9yfx | pdb_00009yfx

KrKA retaining Kdo transferase CMP complex

spinqualitylabelsall models 9yfx, resolution 2.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9yfx is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.7Å Ligands: C5P, CL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A854BIM6_ECOLX Publication Abstract from PubMed 3-Deoxy-D-manno-octulosonic acid (Kdo) is an eight-carbon monosaccharide that, in Gram-negative bacteria, is an essential structural component of both lipopolysaccharide and the polymeric linker in Group 2 and 3 capsules. Kdo is also an important building block of the variable region of various capsular structures, but the responsible enzymes have, to date, not been investigated. Here, we structurally and functionally characterize the protein KrkA from Escherichia coli capsular serotype K13, showing that it has both ribosyltransferase and Kdo-transferase activity, consistent with this protein being solely responsible for synthesizing the K13 (and the closely related K20 and K23) capsular polysaccharide repeat. We show that the N-terminal module of this protein is the Kdo-transferase. This module's x-ray structure (at 2.7 A resolution) resembles that of two characterized Kdo-transferases: the GT99 module of WbbB, and the GT107 module of KpsC, despite sharing negligible sequence similarity. KrkA is therefore the founding member of a new GT family, GT140. KrkA(GT)(140) is organized into a trimer, where a single residue contributes to a neighboring protomer's acceptor binding site. Using a D193C mutation, we determined the Kdo adduct and ternary complex structures at 2.0 and 2.2 A resolution, respectively. These structures, along with site-directed mutagenesis, confirm the critical nature of the nucleophile Asp193 and the general base Glu102 (contributed by a secondary structure element distinct from that in GT99 and GT107), as well as important adduct and acceptor binding residues. Escherichia coli isolates collectively encode four distinct clusters of related proteins, suggesting polyphyletic origins for this capsular serotype. The retaining kdo transferase that synthesizes Escherichia coli K13 capsule is deeply divergent from structurally homologous enzymes.,Govind M, Allas MJ, Huang BS, Lowary TL, Kimber MS J Biol Chem. 2026 Jan 13;302(3):111162. doi: 10.1016/j.jbc.2026.111162. PMID:41539565 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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