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Multifunctional non-homologous end joining DNA repair protein LigD (NHEJ DNA repair protein D) (Mt-Lig) (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]

 LIGD_MYCTU              Reviewed;         759 AA.
P9WNV3; L0T5C5; O05865; P71571;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
15-MAR-2017, entry version 30.
RecName: Full=Multifunctional non-homologous end joining DNA repair protein LigD;
Short=NHEJ DNA repair protein D;
AltName: Full=Mt-Lig;
AltName: Full=NHEJ DNA polymerase;
Includes:
RecName: Full=DNA repair polymerase;
Short=Pol;
AltName: Full=Polymerase/primase;
Includes:
RecName: Full=3'-phosphoesterase;
Short=3'-ribonuclease/3'-phosphatase;
Short=PE;
Includes:
RecName: Full=DNA ligase;
Short=Lig;
EC=6.5.1.1 {ECO:0000269|PubMed:12215643, ECO:0000269|PubMed:16023671, ECO:0000269|PubMed:16476729};
AltName: Full=Polydeoxyribonucleotide synthase [ATP];
Name=ligD; OrderedLocusNames=Rv0938;
ORFNames=MTCY08D9.01c, MTCY10D7.36c;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
FUNCTION AS A LIGASE, CATALYTIC ACTIVITY, ENZYME REGULATION,
INTERACTION WITH MKU, SUBUNIT, DNA-BINDING, ACTIVE SITE, AND
MUTAGENESIS OF LYS-481.
STRAIN=ATCC 25618 / H37Rv;
PubMed=12215643; DOI=10.1126/science.1074584;
Weller G.R., Kysela B., Roy R., Tonkin L.M., Scanlan E., Della M.,
Devine S.K., Day J.P., Wilkinson A., d'Adda di Fagagna F.,
Devine K.M., Bowater R.P., Jeggo P.A., Jackson S.P., Doherty A.J.;
"Identification of a DNA nonhomologous end-joining complex in
bacteria.";
Science 297:1686-1689(2002).
[3]
FUNCTION, COFACTOR, SUBUNIT, DOMAIN, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=14985346; DOI=10.1074/jbc.M401841200;
Gong C., Martins A., Bongiorno P., Glickman M., Shuman S.;
"Biochemical and genetic analysis of the four DNA ligases of
mycobacteria.";
J. Biol. Chem. 279:20594-20606(2004).
[4]
FUNCTION IN DNA REPAIR, COFACTOR, SUBUNIT, AND MUTAGENESIS OF
137-ASP--ASP-139 AND HIS-373.
STRAIN=ATCC 25618 / H37Rv;
PubMed=15499016; DOI=10.1126/science.1099824;
Della M., Palmbos P.L., Tseng H.M., Tonkin L.M., Daley J.M.,
Topper L.M., Pitcher R.S., Tomkinson A.E., Wilson T.E., Doherty A.J.;
"Mycobacterial Ku and ligase proteins constitute a two-component NHEJ
repair machine.";
Science 306:683-685(2004).
[5]
FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, INTERACTION WITH MKU,
SUBUNIT, COFACTOR, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF
137-ASP--ASP-139 AND LYS-481.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16023671; DOI=10.1016/j.jmb.2005.06.038;
Pitcher R.S., Tonkin L.M., Green A.J., Doherty A.J.;
"Domain structure of a NHEJ DNA repair ligase from Mycobacterium
tuberculosis.";
J. Mol. Biol. 351:531-544(2005).
[6]
FUNCTION, INTERACTION WITH KU, AND DOMAIN.
PubMed=15778718; DOI=10.1038/nsmb915;
Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S.,
Glickman M.S.;
"Mechanism of nonhomologous end-joining in mycobacteria: a low-
fidelity repair system driven by Ku, ligase D and ligase C.";
Nat. Struct. Mol. Biol. 12:304-312(2005).
