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Structure paper

TitleThe missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.
Journal, issue, pagesNucleic Acids Res, Vol. 52, Issue 5, Page 2530-2545, Year 2024
Publish dateMar 21, 2024
AuthorsElena Manakova / Edvardas Golovinas / Reda Pocevičiūtė / Giedrius Sasnauskas / Arunas Silanskas / Danielis Rutkauskas / Marija Jankunec / Evelina Zagorskaitė / Edvinas Jurgelaitis / Algirdas Grybauskas / Česlovas Venclovas / Mindaugas Zaremba
PubMed AbstractArgonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid ...Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.
External linksNucleic Acids Res / PubMed:38197228 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.4 - 3.43 Å
Structure data

17973

8pvv

EMDB-17973, PDB-8pvv:
Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 30 nt RNA guide and 51 nt DNA target
Method: EM (single particle) / Resolution: 2.81 Å

18386

8qg0

EMDB-18386, PDB-8qg0:
Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 17 nt RNA guide and 17 nt DNA target
Method: EM (single particle) / Resolution: 3.43 Å

PDB-8ok9:
Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-8old:
Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-8olj:
Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ACY:
ACETIC ACID / Acetic acid

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-HOH:
WATER / Water

ChemComp-CAC:
CACODYLATE ION / Cacodylic acid

ChemComp-CL:
Unknown entry / Chloride

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM / 2-Methyl-2,4-pentanediol

ChemComp-NA:
Unknown entry

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-IPA:
ISOPROPYL ALCOHOL / alkaloid*YM / Isopropyl alcohol

ChemComp-K:
Unknown entry

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

Source
  • archaeoglobus fulgidus (archaea)
  • archaeoglobus fulgidus dsm 8774 (archaea)
  • escherichia coli (E. coli)
  • archaeoglobus fulgidus dsm 4304 (archaea)
KeywordsRNA BINDING PROTEIN / Protein-nucleic acid interactions / Argonaute / pAgo / guide and target specificity / PROTEIN BINDING / DNA BINDING PROTEIN / PIWI DOMAIN / PROTEIN-DNA COMPLEX

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