4.6 Article

Cryogenic and Laser Photoexcitation Studies Identify Multiple Roles for Active Site Residues in the Light-driven Enzyme Protochlorophyllide Oxidoreductase

Journal

JOURNAL OF BIOLOGICAL CHEMISTRY
Volume 284, Issue 27, Pages 18160-18166

Publisher

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
DOI: 10.1074/jbc.M109.020719

Keywords

-

Funding

  1. Biotechnology and Biological Sciences Research Council, Swindon, United Kingdom
  2. BBSRC [BB/D01798X/1, BB/D01963X/1] Funding Source: UKRI
  3. Biotechnology and Biological Sciences Research Council [BB/D01798X/1, BB/D01963X/1] Funding Source: researchfish

Ask authors/readers for more resources

The light-activated enzyme NADPH-protochlorophyllide oxidoreductase (POR) catalyzes the trans addition of hydrogen across the C-17-C-18 double bond of protochlorophyllide ( Pchlide), a key step in chlorophyll biosynthesis. Similar to other members of the short chain alcohol dehydrogenase/reductase family of enzymes, POR contains a conserved Tyr and Lys residue in the enzyme active site, which are implicated in a proposed reaction mechanism involving proton transfer from the Tyr hydoxyl group to Pchlide. We have analyzed a number of POR variant enzymes altered in these conserved residues using a combination of steady-state turnover, laser photoexcitation studies, and low temperature fluorescence spectroscopy. None of the mutations completely abolished catalytic activity. We demonstrate their importance to catalysis by defining multiple roles in the overall reaction pathway. Mutation of either residue impairs formation of the ground state ternary enzyme-substrate complex, pointing to a key role in substrate binding. By analyzing the most active variant (Y193F), we show that Tyr-193 participates in proton transfer to Pchlide and stabilizes the Pchlide excited state, enabling hydride transfer from NADPH to Pchilde. Thus, in addition to confirming the probable identity of the proton donor in Pchlide reduction, our work defines additional roles for these residues in facilitating hydride transfer through stabilization of the ground and excited states of the ternary enzyme complex.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Review Chemistry, Physical

Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals

Binuraj R. K. Menon, Daniel Richmond, Navya Menon

Summary: Bio-halogenase enzymes have the ability to selectively halogenate molecules during biosynthesis, providing opportunities for C-H activation and functionalization of molecular structures.

CATALYSIS REVIEWS-SCIENCE AND ENGINEERING (2022)

Article Biochemistry & Molecular Biology

Insights into the H2O2-driven catalytic mechanism of fungal lytic polysaccharide monooxygenases

Tobias M. Hedison, Erik Breslmayr, Muralidharan Shanmugam, Kwankao Karnpakdee, Derren J. Heyes, Anthony P. Green, Roland Ludwig, Nigel S. Scrutton, Daniel Kracher

Summary: Understanding the reaction mechanism of fungal LPMOs with H2O2 is crucial for their application in biotechnological settings. Research shows that a 'priming' electron transfer reaction from the cellobiose dehydrogenase partner protein supports up to 20 catalytic cycles of LPMOs.

FEBS JOURNAL (2021)

Editorial Material Chemistry, Multidisciplinary

The missing colours of chemistry

Binuraj R. K. Menon

NATURE CHEMISTRY (2021)

Review Biochemistry & Molecular Biology

A Guide to time-resolved structural analysis of light-activated proteins

Harshwardhan Poddar, Derren J. Heyes, Giorgio Schiro, Martin Weik, David Leys, Nigel S. Scrutton

Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.

FEBS JOURNAL (2022)

Article Chemistry, Physical

An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition

Angus J. Robertson, F. Aaron Cruz-Navarrete, Henry P. Wood, Nikita Vekaria, Andrea M. Hounslow, Claudine Bisson, Matthew J. Cliff, Nicola J. Baxter, Jonathan P. Waltho

Summary: Understanding the factors contributing to the high catalytic efficiencies of enzymes is crucial for catalysis and enzyme design. This study investigates the relationship between binding a phosphodianion group in a distal site, adopting a closed enzyme form, and catalytic proficiency. The results suggest that binding of a phosphodianion group in the distal site stimulates domain closure and stabilizes the closed active form, leading to high catalytic efficiencies.

