8S8S

An induced-fit motion of a mobile loop

8S8S の概要

• エントリーDOI: 10.2210/pdb8s8s/pdb
• 分子名称: Imidazole glycerol phosphate synthase subunit HisF (2 entities in total)
• 機能のキーワード: histidine and purine biosynthesis, structural protein
• 由来する生物種: Thermotoga maritima
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27605.69

構造登録者

Rajendran, C. (登録日: 2024-03-07, 公開日: 2025-02-19)

主引用文献

Hupfeld, E.,Schlee, S.,Wurm, J.P.,Rajendran, C.,Yehorova, D.,Vos, E.,Ravindra Raju, D.,Kamerlin, S.C.L.,Sprangers, R.,Sterner, R.
Conformational Modulation of a Mobile Loop Controls Catalysis in the ( beta alpha ) 8 -Barrel Enzyme of Histidine Biosynthesis HisF.
Jacs Au, 4:3258-3276, 2024

PubMed Abstract: The overall significance of loop motions for enzymatic activity is generally accepted. However, it has largely remained unclear whether and how such motions can control different steps of catalysis. We have studied this problem on the example of the mobile active site βα-loop (loop1) of the (βα)-barrel enzyme HisF, which is the cyclase subunit of imidazole glycerol phosphate synthase. Loop1 variants containing single mutations of conserved amino acids showed drastically reduced rates for the turnover of the substrates '-[(5'-phosphoribulosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) and ammonia to the products imidazole glycerol phosphate (ImGP) and 5-aminoimidazole-4-carboxamide-ribotide (AICAR). A comprehensive mechanistic analysis including stopped-flow kinetics, X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations detected three conformations of loop1 (open, detached, closed) whose populations differed between wild-type HisF and functionally affected loop1 variants. Transient stopped-flow kinetic experiments demonstrated that wt-HisF binds PrFAR by an induced-fit mechanism whereas catalytically impaired loop1 variants bind PrFAR by a simple two-state mechanism. Our findings suggest that PrFAR-induced formation of the closed conformation of loop1 brings active site residues in a productive orientation for chemical turnover, which we show to be the rate-limiting step of HisF catalysis. After the cyclase reaction, the closed loop conformation is destabilized, which favors the formation of detached and open conformations and hence facilitates the release of the products ImGP and AICAR. Our data demonstrate how different conformations of active site loops contribute to different catalytic steps, a finding that is presumably of broad relevance for the reaction mechanisms of (βα)-barrel enzymes and beyond.

PubMed: 39211614
DOI: 10.1021/jacsau.4c00558

実験手法

X-RAY DIFFRACTION (1.314 Å)