[7]
FUNCTION, AND PROBABLE INTERACTION WITH VIRAL KU.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16949369; DOI=10.1016/j.molcel.2006.07.009;
Pitcher R.S., Tonkin L.M., Daley J.M., Palmbos P.L., Green A.J.,
Velting T.L., Brzostek A., Korycka-Machala M., Cresawn S., Dziadek J.,
Hatfull G.F., Wilson T.E., Doherty A.J.;
"Mycobacteriophage exploit NHEJ to facilitate genome
circularization.";
Mol. Cell 23:743-748(2006).
[8]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[9]
INTERACTION WITH SIR2, AND SUBUNIT.
PubMed=21637345; DOI=10.1371/journal.pone.0020045;
Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X.,
Sui L., Bi L.J., Zhang X.E.;
"A Sir2-like protein participates in mycobacterial NHEJ.";
PLoS ONE 6:E20045-E20045(2011).
[10]
X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 452-759 IN COMPLEX WITH
DIVALENT CATION, CATALYTIC ACTIVITY FOR LIGASE, ACTIVE SITE, AND
MUTAGENESIS OF LYS-481; ASP-483; GLU-530; GLU-613; LYS-635 AND
LYS-637.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16476729; DOI=10.1074/jbc.M513550200;
Akey D., Martins A., Aniukwu J., Glickman M.S., Shuman S.,
Berger J.M.;
"Crystal structure and nonhomologous end-joining function of the
ligase component of Mycobacterium DNA ligase D.";
J. Biol. Chem. 281:13412-13423(2006).
[11]
X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 1-300 OF APOENZYME AND IN
COMPLEX WITH MANGANESE AND SUBSTRATE, FUNCTION, COFACTOR, AND
DNA-BINDING.
PubMed=17174332; DOI=10.1016/j.jmb.2006.10.046;
Pitcher R.S., Brissett N.C., Picher A.J., Andrade P., Juarez R.,
Thompson D., Fox G.C., Blanco L., Doherty A.J.;
"Structure and function of a mycobacterial NHEJ DNA repair
polymerase.";
J. Mol. Biol. 366:391-405(2007).
[12]
X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 1-300 IN COMPLEX WITH DNA,
FUNCTION, SUBUNIT, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF LYS-16 AND
83-HIS--SER-85.
PubMed=17947582; DOI=10.1126/science.1145112;
Brissett N.C., Pitcher R.S., Juarez R., Picher A.J., Green A.J.,
Dafforn T.R., Fox G.C., Blanco L., Doherty A.J.;
"Structure of a NHEJ polymerase-mediated DNA synaptic complex.";
Science 318:456-459(2007).
[13]
X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS) OF 1-300 IN PRETERNARY COMPLEX
WITH DNA, SUBSTRATE AND MANGANESE, COFACTOR, DNA-BINDING, AND
MUTAGENESIS OF ARG-220.
PubMed=21255731; DOI=10.1016/j.molcel.2010.12.026;
Brissett N.C., Martin M.J., Pitcher R.S., Bianchi J., Juarez R.,
Green A.J., Fox G.C., Blanco L., Doherty A.J.;
"Structure of a preternary complex involving a prokaryotic NHEJ DNA
polymerase.";
Mol. Cell 41:221-231(2011).
[14]
X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 1-300 IN COMPLEX WITH DNA,
REACTION MECHANISM, DNA-BINDING, AND MUTAGENESIS OF ARG-53; PHE-63;
PHE-64; 83-HIS--SER-85; LYS-217; GLN-230 AND LYS-235.
PubMed=24239356; DOI=10.1016/j.celrep.2013.10.016;
Brissett N.C., Martin M.J., Bartlett E.J., Bianchi J., Blanco L.,
Doherty A.J.;
"Molecular basis for DNA double-strand break annealing and primer
extension by an NHEJ DNA polymerase.";
Cell Rep. 5:1108-1120(2013).