ACS CATALYSIS (2022)

Article Chemistry, Physical

Versatile and Facile One-Pot Biosynthesis for Amides and Carboxylic Acids in E. coli by Engineering Auxin Pathways of Plant Microbiomes

Navya Menon, Daniel Richmond, Mohammad Rejaur Rahman, Binuraj R. K. Menon

Summary: The development of enzymatic routes for the synthesis of amide and carboxylic acid bonds in bioactive molecular scaffolds under aqueous conditions poses a major challenge for the biopharmaceutical and fine chemical industries. In this study, we characterized and studied the kinetics of two enzymes, tryptophan-2-monooxygenase (iaaM) and indole-3-acetamide hydrolase (iaaH), present in plant microbiomes, which catalyze the conversion of tryptophan to indole-3-acetamide and subsequent hydrolysis to form carboxylic acid. These enzymes have the potential to produce indole-3-acetic acid (IAA), a natural plant hormone and an important synthon for agrochemical and pharmaceutical applications. Additionally, we demonstrated the synthesis of IAA derivatives using a one-pot multienzyme biosynthetic cascade and the de novo biosynthesis of IAA and its derivatives from glucose or indoles in Escherichia coli.

ACS CATALYSIS (2022)

Article Chemistry, Physical

The Relationship between Enzyme Conformational Change, Proton Transfer, and Phosphoryl Transfer in β-Phosphoglucomutase

Angus J. Robertson, Alex L. Wilson, Matthew J. Burn, Matthew J. Cliff, Paul L. A. Popelier, Jonathan P. Waltho

Summary: The study using QM models, experimental NMR measurements, and X-ray structures revealed that the transition of an archetypal phosphoryl transfer enzyme, beta PGM, triggers partial proton transfer and partial dissociation of phosphoryl group. Proton transfer continues but is not completed during the reaction with the enzyme in the TSA conformation. Changes in proton position and electrostatic repulsion stimulate phosphoryl transfer.

ACS CATALYSIS (2021)

Article Chemistry, Physical

Solution-State Inter-Copper Distribution of Redox Partner-Linked Copper Nitrite Reductases: A Pulsed Electron-Electron Double Resonance Spectroscopy Study

Tobias M. Hedison, Andreea I. Iorgu, Donato Calabrese, Derren J. Heyes, Muralidharan Shanmugam, Nigel S. Scrutton

Summary: This study investigates the structural, dynamical, and functional relationship of copper nitrite reductases (CuNiRs) through combining crystallographic techniques and solution-state approaches. The findings shed light on the catalytic mechanisms of these enzymes and suggest the involvement of protein dynamics. The importance of integrating high-resolution crystallographic techniques and low-resolution solution-state approaches in studying metalloenzymes is emphasized.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2022)

Article Multidisciplinary Sciences

A designed photoenzyme for enantioselective [2+2] cycloadditions

Jonathan S. Trimble, Rebecca Crawshaw, Florence J. Hardy, Colin W. Levy, Murray J. B. Brown, Douglas E. Fuerst, Derren J. Heyes, Richard Obexer, Anthony P. Green

Summary: The ability to program new modes of catalysis into proteins using genetic code expansion methodology has led to the development of photoenzymes that operate through triplet energy transfer catalysis. This allows for versatile reactivity in organic synthesis that is not possible with current biocatalysis methods. The study demonstrates the successful installation of a genetically encoded photosensitizer into a protein scaffold, resulting in a photoenzyme that can perform cycloadditions with high efficiency and selectivity. The photoenzyme outperforms small-molecule catalysts by being able to operate under aerobic conditions and at ambient temperatures. This research opens up new possibilities for excited-state chemistry in protein active sites and provides a foundation for the development of enantioselective photocatalysts.

