAND 743..747
FT /evidence="ECO:0007829|PDB:1VS0"
FT HELIX 753..755
FT /evidence="ECO:0007829|PDB:1VS0"
SQ SEQUENCE 759 AA; 83572 MW; 81BD49222EE09E36 CRC64;
MGSASEQRVT LTNADKVLYP ATGTTKSDIF DYYAGVAEVM LGHIAGRPAT RKRWPNGVDQ
PAFFEKQLAL SAPPWLSRAT VAHRSGTTTY PIIDSATGLA WIAQQAALEV HVPQWRFVAE
PGSGELNPGP ATRLVFDLDP GEGVMMAQLA EVARAVRDLL ADIGLVTFPV TSGSKGLHLY
TPLDEPVSSR GATVLAKRVA QRLEQAMPAL VTSTMTKSLR AGKVFVDWSQ NSGSKTTIAP
YSLRGRTHPT VAAPRTWAEL DDPALRQLSY DEVLTRIARD GDLLERLDAD APVADRLTRY
RRMRDASKTP EPIPTAKPVT GDGNTFVIQE HHARRPHYDF RLECDGVLVS WAVPKNLPDN
TSVNHLAIHT EDHPLEYATF EGAIPSGEYG AGKVIIWDSG TYDTEKFHDD PHTGEVIVNL
HGGRISGRYA LIRTNGDRWL AHRLKNQKDQ KVFEFDNLAP MLATHGTVAG LKASQWAFEG
KWDGYRLLVE ADHGAVRLRS RSGRDVTAEY PQLRALAEDL ADHHVVLDGE AVVLDSSGVP
SFSQMQNRGR DTRVEFWAFD LLYLDGRALL GTRYQDRRKL LETLANATSL TVPELLPGDG
AQAFACSRKH GWEGVIAKRR DSRYQPGRRC ASWVKDKHWN TQEVVIGGWR AGEGGRSSGV
GSLLMGIPGP GGLQFAGRVG TGLSERELAN LKEMLAPLHT DESPFDVPLP ARDAKGITYV
KPALVAEVRY SEWTPEGRLR QSSWRGLRPD KKPSEVVRE
