ID   LTRA_LACLM              Reviewed;         599 AA.
AC   P0A3U1; A2RKZ3; Q57005; Q9FB65;
DT   15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   15-MAR-2005, sequence version 1.
DT   03-AUG-2022, entry version 80.
DE   RecName: Full=Group II intron-encoded protein LtrA;
DE   Includes:
DE     RecName: Full=Reverse-transcriptase;
DE              EC=2.7.7.49;
DE   Includes:
DE     RecName: Full=RNA maturase;
DE              EC=3.1.-.-;
DE   Includes:
DE     RecName: Full=DNA endonuclease;
DE              EC=3.1.-.-;
DE     AltName: Full=Homing endonuclease I-LlaI {ECO:0000303|PubMed:12654995};
GN   Name=ltrA; Synonyms=matR {ECO:0000303|PubMed:8843433};
GN   OrderedLocusNames=llmg_1371;
OS   Lactococcus lactis subsp. cremoris (strain MG1363).
OC   Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC   Lactococcus; Lactococcus cremoris subsp. cremoris.
OX   NCBI_TaxID=416870;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX   PubMed=8843433; DOI=10.1046/j.1365-2958.1996.00610.x;
RA   Shearman C., Godon J.-J., Gasson M.;
RT   "Splicing of a group II intron in a functional transfer gene of Lactococcus
RT   lactis.";
RL   Mol. Microbiol. 21:45-53(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=MG1363;
RX   PubMed=17307855; DOI=10.1128/jb.01768-06;
RA   Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C.,
RA   Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P.,
RA   van Sinderen D., Kok J.;
RT   "The complete genome sequence of the lactic acid bacterial paradigm
RT   Lactococcus lactis subsp. cremoris MG1363.";
RL   J. Bacteriol. 189:3256-3270(2007).
RN   [3]
RP   NOMENCLATURE.
RX   PubMed=12654995; DOI=10.1093/nar/gkg274;
RA   Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A.,
RA   Bitinaite J., Blumenthal R.M., Degtyarev S.K., Dryden D.T., Dybvig K.,
RA   Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S.,
RA   Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A.,
RA   Klaenhammer T.R., Kobayashi I., Kong H., Krueger D.H., Lacks S.,
RA   Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V.,
RA   Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E.,
RA   Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W.,
RA   Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., Xu S.Y.;
RT   "A nomenclature for restriction enzymes, DNA methyltransferases, homing
RT   endonucleases and their genes.";
RL   Nucleic Acids Res. 31:1805-1812(2003).
CC   -!- FUNCTION: Multifunctional protein that promotes group II intron
CC       splicing and mobility by acting both on RNA and DNA. It has three
CC       activities: reverse transcriptase (RT) for intron duplication, maturase
CC       to promote splicing, and DNA endonuclease for site-specific cleavage of
CC       recipient alleles. The intron-encoded protein promotes splicing by
CC       facilitating the formation of the catalytically active structure of the
CC       intron RNA. After splicing, the protein remains bound to the excised
CC       intron lariat RNA, forming ribonucleoprotein particles, and cleaving
CC       the antisense strand of the recipient DNA in the 3' exon. After DNA
CC       cleavage, retrohoming occurs by a target DNA-primed reverse
CC       transcription of the intron RNA that had reverse spliced into the sense
CC       strand of the recipient DNA. It also contributes to the recognition of
CC       the DNA target site and acts as a repressor of its own translation.
CC       {ECO:0000305|PubMed:8843433}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.49; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU00405};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC   -!- SUBUNIT: Homodimer. {ECO:0000305}.
CC   -!- BIOTECHNOLOGY: Mobile group II introns can be retargeted and used for
CC       highly specific chromosomal gene disruption in bacteria. Could be
CC       useful for genetic engineering and functional genomics in a wide
CC       variety of bacteria.
