Reviewed, UniProtKB/Swiss-Prot P0A3U0 (LTRA_LACLC)

Names and origin

Protein names

Recommended name:
Group II intron-encoded protein ltrA

Including the following 3 domains:

1. Reverse-transcriptase
   EC=2.7.7.49
2. RNA maturase
   EC=3.1.-.-
3. DNA endonuclease
   EC=3.1.-.-

Gene names

Name:	ltrA
Synonyms:	matR

Encoded on

Plasmid pRS01 Ref.1 Ref.6
Plasmid pAH82 Ref.2

Organism

Lactococcus lactis subsp. cremoris (Streptococcus cremoris)

Taxonomic identifier

1359 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Lactococcus

Protein attributes

Sequence length	599 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Multifunctional protein that promotes group II intron splicing and mobility by acting both on RNA and DNA. It has three activities: reverse transcriptase (RT) for intron duplication, maturase to promote splicing, and DNA endonuclease for site-specific cleavage of recipient alleles. The intron-encoded protein promotes splicing by facilitating the formation of the catalytically active structure of the intron RNA. After splicing, the protein remains bound to the excised intron lariat RNA, forming ribonucleoprotein particles, and cleaving the antisense strand of the recipient DNA in the 3' exon. After DNA cleavage, retrohoming occurs by a target DNA-primed reverse transcription of the intron RNA that had reverse spliced into the sense strand of the recipient DNA. It also contributes to the recognition of the DNA target site and acts as a repressor of its own translation.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Cofactor	Magnesium.
Subunit structure	Homodimer Probable.
Biotechnological use	Mobile group II introns can be retargeted and used for highly specific chromosomal gene disruption in bacteria. Could be useful for genetic engineering and functional genomics in a wide variety of bacteria.
Miscellaneous	The correct folding of ltrA seems to be facilitated by binding to the unspliced precursor or intron RNA. RNA would serve in part as a chaperone that promotes folding of the protein into an active conformation. Purified protein lacks endonuclease activity unless complexed with intron lariat RNA. It may preferentially function in cis by binding to the intron RNA from which it was translated.
Sequence similarities	Contains 1 reverse transcriptase domain.

Ontologies

Keywords
Biological process	Intron homing
Ligand	Magnesium
Molecular function	Endonuclease Hydrolase Nuclease Nucleotidyltransferase RNA-directed DNA polymerase Transferase
Technical term	Multifunctional enzyme Plasmid
Gene Ontology (GO)
Biological process	RNA splicing Inferred from electronic annotation. Source: InterPro RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro intron homing Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 599	599	Group II intron-encoded protein ltrA		PRO_0000084512
Regions
	Domain	70 – 361	292	Reverse transcriptase
	Region	381 – 549	169	Intron maturase type-2
Experimental info
	Mutagenesis	308 – 309	2	DD → AA: Loss of RT function. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P0A3U0-1 [UniParc]. Last modified March 15, 2005. Version 1. Checksum: 52A286BD5F504589	FASTA	599	70,163
	10 20 30 40 50 60 MKPTMAILER ISKNSQENID EVFTRLYRYL LRPDIYYVAY QNLYSNKGAS TKGILDDTAD 70 80 90 100 110 120 GFSEEKIKKI IQSLKDGTYY PQPVRRMYIA KKNSKKMRPL GIPTFTDKLI QEAVRIILES 130 140 150 160 170 180 IYEPVFEDVS HGFRPQRSCH TALKTIKREF GGARWFVEGD IKGCFDNIDH VTLIGLINLK 190 200 210 220 230 240 IKDMKMSQLI YKFLKAGYLE NWQYHKTYSG TPQGGILSPL LANIYLHELD KFVLQLKMKF 250 260 270 280 290 300 DRESPERITP EYRELHNEIK RISHRLKKLE GEEKAKVLLE YQEKRKRLPT LPCTSQTNKV 310 320 330 340 350 360 LKYVRYADDF IISVKGSKED CQWIKEQLKL FIHNKLKMEL SEEKTLITHS SQPARFLGYD 370 380 390 400 410 420 IRVRRSGTIK RSGKVKKRTL NGSVELLIPL QDKIRQFIFD KKIAIQKKDS SWFPVHRKYL 430 440 450 460 470 480 IRSTDLEIIT IYNSELRGIC NYYGLASNFN QLNYFAYLME YSCLKTIASK HKGTLSKTIS 490 500 510 520 530 540 MFKDGSGSWG IPYEIKQGKQ RRYFANFSEC KSPYQFTDEI SQAPVLYGYA RNTLENRLKA 550 560 570 580 590 KCCELCGTSD ENTSYEIHHV NKVKNLKGKE KWEMAMIAKQ RKTLVVCFHC HRHVIHKHK

References

[1]	"Splicing of a group II intron involved in the conjugative transfer of pRS01 in Lactococci." Mills D.A., McKay L.L., Dunny G.M. J. Bacteriol. 178:3531-3538(1996) [PubMed: 8655550] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: NCDO 763 / ML3.
[2]	"Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable marker." O'Sullivan D., Ross R.P., Twomey D.P., Fitzgerald G.F., Hill C., Coffey A. Appl. Environ. Microbiol. 67:929-937(2001) [PubMed: 11157264] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA." Wank H., SanFilippo J., Singh R.N., Matsuura M., Lambowitz A.M. Mol. Cell 4:239-250(1999) [PubMed: 10488339] [Abstract] Cited for: CHARACTERIZATION.
[4]	"A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron." Matsuura M., Saldanha R., Ma H., Wank H., Yang J., Mohr G., Cavanagh S., Dunny G.M., Belfort M., Lambowitz A.M. Genes Dev. 11:2910-2924(1997) [PubMed: 9353259] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF 308-ASP-ASP-309.
[5]	"RNA and protein catalysis in group II intron splicing and mobility reactions using purified components." Saldanha R., Chen B., Wank H., Matsuura M., Edwards J., Lambowitz A.M. Biochemistry 38:9069-9083(1999) [PubMed: 10413481] [Abstract] Cited for: CHARACTERIZATION.
[6]	"Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria." Karberg M., Guo H., Zhong J., Coon R., Perutka J., Lambowitz A.M. Nat. Biotechnol. 19:1162-1167(2001) [PubMed: 11731786] [Abstract] Cited for: INTRON RETARGETING. Strain: NCDO 763 / ML3.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U50902 Genomic DNA. Translation: AAB06503.1. AF243383 Genomic DNA. Translation: AAF98310.1.
3D structure databases
ModBase	Search...
Phylogenomic databases
ProtClustDB	CLSK862318.
Enzyme and pathway databases
BRENDA	2.7.7.49. 289716.
Family and domain databases
InterPro	IPR003615. HNH_nuc. IPR000442. Intron_maturse2. IPR000477. Reverse_transcriptase. [Graphical view]
Pfam	PF01348. Intron_maturas2. 1 hit. PF00078. RVT_1. 1 hit. [Graphical view]
SMART	SM00507. HNHc. 1 hit. [Graphical view]
PROSITE	PS50878. RT_POL. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

LTRA_LACLC

Accession

Primary (citable) accession number: P0A3U0
Secondary accession number(s): Q57005, Q9FB65

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	March 15, 2005
Last modified:	March 2, 2010
This is version 22 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)