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Hupfeld, Enrico ; Schlee, Sandra ; Wurm, Jan Philip ; Rajendran, Chitra ; Yehorova, Dariia ; Vos, Eva ; Ravindra Raju, Dinesh ; Kamerlin, Shina Caroline Lynn ; Sprangers, Remco ; Sterner, Reinhard

Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα)8-Barrel Enzyme of Histidine Biosynthesis HisF

Hupfeld, Enrico, Schlee, Sandra, Wurm, Jan Philip , Rajendran, Chitra, Yehorova, Dariia, Vos, Eva, Ravindra Raju, Dinesh, Kamerlin, Shina Caroline Lynn, Sprangers, Remco and Sterner, Reinhard (2024) Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα)8-Barrel Enzyme of Histidine Biosynthesis HisF. JACS Au 4 (8), pp. 3258-3276.

Date of publication of this fulltext: 30 Sep 2024 13:03
Article
DOI to cite this document: 10.5283/epub.59288


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 β1α1-loop (loop1) of the (βα)8-barrel enzyme HisF, which is the cyclase subunit of imidazole glycerol phosphate synthase. Loop1 ...

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 β1α1-loop (loop1) of the (βα)8-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 N′-[(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)8-barrel enzymes and beyond.



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Details

Item typeArticle
Journal or Publication TitleJACS Au
Publisher:American Chemical Society (ACS)
Volume:4
Number of Issue or Book Chapter:8
Page Range:pp. 3258-3276
Date15 August 2024
InstitutionsBiology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie
Projects
Funded by: Deutsche Forschungsgemeinschaft (DFG) (273747520)
Identification Number
ValueType
10.1021/jacsau.4c00558DOI
Keywords(βα)8-barrel, protein dynamics, loop motion, enzyme kinetics, enzyme mechanism, stopped-flow analysis, nuclear magnetic resonance spectroscopy, molecular dynamics simulation
Dewey Decimal Classification500 Science > 540 Chemistry & allied sciences
StatusPublished
RefereedYes, this version has been refereed
Created at the University of RegensburgYes
URN of the UB Regensburgurn:nbn:de:bvb:355-epub-592880
Item ID59288

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