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Protein

Group II intron-encoded protein LtrA

Gene

ltrA

Organism
Lactococcus lactis subsp. cremoris (Streptococcus cremoris)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.

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.

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation

Cofactori

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionEndonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, RNA-directed DNA polymerase, Transferase
Biological processIntron homing
LigandMagnesium

Protein family/group databases

REBASEi3057 I-LlaI

Names & Taxonomyi

Protein namesi
Recommended name:
Group II intron-encoded protein LtrA
Including the following 3 domains:
Reverse-transcriptase (EC:2.7.7.49)
RNA maturase (EC:3.1.-.-)
DNA endonuclease (EC:3.1.-.-)
Gene namesi
Name:ltrA
Synonyms:matR
Encoded oniPlasmid pRS012 Publications
Plasmid pAH821 Publication
OrganismiLactococcus lactis subsp. cremoris (Streptococcus cremoris)
Taxonomic identifieri1359 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus

Pathology & Biotechi

Biotechnological usei

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.

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi308 – 309DD → AA: Loss of RT function. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000845121 – 599Group II intron-encoded protein LtrAAdd BLAST599

Proteomic databases

PRIDEiP0A3U0

Interactioni

Subunit structurei

Homodimer.Curated

Structurei

3D structure databases

SMRiP0A3U0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini70 – 361Reverse transcriptasePROSITE-ProRule annotationAdd BLAST292

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni381 – 549Intron maturase type-2Add BLAST169

Phylogenomic databases

eggNOGiENOG4105EKQ Bacteria
COG3344 LUCA

Family and domain databases

InterProiView protein in InterPro
IPR024937 Domain_X
IPR000477 RT_dom
PfamiView protein in Pfam
PF01348 Intron_maturas2, 1 hit
PF00078 RVT_1, 1 hit
PROSITEiView protein in PROSITE
PS50878 RT_POL, 1 hit

Sequencei

Sequence statusi: Complete.

P0A3U0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKPTMAILER ISKNSQENID EVFTRLYRYL LRPDIYYVAY QNLYSNKGAS
60 70 80 90 100
TKGILDDTAD GFSEEKIKKI IQSLKDGTYY PQPVRRMYIA KKNSKKMRPL
110 120 130 140 150
GIPTFTDKLI QEAVRIILES IYEPVFEDVS HGFRPQRSCH TALKTIKREF
160 170 180 190 200
GGARWFVEGD IKGCFDNIDH VTLIGLINLK IKDMKMSQLI YKFLKAGYLE
210 220 230 240 250
NWQYHKTYSG TPQGGILSPL LANIYLHELD KFVLQLKMKF DRESPERITP
260 270 280 290 300
EYRELHNEIK RISHRLKKLE GEEKAKVLLE YQEKRKRLPT LPCTSQTNKV
310 320 330 340 350
LKYVRYADDF IISVKGSKED CQWIKEQLKL FIHNKLKMEL SEEKTLITHS
360 370 380 390 400
SQPARFLGYD IRVRRSGTIK RSGKVKKRTL NGSVELLIPL QDKIRQFIFD
410 420 430 440 450
KKIAIQKKDS SWFPVHRKYL IRSTDLEIIT IYNSELRGIC NYYGLASNFN
460 470 480 490 500
QLNYFAYLME YSCLKTIASK HKGTLSKTIS MFKDGSGSWG IPYEIKQGKQ
510 520 530 540 550
RRYFANFSEC KSPYQFTDEI SQAPVLYGYA RNTLENRLKA KCCELCGTSD
560 570 580 590
ENTSYEIHHV NKVKNLKGKE KWEMAMIAKQ RKTLVVCFHC HRHVIHKHK
Length:599
Mass (Da):70,163
Last modified:March 15, 2005 - v1
Checksum:i52A286BD5F504589
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50902 Genomic DNA Translation: AAB06503.1
AF243383 Genomic DNA Translation: AAF98310.1
RefSeqiWP_011835237.1, NZ_LITG01000148.1

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50902 Genomic DNA Translation: AAB06503.1
AF243383 Genomic DNA Translation: AAF98310.1
RefSeqiWP_011835237.1, NZ_LITG01000148.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5G2Xelectron microscopy3.80C1-599[»]
SMRiP0A3U0
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

REBASEi3057 I-LlaI

Proteomic databases

PRIDEiP0A3U0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105EKQ Bacteria
COG3344 LUCA

Family and domain databases

InterProiView protein in InterPro
IPR024937 Domain_X
IPR000477 RT_dom
PfamiView protein in Pfam
PF01348 Intron_maturas2, 1 hit
PF00078 RVT_1, 1 hit
PROSITEiView protein in PROSITE
PS50878 RT_POL, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLTRA_LACLC
AccessioniPrimary (citable) accession number: P0A3U0
Secondary accession number(s): Q57005, Q9FB65
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: July 5, 2017
This is version 53 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Plasmid

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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