ID   LTRA_LACLC              Reviewed;         599 AA.
AC   P0A3U0; Q57005; Q9FB65;
DT   15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   15-MAR-2005, sequence version 1.
DT   28-JUL-2009, entry version 21.
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.-.-;
GN   Name=ltrA; Synonyms=matR;
OS   Lactococcus lactis subsp. cremoris (Streptococcus cremoris).
OG   Plasmid pRS01, and Plasmid pAH82.
OC   Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Lactococcus.
OX   NCBI_TaxID=1359;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=NCDO 763 / ML3; PLASMID=pRS01;
RX   MEDLINE=96256606; PubMed=8655550;
RA   Mills D.A., McKay L.L., Dunny G.M.;
RT   "Splicing of a group II intron involved in the conjugative transfer of
RT   pRS01 in Lactococci.";
RL   J. Bacteriol. 178:3531-3538(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   PLASMID=pAH82;
RX   MEDLINE=21091990; PubMed=11157264; DOI=10.1128/AEM.67.2.929-937.2001;
RA   O'Sullivan D., Ross R.P., Twomey D.P., Fitzgerald G.F., Hill C.,
RA   Coffey A.;
RT   "Naturally occurring lactococcal plasmid pAH90 links bacteriophage
RT   resistance and mobility functions to a food-grade selectable marker.";
RL   Appl. Environ. Microbiol. 67:929-937(2001).
RN   [3]
RP   CHARACTERIZATION.
RX   MEDLINE=99417963; PubMed=10488339; DOI=10.1016/S1097-2765(00)80371-8;
RA   Wank H., SanFilippo J., Singh R.N., Matsuura M., Lambowitz A.M.;
RT   "A reverse transcriptase/maturase promotes splicing by binding at its
RT   own coding segment in a group II intron RNA.";
RL   Mol. Cell 4:239-250(1999).
RN   [4]
RP   CHARACTERIZATION, AND MUTAGENESIS OF 308-ASP-ASP-309.
RX   MEDLINE=98019170; PubMed=9353259;
RA   Matsuura M., Saldanha R., Ma H., Wank H., Yang J., Mohr G.,
RA   Cavanagh S., Dunny G.M., Belfort M., Lambowitz A.M.;
RT   "A bacterial group II intron encoding reverse transcriptase, maturase,
RT   and DNA endonuclease activities: biochemical demonstration of maturase
RT   activity and insertion of new genetic information within the intron.";
RL   Genes Dev. 11:2910-2924(1997).
RN   [5]
RP   CHARACTERIZATION.
RX   MEDLINE=99343933; PubMed=10413481; DOI=10.1021/bi982799l;
RA   Saldanha R., Chen B., Wank H., Matsuura M., Edwards J.,
RA   Lambowitz A.M.;
RT   "RNA and protein catalysis in group II intron splicing and mobility
RT   reactions using purified components.";
RL   Biochemistry 38:9069-9083(1999).
RN   [6]
RP   INTRON RETARGETING.
RC   STRAIN=NCDO 763 / ML3; PLASMID=pRS01;
RX   MEDLINE=21588758; PubMed=11731786; DOI=10.1038/nbt1201-1162;
RA   Karberg M., Guo H., Zhong J., Coon R., Perutka J., Lambowitz A.M.;
RT   "Group II introns as controllable gene targeting vectors for genetic
RT   manipulation of bacteria.";
RL   Nat. Biotechnol. 19:1162-1167(2001).
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,
CC       maturase to promote splicing, and DNA endonuclease for site-
CC       specific cleavage of recipient alleles. The intron-encoded protein
CC       promotes splicing by facilitating the formation of the
CC       catalytically active structure of the intron RNA. After splicing,
CC       the protein remains bound to the excised intron lariat RNA,
CC       forming ribonucleoprotein particles, and cleaving the antisense
CC       strand of the recipient DNA in the 3' exon. After DNA cleavage,
CC       retrohoming occurs by a target DNA-primed reverse transcription of
CC       the intron RNA that had reverse spliced into the sense strand of
CC       the recipient DNA. It also contributes to the recognition of the
CC       DNA target site and acts as a repressor of its own translation.
CC   -!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
CC       diphosphate + DNA(n+1).
CC   -!- COFACTOR: Magnesium.
CC   -!- SUBUNIT: Homodimer (Probable).
CC   -!- BIOTECHNOLOGY: Mobile group II introns can be retargeted and used
CC       for highly specific chromosomal gene disruption in bacteria. Could
CC       be useful for genetic engineering and functional genomics in a
CC       wide variety of bacteria.
CC   -!- MISCELLANEOUS: The correct folding of ltrA seems to be facilitated
CC       by binding to the unspliced precursor or intron RNA. RNA would
CC       serve in part as a chaperone that promotes folding of the protein
CC       into an active conformation. Purified protein lacks endonuclease
CC       activity unless complexed with intron lariat RNA. It may
CC       preferentially function in cis by binding to the intron RNA from
CC       which it was translated.
CC   -!- SIMILARITY: Contains 1 reverse transcriptase domain.
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DR   EMBL; U50902; AAB06503.1; -; Genomic_DNA.
DR   EMBL; AF243383; AAF98310.1; -; Genomic_DNA.
DR   BRENDA; 2.7.7.49; 289716.
DR   GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
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:0008380; P:RNA splicing; IEA:InterPro.
DR   GO; GO:0006278; P:RNA-dependent DNA replication; IEA:InterPro.
DR   InterPro; IPR003615; HNH_nuc.
DR   InterPro; IPR000442; Intron_maturse2.
DR   InterPro; IPR000477; Reverse_transcriptase.
DR   Pfam; PF01348; Intron_maturas2; 1.
DR   Pfam; PF00078; RVT_1; 1.
DR   SMART; SM00507; HNHc; 1.
DR   PROSITE; PS50878; RT_POL; 1.
PE   1: Evidence at protein level;
KW   Endonuclease; Hydrolase; Intron homing; Magnesium;
KW   Multifunctional enzyme; Nuclease; Nucleotidyltransferase; Plasmid;
KW   RNA-directed DNA polymerase; Transferase.
FT   CHAIN         1    599       Group II intron-encoded protein ltrA.
FT                                /FTId=PRO_0000084512.
FT   DOMAIN       70    361       Reverse transcriptase.
FT   REGION      381    549       Intron maturase type-2.
FT   MUTAGEN     308    309       DD->AA: Loss of RT function.
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
//