-!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) repair
enzyme which repairs DNA double-strand breaks (DSB) with reduced
fidelity. Recognizes, processes and reseals DSBs, including
repairs on incompatible DSB which require 3'-resection, gap
filling and ligation. Anneals the 3' overhanging strands from
opposing breaks to form a gapped intermediate, which then can be
extended in trans by using the termini as primers for extension of
the annealed break. Binds to the recessed 5'-phosphate moiety of
the downstream DNA strand forming a stable synaptic complex even
when the 3'-protruding ends of the template DNA strands are not
complementary. Has numerous activites; gap filling copies the
template strand, and prefers a 5'-phosphate in the gap and rNTPS
(PubMed:17174332, PubMed:17947582), DNA-directed DNA or RNA
polymerase on 5'-overhangs, terminal transferase (extending ssDNA
or blunt dsDNA in a non-templated fashion, preferentially with
rNTPs), DNA-dependent RNA primase (synthesizes short RNAs on
unprimed closed ssDNA) and 3'- to 5'-exonuclease on ssDNA
(PubMed:15499016). Isolated Pol domain (and presumably the
holoenzyme) is able to form complexes between 2 noncompatible
protruding 3'-ends DNA ends via microhomologous DNA strands, in a
end-bridging function to which it adds a templated nucleotide
(PubMed:17947582). Minimal primer length is 2 nucleotides
(PubMed:21255731). {ECO:0000269|PubMed:15499016,
ECO:0000269|PubMed:17174332, ECO:0000269|PubMed:17947582,
ECO:0000269|PubMed:21255731}.
-!- FUNCTION: The preference of the polymerase domain for rNTPs over
dNTPs may be advantageous in dormant cells, where the dNTP pool is
limiting.
-!- FUNCTION: In conjunction with endogenous or Mycobacterium phage
Omega Ku (AC Q853W0) can reconstitute NHEJ in Saccharomyces
cerevisiae.
-!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
AMP + diphosphate. {ECO:0000269|PubMed:12215643,
ECO:0000269|PubMed:16023671, ECO:0000269|PubMed:16476729}.
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000305|PubMed:14985346,
ECO:0000305|PubMed:15499016, ECO:0000305|PubMed:16023671,
ECO:0000305|PubMed:17174332, ECO:0000305|PubMed:21255731};
Note=Binds 4 Mn(2+); 2 Mn(2+) for polymerase/primase activity, 1
each for 3-phosphoesterase and ligase.
{ECO:0000305|PubMed:14985346, ECO:0000305|PubMed:15499016,
ECO:0000305|PubMed:16023671, ECO:0000305|PubMed:17174332,
ECO:0000305|PubMed:21255731};
-!- ENZYME REGULATION: The polymerase, exonuclease and ligase
activities are stimulated by Ku. Polymerase activity is inhibited
by EDTA. {ECO:0000269|PubMed:12215643,
ECO:0000269|PubMed:16023671}.
-!- SUBUNIT: Monomer. Component of the NHEJ repair enzyme with mKu.
Interacts with Ku in the absence of DSB via the Pol domain. In
structures of the Pol domain with template DNA 2 Pol domains are
bound to microhomologous DNA complexes to form an end-bridging
complex. Probably interacts with Mycobacterium phage Omega and
Corndog Ku homologs (AC Q853W0, AC Q856K7). Interacts with Sir2;
may form a trimeric complex with LigD during NHEJ.
{ECO:0000269|PubMed:12215643, ECO:0000269|PubMed:14985346,
ECO:0000269|PubMed:15499016, ECO:0000269|PubMed:15778718,
ECO:0000269|PubMed:16023671, ECO:0000269|PubMed:16476729,
ECO:0000269|PubMed:17174332, ECO:0000269|PubMed:17947582,
ECO:0000269|PubMed:21637345, ECO:0000269|PubMed:24239356}.
-!- DOMAIN: The N-terminal Mn(2+)-dependent polymerase/primase domain
(Pol) functions as an independent domain, binds DNA, is sufficient
for DNA-directed and non-DNA-directed DNA synthesis
(PubMed:15778718) and interacts with Ku (PubMed:16023671).
{ECO:0000269|PubMed:15778718, ECO:0000269|PubMed:16023671}.