CC   -!- MISCELLANEOUS: The correct folding of LtrA seems to be facilitated by
CC       binding to the unspliced precursor or intron RNA. RNA would serve in
CC       part as a chaperone that promotes folding of the protein into an active
CC       conformation. Purified protein lacks endonuclease activity unless
CC       complexed with intron lariat RNA. It may preferentially function in cis
CC       by binding to the intron RNA from which it was translated.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the bacterial reverse
CC       transcriptase family. {ECO:0000305}.
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DR   EMBL; X89922; CAA61996.1; -; Genomic_DNA.
DR   EMBL; AM406671; CAL97959.1; -; Genomic_DNA.
DR   PIR; S77648; S77648.
DR   RefSeq; WP_011835237.1; NZ_WJVF01000011.1.
DR   RefSeq; YP_009091786.1; NC_025249.1.
DR   AlphaFoldDB; P0A3U1; -.
DR   SMR; P0A3U1; -.
DR   STRING; 416870.llmg_1371; -.
DR   REBASE; 3057; I-LlaI.
DR   EnsemblBacteria; CAL97959; CAL97959; llmg_1371.
DR   KEGG; llm:llmg_1371; -.
DR   eggNOG; COG3344; Bacteria.
DR   HOGENOM; CLU_013584_3_1_9; -.
DR   OMA; YNYYCLA; -.
DR   PhylomeDB; P0A3U1; -.
DR   BioCyc; LLAC416870:LLMG_RS06945-MON; -.
DR   Proteomes; UP000000364; Chromosome.
DR   GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR   GO; GO:0006397; P:mRNA processing; IEA:InterPro.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR024937; Domain_X.
DR   InterPro; IPR000477; RT_dom.
DR   Pfam; PF01348; Intron_maturas2; 1.
DR   Pfam; PF00078; RVT_1; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS50878; RT_POL; 1.
PE   1: Evidence at protein level;
KW   Endonuclease; Hydrolase; Intron homing; Magnesium; Multifunctional enzyme;
KW   Nuclease; Nucleotidyltransferase; RNA-directed DNA polymerase; Transferase.
FT   CHAIN           1..599
FT                   /note="Group II intron-encoded protein LtrA"
FT                   /id="PRO_0000084513"
FT   DOMAIN          70..361
FT                   /note="Reverse transcriptase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT   REGION          381..549
FT                   /note="Intron maturase type-2"
SQ   SEQUENCE   599 AA;  70163 MW;  52A286BD5F504589 CRC64;
     MKPTMAILER ISKNSQENID EVFTRLYRYL LRPDIYYVAY QNLYSNKGAS TKGILDDTAD
     GFSEEKIKKI IQSLKDGTYY PQPVRRMYIA KKNSKKMRPL GIPTFTDKLI QEAVRIILES
     IYEPVFEDVS HGFRPQRSCH TALKTIKREF GGARWFVEGD IKGCFDNIDH VTLIGLINLK
     IKDMKMSQLI YKFLKAGYLE NWQYHKTYSG TPQGGILSPL LANIYLHELD KFVLQLKMKF
     DRESPERITP EYRELHNEIK RISHRLKKLE GEEKAKVLLE YQEKRKRLPT LPCTSQTNKV
     LKYVRYADDF IISVKGSKED CQWIKEQLKL FIHNKLKMEL SEEKTLITHS SQPARFLGYD
     IRVRRSGTIK RSGKVKKRTL NGSVELLIPL QDKIRQFIFD KKIAIQKKDS SWFPVHRKYL
     IRSTDLEIIT IYNSELRGIC NYYGLASNFN QLNYFAYLME YSCLKTIASK HKGTLSKTIS
     MFKDGSGSWG IPYEIKQGKQ RRYFANFSEC KSPYQFTDEI SQAPVLYGYA RNTLENRLKA
     KCCELCGTSD ENTSYEIHHV NKVKNLKGKE KWEMAMIAKQ RKTLVVCFHC HRHVIHKHK