9vis | pdb_00009vis

Crystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU from Akkermansia muciniphila in complex with AdoCbi-GDP

spinqualitylabelsall models 9vis, resolution 1.85Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9vis is a 1 chain structure with sequence from Akkermansia muciniphila ATCC BAA-835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.85Å Ligands: GOL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function B2UM52_AKKM8 Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate.[ARBA:ARBA00003889] Publication Abstract from PubMed Cobamides are a family of complex nutrients that are essential for animals and some bacteria and archaea. The intestinal probiotic Akkermansia muciniphila cannot synthesize cobamide de novo, but was reported to synthesize cobamide through a salvage pathway starting with the generation of cobamide precursor AdoCbi-P by CbiR. However, the downstream of this pathway remains unclear. In this work, we demonstrated that AmCobU possesses AdoCbi-P guanylyltransferase activity, which implied that AdoCbi-P can be activated to AdoCbi-GDP, an intermediate that can incorporate new lower ligands, in A. muciniphila. Further, we determined the crystal structures of AmCobU and its complex with the product AdoCbi-GDP, as well as its H49A mutant in complex with the substrate GTP. The structural results revealed that GTP binds in a pocket formed by helix alpha2, the core beta-sheets, and the P-loop, and AdoCbi-P binds in a pocket involving the trimerization interface, suggesting that trimerization is essential for CobU activity. In addition, we found a significant positional variation of alpha2 in the GTP complex and the AdoCbi-GDP complex structures, suggesting a conformational change of alpha2 during the catalytic process. Our findings improved the understanding of the cobamide synthesis pathway in A. muciniphila, as well as the catalytic mechanism of the AdoCbi-P guanylyltransferase activity of CobU. Structural insights into the adenosylcobinamide-phosphate guanylyltransferase activity of CobU from Akkermansia muciniphila.,Jiang M, Kong C, Wei Q, Guo S, Chen X, Li Q, Wang M Int J Biol Macromol. 2025 Sep 19;329(Pt 1):147810. doi: , 10.1016/j.ijbiomac.2025.147810. PMID:40976292 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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