-!- DOMAIN: The central 3'-phosphoesterase domain (PE) has exonuclease
activity probably constituted of 3'-ribonuclease and 3'-
phosphatase activity (PubMed:15499016). It does not function as an
independent domain (PubMed:16023671).
{ECO:0000269|PubMed:15499016, ECO:0000269|PubMed:16023671}.
-!- DOMAIN: The C-terminal ligase domain (Lig) binds dsDNA and
functions as an independent domain (PubMed:14985346,
PubMed:16023671). {ECO:0000269|PubMed:14985346,
ECO:0000269|PubMed:16023671}.
-!- DISRUPTION PHENOTYPE: Not essential for growth, 80% reduction in
NHEJ (in strain Erdman). {ECO:0000269|PubMed:14985346}.
-!- MISCELLANEOUS: LigD has variable architecture; domain order can be
permutated, domains can be independently encoded, while some
bacteria lack the 3'-phosphoesterase domain entirely.
-!- MISCELLANEOUS: It is not clear whether there is a 5- to 3'-
exonuclease activity associated with the enzyme.
-!- SIMILARITY: In the N-terminal section; belongs to the LigD
polymerase family. {ECO:0000305}.
-!- SIMILARITY: In the central section; belongs to the LigD 3'-
phosphoesterase family. {ECO:0000305}.
-!- SIMILARITY: In the C-terminal section; belongs to the ATP-
dependent DNA ligase family. {ECO:0000305}.
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EMBL; AL123456; CCP43686.1; -; Genomic_DNA.
PIR; B70585; B70585.
RefSeq; NP_215453.1; NC_000962.3.
RefSeq; WP_003911307.1; NZ_KK339370.1.
PDB; 1VS0; X-ray; 2.40 A; A/B=452-759.
PDB; 2IRU; X-ray; 1.65 A; A/B=1-300.
PDB; 2IRX; X-ray; 1.80 A; A=1-300.
PDB; 2IRY; X-ray; 1.78 A; A/B=1-300.
PDB; 2R9L; X-ray; 2.40 A; A/B=1-300.
PDB; 3PKY; X-ray; 3.10 A; A/B=1-300.
PDB; 4MKY; X-ray; 2.40 A; A/B/C/D=1-300.
PDBsum; 1VS0; -.
PDBsum; 2IRU; -.
PDBsum; 2IRX; -.
PDBsum; 2IRY; -.
PDBsum; 2R9L; -.
PDBsum; 3PKY; -.
PDBsum; 4MKY; -.
ProteinModelPortal; P9WNV3; -.
SMR; P9WNV3; -.
STRING; 83332.Rv0938; -.
PaxDb; P9WNV3; -.
EnsemblBacteria; CCP43686; CCP43686; Rv0938.
GeneID; 885561; -.
KEGG; mtu:Rv0938; -.
TubercuList; Rv0938; -.
eggNOG; ENOG4105DQE; Bacteria.
eggNOG; COG1793; LUCA.
eggNOG; COG3285; LUCA.
KO; K01971; -.
OMA; AAPRTWD; -.
PhylomeDB; P9WNV3; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
GO; GO:0005524; F:ATP binding; IDA:MTBBASE.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003910; F:DNA ligase (ATP) activity; IDA:MTBBASE.
GO; GO:0003909; F:DNA ligase activity; IDA:MTBBASE.
GO; GO:0003896; F:DNA primase activity; IDA:MTBBASE.
GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IDA:MTBBASE.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:MTBBASE.
GO; GO:0000287; F:magnesium ion binding; IDA:MTBBASE.
GO; GO:0030145; F:manganese ion binding; IDA:MTBBASE.
GO; GO:0004652; F:polynucleotide adenylyltransferase activity; IDA:MTBBASE.
GO; GO:0008310; F:single-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:MTBBASE.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0006269; P:DNA replication, synthesis of RNA primer; IDA:MTBBASE.
GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:MTBBASE.
GO; GO:0016032; P:viral process; IEA:UniProtKB-KW.
CDD; cd04863; MtLigD_Pol_like; 1.
InterPro; IPR012309; DNA_ligase_ATP-dep_C.
InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
InterPro; IPR014146; LigD_ligase_dom.
InterPro; IPR014144; LigD_PE_domain.
InterPro; IPR014145; LigD_pol_dom.
InterPro; IPR033649; MtLigD_Pol-like.
InterPro; IPR012340; NA-bd_OB-fold.
Pfam; PF04679; DNA_ligase_A_C; 1.
Pfam; PF01068; DNA_ligase_A_M; 1.
Pfam; PF13298; LigD_N; 1.
SUPFAM; SSF50249; SSF50249; 1.
TIGRFAMs; TIGR02777; LigD_PE_dom; 1.
TIGRFAMs; TIGR02778; ligD_pol; 1.
TIGRFAMs; TIGR02779; NHEJ_ligase_lig; 1.
PROSITE; PS50160; DNA_LIGASE_A3; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; DNA damage;
DNA recombination; DNA repair; DNA-binding;
DNA-directed DNA polymerase; Exonuclease; Host-virus interaction;
Hydrolase; Ligase; Manganese; Metal-binding; Multifunctional enzyme;
Nuclease; Nucleotide-binding; Nucleotidyltransferase;
Reference proteome; Transferase.
CHAIN 1 759 Multifunctional non-homologous end
joining DNA repair protein LigD.
/FTId=PRO_0000059627.
DNA_BIND 13 16 Interaction with target DNA.
DNA_BIND 26 26 Interaction with target DNA.
DNA_BIND 53 55 Interaction with target DNA.
DNA_BIND 63 67 Interaction with target DNA.
DNA_BIND 71 71 Interaction with target DNA.
DNA_BIND 83 88 Interaction with target DNA.
DNA_BIND 104 104 Interaction with target DNA.
NP_BIND 137 139 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
DNA_BIND 137 137 Interaction with target DNA.
NP_BIND 172 178 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
DNA_BIND 215 220 Interaction with target DNA.
DNA_BIND 227 235 Interaction with target DNA.
REGION 1 411 Not required for ligase activity.
REGION 9 261 DNA repair polymerase domain (Pol);
interacts with Ku.
REGION 297 446 3-phosphoesterase domain (PE).
REGION 460 757 Ligase domain (Lig).
ACT_SITE 481 481 N6-AMP-lysine intermediate; for ligase
activity. {ECO:0000269|PubMed:12215643,
ECO:0000269|PubMed:16476729}.
METAL 137 137 Manganese 1.
{ECO:0000269|PubMed:17174332}.
METAL 137 137 Manganese 2.
{ECO:0000269|PubMed:17174332}.
METAL 139 139 Manganese 1.
{ECO:0000269|PubMed:17174332}.
METAL 139 139 Manganese 2.
{ECO:0000269|PubMed:17174332}.
METAL 227 227 Manganese 2.
{ECO:0000269|PubMed:17174332}.
METAL 331 331 Manganese 3; via pros nitrogen;
catalytic; for 3'-phosphoesterase
activity. {ECO:0000250}.
METAL 337 337 Manganese 3; via tele nitrogen;
catalytic; for 3'-phosphoesterase
activity. {ECO:0000250}.
METAL 339 339 Manganese 3; catalytic; for 3'-
phosphoesterase activity. {ECO:0000250}.
METAL 483 483 Manganese 4.
{ECO:0000305|PubMed:17174332}.
METAL 613 613 Manganese 4.
{ECO:0000305|PubMed:17174332}.
BINDING 52 52 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
BINDING 111 111 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
BINDING 230 230 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
BINDING 236 236 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
BINDING 244 244 Substrate; for polymerase activity.
{ECO:0000269|PubMed:17174332}.
SITE 373 373 Transition state stabilizer; for 3'-
phosphoesterase activity. {ECO:0000250}.
MUTAGEN 16 16 K->A: Loss of DNA-binding, no polymerase
activity, no effect of gap-filling (in
Pol domain).
{ECO:0000269|PubMed:17947582}.