NATURE (2022)

Article Biochemistry & Molecular Biology

Loss of Residues 119-136, Including the First b-strand of Human Prion Protein, Generates an Aggregation-competent Partially Open Form

Laszlo L. P. Hosszu, Daljit Sangar, Mark Batchelor, Emmanuel Risse, Andrea M. Hounslow, John Collinge, Jonathan P. Waltho, Jan Bieschke

Summary: In prion replication, the conversion of cellular form of prion protein (PrPC) to its disease-associated fibrillar form is achieved through a full conformational transition. Transmembrane forms of PrP play a role in this structural conversion. Removing residues 119-136 of PrP, which includes the first β-strand and a large portion of the conserved hydrophobic region associated with the ER membrane, resulted in an open native-like conformer of PrPC with increased solvent exposure and enhanced fibril formation. These findings suggest a stepwise folding transition initiated by the conformational switch to this open form of PrPC.

JOURNAL OF MOLECULAR BIOLOGY (2023)

Article Multidisciplinary Sciences

Redox driven B12-ligand switch drives CarH photoresponse

Harshwardhan Poddar, Ronald Rios-Santacruz, Derren J. J. Heyes, Muralidharan Shanmugam, Adam Brookfield, Linus O. O. Johannissen, Colin W. W. Levy, Laura N. N. Jeffreys, Shaowei Zhang, Michiyo Sakuma, Jacques-Philippe Colletier, Sam Hay, Giorgio Schiro, Martin Weik, Nigel S. S. Scrutton, David Leys

Summary: This study provides insights into the mechanism of CarH, a photoreceptor involved in transcriptional regulation. The authors show that the response of CarH to light integrates both B-12 photochemistry and redox changes to drive large-scale conformational changes.

NATURE COMMUNICATIONS (2023)

Article Chemistry, Multidisciplinary

A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase

Mary Ortmayer, Florence J. Hardy, Matthew G. Quesne, Karl Fisher, Colin Levy, Derren J. Heyes, C. Richard A. Catlow, Sam P. de Visser, Stephen E. J. Rigby, Sam Hay, Anthony P. Green

Summary: This study utilizes an expanded genetic code to investigate the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, revealing that modifications to the active site amino acid Trp51 can significantly affect the reactivity of ferryl heme intermediates and regulate catalytic function.

JACS AU (2021)

Article Chemistry, Multidisciplinary

Interplay between chromophore binding and domain assembly by the B12-dependent photoreceptor protein, CarH

Ines S. Camacho, Rachelle Black, Derren J. Heyes, Linus O. Johannissen, Lennart A. I. Ramakers, Bruno Bellina, Perdita E. Barran, Sam Hay, Alex R. Jones

Summary: A study using molecular dynamics simulations, native ion mobility mass spectrometry and time-resolved spectroscopy has revealed the mechanism of B-12-dependent photoreceptor CarH in the dark and how B-12 drives domain assembly in CarH. When B-12 is in excess, it can form head-to-tail dimers that quickly combine to form tetramers; while when B-12 is scarce, tetramers can still form without a complete B-12 complement to each dimer.

CHEMICAL SCIENCE (2021)

Review Plant Sciences

Photocatalysis as the 'master switch' of photomorphogenesis in early plant development

Derren J. Heyes, Shaowei Zhang, Aoife Taylor, Linus O. Johannissen, Samantha J. O. Hardman, Sam Hay, Nigel S. Scrutton

Summary: LPOR is a light-activated enzyme essential for chlorophyll biosynthesis and plant greening. It catalyzes the conversion of protochlorophyllide to chlorophyllide, playing a crucial role in early plant development. Through photocatalysis, LPOR acts as a master switch for plant photomorphogenesis, triggering complex molecular and cellular events that lead to plant morphological changes.

NATURE PLANTS (2021)

Article Chemistry, Multidisciplinary

Enzymatic production of β-glucose 1,6-bisphosphate through manipulation of catalytic magnesium coordination

Henry P. Wood, Nicola J. Baxter, F. Aaron Cruz-Navarrete, Clare R. Trevitt, Andrea M. Hounslow, Jonathan P. Waltho

Summary: The study demonstrated an efficient enzymatic synthesis method for anomer-specific beta G16BP using the D170N variant of beta PGM. The perturbation of catalytic magnesium ion coordination by the substitution at residue 170 in the enzyme was found to contribute to the accumulation of beta G16BP. The purification process employed a simple and environmentally friendly precipitation procedure, resulting in a high purity and yield of the beta G16BP product.

GREEN CHEMISTRY (2021)

No Data Available