P0A3U1 (LTRA_LACLM) Reviewed, UniProtKB/Swiss-Prot

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
Ordered Locus Names:	llmg_1371

Organism

Lactococcus lactis subsp. cremoris (strain MG1363) [Complete proteome] [HAMAP]

Taxonomic identifier

416870 [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	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro intron homing Inferred from electronic annotation. Source: UniProtKB-KW mRNA processing Inferred from electronic annotation. Source: InterPro
Cellular component	chloroplast Inferred from electronic annotation. Source: InterPro
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
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_0000084513
Regions
	Domain	70 – 361	292	Reverse transcriptase
	Region	381 – 549	169	Intron maturase type-2

Sequences

	Sequence		Length	Mass (Da)
	P0A3U1 [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

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Splicing of a group II intron in a functional transfer gene of Lactococcus lactis." Shearman C., Godon J.-J., Gasson M. Mol. Microbiol. 21:45-53(1996) [PubMed: 8843433] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363." Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J. J. Bacteriol. 189:3256-3270(2007) [PubMed: 17307855] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: MG1363.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X89922 Genomic DNA. Translation: CAA61996.1. AM406671 Genomic DNA. Translation: CAL97959.1.
PIR	S77648.
RefSeq	YP_001032672.1. NC_009004.1.
3D structure databases
ModBase	Search...
Protein family/group databases
REBASE	3057. I-LlaI.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4797413.
GenomeReviews	Gene locus llmg_1371 in contig AM406671_GR.
KEGG	llm:llmg_1371.
PATRIC	22283919. VBILacLac4574_1415.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG3344.
HOGENOM	HBG343449.
OMA	YLMEYSC.
ProtClustDB	CLSK862318.
Family and domain databases
InterPro	IPR003615. HNH_nuc. IPR000477. RVT. [Graphical view]
Pfam	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_LACLM

Accession

Primary (citable) accession number: P0A3U1
Secondary accession number(s): A2RKZ3, Q57005, Q9FB65

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	March 15, 2005
Last modified:	January 25, 2012
This is version 33 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program