MUTAGEN 53 53 R->A: On substrate with 5'-phosphate, 1
base pair (bp) complementarity and 1
nucleotide (nt) gap, greatly reduced DNA-
binding and gap-filling. Barely
detectable activity on substrate with
high complementarity and 3'-overhang (in
Pol domain).
{ECO:0000269|PubMed:24239356}.
MUTAGEN 63 63 F->A: On substrate with 5'-phosphate, 1
bp complementarity and 1 nt gap, greatly
reduced DNA-binding and gap-filling. No
activity on substrate with high
complementarity and 3'-overhang (in Pol
domain). {ECO:0000269|PubMed:24239356}.
MUTAGEN 64 64 F->A: On substrate with 5'-phosphate, 1
bp complementarity and 1 nt gap, greatly
reduced DNA-binding and gap-filling.
Barely detectable activity on substrate
with high complementarity and 3'-overhang
(in Pol domain).
{ECO:0000269|PubMed:24239356}.
MUTAGEN 83 85 HRS->AAA: Binds DNA, no formation of DNA
end-bridging complex, no polymerase
activity. Significantly decreased ability
to fill in 2 nt gaps (in Pol domain).
{ECO:0000269|PubMed:17947582,
ECO:0000269|PubMed:24239356}.
MUTAGEN 137 139 DLD->ALA: Loss of polymerase activities,
no DNA repair (in Pol domain).
{ECO:0000269|PubMed:15499016,
ECO:0000269|PubMed:16023671}.
MUTAGEN 217 217 K->A: Better than wild-type DNA-binding
and filling on single nt gaps, impaired
gap filling on more complicated templates
(in Pol domain).
{ECO:0000269|PubMed:24239356}.
MUTAGEN 220 220 R->A: Binds DNA, no gap-filling (in Pol
domain). {ECO:0000269|PubMed:21255731}.
MUTAGEN 230 230 Q->A: Wild-type filling on single nt
gaps, impaired gap filling on more
complicated templates (in Pol domain).
{ECO:0000269|PubMed:24239356}.
MUTAGEN 235 235 K->A: Wild-type filling on single nt
gaps, impaired gap filling on more
complicated templates (in Pol domain).
{ECO:0000269|PubMed:24239356}.
MUTAGEN 373 373 H->A: Loss of exonuclease, no DNA repair.
{ECO:0000269|PubMed:15499016}.
MUTAGEN 481 481 K->A: Loss of adenyltransferase activity,
no N6-AMP-lysine formation and loss of
ligase activity. No effect on
phosphodiester bond formation on pre-
adenylated nicked DNA, or on DNA
polymerase. {ECO:0000269|PubMed:12215643,
ECO:0000269|PubMed:16023671,
ECO:0000269|PubMed:16476729}.
MUTAGEN 483 483 D->A: No ligase of singly nicked dsDNA
activity, no N6-AMP-lysine intermediate
formed, decreased phosphodiester bond
formation on pre-adenylated nicked DNA,
no effect on DNA polymerase.
{ECO:0000269|PubMed:16476729}.
MUTAGEN 530 530 E->A: No ligase of singly nicked dsDNA
activity, no N6-AMP-lysine intermediate
formed, no phosphodiester bond formation
on pre-adenylated nicked DNA, no effect
on DNA polymerase.
{ECO:0000269|PubMed:16476729}.
MUTAGEN 613 613 E->A: No ligase of singly nicked dsDNA
activity, no N6-AMP-lysine intermediate
formed, decreased phosphodiester bond
formation on pre-adenylated nicked DNA,
no effect on DNA polymerase.
{ECO:0000269|PubMed:16476729}.
MUTAGEN 635 635 K->A: 20% ligase activity for singly
nicked dsDNA, normal N6-AMP-lysine
intermediate formed, no effect on
phosphodiester bond formation, no effect
on DNA polymerase.
{ECO:0000269|PubMed:16476729}.
MUTAGEN 637 637 K->A: No ligase of singly nicked dsDNA
activity, 25% N6-AMP-lysine intermediate
formed, decreased phosphodiester bond
formation, no effect on DNA polymerase.
