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8x46

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Crystal structure of DIMT1 in complex with adenosylornithine (SFG) from Pyrococcus horikoshii

Structural highlights

8x46 is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RSMA_PYRHO Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]

Publication Abstract from PubMed

Dimethyladenosine transferase 1 (DIMT1), an ortholog of bacterial KsgA is a conserved protein that assists in ribosome biogenesis by modifying two successive adenosine bases near the 3' end of small subunit (SSU) rRNA. Although KsgA/DIMT1 proteins have been characterized in bacteria and eukaryotes, they are yet unexplored in archaea. Also, their dynamics are not well understood. Here, we structurally and functionally characterized the apo and holo forms of archaeal DIMT1 from Pyrococcus horikoshii. Wild-type protein and mutants were analyzed to capture different transition states, including open, closed, and intermediate states. This study reports a unique inter-domain movement that is needed for substrate (RNA) positioning in the catalytic pocket, and is only observed in the presence of the cognate cofactors S-adenosyl-L-methionine (SAM) or S-adenosyl-L-homocysteine (SAH). The binding of the inhibitor sinefungine, an analog of SAM or SAH, to archaeal DIMT1 blocks the catalytic pocket and renders the enzyme inactive.

Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.,Saha S, Kanaujia SP Structure. 2024 Aug 2:S0969-2126(24)00276-4. doi: 10.1016/j.str.2024.07.013. PMID:39146930^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Saha S, Kanaujia SP. Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis. Structure. 2024 Aug 2:S0969-2126(24)00276-4. PMID:39146930 doi:10.1016/j.str.2024.07.013