9C6D

Crystal structure of mutant NonPro1 Tautomerase Superfamily Member 8U6-S1P in complex with 3-bromopropiolate inhibitor

This is a non-PDB format compatible entry.

Summary for 9C6D

• Entry DOI: 10.2210/pdb9c6d/pdb
• Descriptor: Tautomerase family protein, 3-bromo-3-oxopropanoic acid (3 entities in total)
• Functional Keywords: tautomerase superfamily inhibitor enzyme msad-like, isomerase, isomerase-inhibitor complex, isomerase/inhibitor
• Biological source: Sulfurovum
• Total number of polymer chains: 6
• Total formula weight: 89691.10

Authors

Hardtke, H.A.,Venkat Ramani, M.K.,Zhang, Y.J. (deposition date: 2024-06-07, release date: 2025-03-05)

Primary citation

Lancaster, E.B.,Hardtke, H.A.,Melkonian, T.R.,Venkat Ramani, M.,Johnson Jr., W.H.,Baas, B.J.,Zhang, Y.J.,Whitman, C.P.
Conversion of Inactive Non-Pro1 Tautomerase Superfamily Members into Active Tautomerases: Analysis of the Pro1 Mutants.
Biochemistry, 64:812-822, 2025

PubMed Abstract: Pro1 is a critical catalytic residue in the characterized activities of tautomerase superfamily (TSF) members. Only a handful of members (∼346) lack Pro1 in a sequence similarity network (SSN) that consists of over 11,000 members. Most (294 members) are in the malonate semialdehyde decarboxylase (MSAD)-like subgroup, but the ones characterized thus far have little or no MSAD activity. Moreover, there is little to no activity with other TSF substrates. Five non-Pro1 members were selected randomly for kinetic [using phenylenolpyruvate (PP) and 2-hydroxymuconate (2HM)], mutagenic, inhibition, and crystallographic analysis. Using PP, / values (∼10-10 M s) could be estimated for three native proteins whereas using 2HM, a / value could only be estimated for one native protein (∼10 M s). The and values could not be determined. However, changing the N-terminal residue to a proline gave a significant improvement in / values for all mutant enzymes using PP or 2HM. For PP, the / values ranged from 10-10 M s and for 2HM, the / values ranged from 10-10 M s. In addition, it was now possible to measure and values for all mutant proteins using PP and one mutant protein using 2HM. Incubation of the Pro1 mutants with 3-bromopropiolate (3BP) results in covalent modification of the prolyl nitrogen of Pro1 by a 3-oxopropanoate adduct. Crystallographic analysis of two mutant enzymes (NJ7V1P and 8U6S1P) modified by the 3-oxopropanoate adduct identified binding ligands and suggest a mechanism for the tautomerase activity involving Pro1, Arg71, Tyr124, and the backbone amide of Phe68.

PubMed: 39914393
DOI: 10.1021/acs.biochem.4c00338

Experimental method

X-RAY DIFFRACTION (2.1 Å)