{ECO:0000269|PubMed:16476729}.
STRAND 17 19 {ECO:0000244|PDB:3PKY}.
TURN 20 22 {ECO:0000244|PDB:2IRU}.
HELIX 26 44 {ECO:0000244|PDB:2IRU}.
STRAND 50 53 {ECO:0000244|PDB:2IRU}.
STRAND 63 65 {ECO:0000244|PDB:2IRU}.
STRAND 76 81 {ECO:0000244|PDB:2IRU}.
STRAND 88 92 {ECO:0000244|PDB:2IRU}.
HELIX 96 104 {ECO:0000244|PDB:2IRU}.
STRAND 109 112 {ECO:0000244|PDB:2IRU}.
STRAND 114 119 {ECO:0000244|PDB:2IRU}.
TURN 121 123 {ECO:0000244|PDB:2IRU}.
STRAND 126 140 {ECO:0000244|PDB:2IRU}.
HELIX 146 161 {ECO:0000244|PDB:2IRU}.
TURN 162 164 {ECO:0000244|PDB:2IRU}.
STRAND 168 171 {ECO:0000244|PDB:2IRU}.
STRAND 173 175 {ECO:0000244|PDB:2IRU}.
STRAND 177 187 {ECO:0000244|PDB:2IRU}.
HELIX 189 206 {ECO:0000244|PDB:2IRU}.
TURN 208 210 {ECO:0000244|PDB:2IRU}.
STRAND 211 214 {ECO:0000244|PDB:2IRU}.
HELIX 217 219 {ECO:0000244|PDB:2IRU}.
STRAND 223 227 {ECO:0000244|PDB:2IRU}.
HELIX 229 231 {ECO:0000244|PDB:2IRU}.
STRAND 246 248 {ECO:0000244|PDB:2IRU}.
HELIX 257 260 {ECO:0000244|PDB:2IRU}.
HELIX 270 280 {ECO:0000244|PDB:2IRU}.
TURN 283 287 {ECO:0000244|PDB:2IRU}.
HELIX 455 457 {ECO:0000244|PDB:1VS0}.
STRAND 462 465 {ECO:0000244|PDB:1VS0}.
TURN 473 475 {ECO:0000244|PDB:1VS0}.
STRAND 476 481 {ECO:0000244|PDB:1VS0}.
STRAND 484 492 {ECO:0000244|PDB:1VS0}.
STRAND 495 500 {ECO:0000244|PDB:1VS0}.
HELIX 507 509 {ECO:0000244|PDB:1VS0}.
HELIX 511 513 {ECO:0000244|PDB:1VS0}.
HELIX 514 519 {ECO:0000244|PDB:1VS0}.
TURN 520 522 {ECO:0000244|PDB:1VS0}.
STRAND 524 532 {ECO:0000244|PDB:1VS0}.
HELIX 542 546 {ECO:0000244|PDB:1VS0}.
STRAND 555 564 {ECO:0000244|PDB:1VS0}.
HELIX 574 587 {ECO:0000244|PDB:1VS0}.
HELIX 600 609 {ECO:0000244|PDB:1VS0}.
STRAND 614 619 {ECO:0000244|PDB:1VS0}.
STRAND 629 650 {ECO:0000244|PDB:1VS0}.
STRAND 662 669 {ECO:0000244|PDB:1VS0}.
STRAND 672 679 {ECO:0000244|PDB:1VS0}.
HELIX 685 695 {ECO:0000244|PDB:1VS0}.
HELIX 696 698 {ECO:0000244|PDB:1VS0}.
STRAND 704 707 {ECO:0000244|PDB:1VS0}.
HELIX 711 714 {ECO:0000244|PDB:1VS0}.
STRAND 717 720 {ECO:0000244|PDB:1VS0}.
STRAND 725 731 {ECO:0000244|PDB:1VS0}.
STRAND 743 747 {ECO:0000244|PDB:1VS0}.
HELIX 753 755 {ECO:0000244|PDB:1VS0}.
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


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