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Grunow AL, Carroll SC, Kreiman AN, Sutherland MC. Structure-function analysis of the heme-binding WWD domain in the bacterial holocytochrome c synthase, CcmFH. mBio 2023; 14:e0150923. [PMID: 37929956 PMCID: PMC10746174 DOI: 10.1128/mbio.01509-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Heme is an essential co-factor for proteins involved with critical cellular functions, such as energy production and oxygen transport. Thus, understanding how heme interacts with proteins and is moved through cells is a fundamental biological question. This work studies the System I cytochrome c biogenesis pathway, which in some species (including Escherichia coli) is composed of eight integral membrane or membrane-associated proteins called CcmA-H that are proposed to function in two steps to transport and attach heme to apocytochrome c. Cytochrome c requires this heme attachment to function in electron transport chains to generate cellular energy. A conserved WWD heme-handling domain in CcmFH is analyzed and residues critical for heme interaction and holocytochrome c synthase activity are identified. CcmFH is the third member of the WWD domain-containing heme-handling protein family to undergo a comprehensive structure-function analysis, allowing for comparison of heme interaction across this protein family.
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Affiliation(s)
- Amber L. Grunow
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Susan C. Carroll
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Alicia N. Kreiman
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Molly C. Sutherland
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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2
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Abstract
While the bottom-up design of enzymes appears to be an intractably complex problem, a minimal approach that combines elementary, de novo-designed proteins with intrinsically reactive cofactors offers a simple means to rapidly access sophisticated catalytic mechanisms. Not only is this method proven in the reproduction of powerful oxidative chemistry of the natural peroxidase enzymes, but we show here that it extends to the efficient, abiological—and often asymmetric—formation of strained cyclopropane rings, nitrogen–carbon and carbon–carbon bonds, and the ring expansion of a simple cyclic molecule to form a precursor for NAD+, a fundamentally important biological cofactor. That the enzyme also functions in vivo paves the way for its incorporation into engineered biosynthetic pathways within living organisms. By constructing an in vivo-assembled, catalytically proficient peroxidase, C45, we have recently demonstrated the catalytic potential of simple, de novo-designed heme proteins. Here, we show that C45’s enzymatic activity extends to the efficient and stereoselective intermolecular transfer of carbenes to olefins, heterocycles, aldehydes, and amines. Not only is this a report of carbene transferase activity in a completely de novo protein, but also of enzyme-catalyzed ring expansion of aromatic heterocycles via carbene transfer by any enzyme.
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Shevket SH, Gonzalez D, Cartwright JL, Kleanthous C, Ferguson SJ, Redfield C, Mavridou DAI. The CcmC-CcmE interaction during cytochrome c maturation by System I is driven by protein-protein and not protein-heme contacts. J Biol Chem 2018; 293:16778-16790. [PMID: 30206118 PMCID: PMC6204919 DOI: 10.1074/jbc.ra118.005024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/07/2018] [Indexed: 12/30/2022] Open
Abstract
Cytochromes c are ubiquitous proteins, essential for life in most organisms. Their distinctive characteristic is the covalent attachment of heme to their polypeptide chain. This post-translational modification is performed by a dedicated protein system, which in many Gram-negative bacteria and plant mitochondria is a nine-protein apparatus (CcmA-I) called System I. Despite decades of study, mechanistic understanding of the protein-protein interactions in this highly complex maturation machinery is still lacking. Here, we focused on the interaction of CcmC, the protein that sources the heme cofactor, with CcmE, the pivotal component of System I responsible for the transfer of the heme to the apocytochrome. Using in silico analyses, we identified a putative interaction site between these two proteins (residues Asp47, Gln50, and Arg55 on CcmC; Arg73, Asp101, and Glu105 on CcmE), and we validated our findings by in vivo experiments in Escherichia coli Moreover, employing NMR spectroscopy, we examined whether a heme-binding site on CcmE contributes to this interaction and found that CcmC and CcmE associate via protein-protein rather than protein-heme contacts. The combination of in vivo site-directed mutagenesis studies and high-resolution structural techniques enabled us to determine at the residue level the mechanism for the formation of one of the key protein complexes for cytochrome c maturation by System I.
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Affiliation(s)
- Shevket H Shevket
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Diego Gonzalez
- the Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, Switzerland
| | - Jared L Cartwright
- the Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Colin Kleanthous
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Stuart J Ferguson
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom,
| | - Christina Redfield
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom,
| | - Despoina A I Mavridou
- From the MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, London SW7 2DD, United Kingdom,
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Sutherland MC, Rankin JA, Kranz RG. Heme Trafficking and Modifications during System I Cytochrome c Biogenesis: Insights from Heme Redox Potentials of Ccm Proteins. Biochemistry 2016; 55:3150-6. [PMID: 27198710 DOI: 10.1021/acs.biochem.6b00427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochromes c require covalent attachment of heme via two thioether bonds at conserved CXXCH motifs, a process accomplished in prokaryotes by eight integral membrane proteins (CcmABCDEFGH), termed System I. Heme is trafficked from inside the cell to outside (via CcmABCD) and chaperoned (holoCcmE) to the cytochrome c synthetase (CcmF/H). Purification of key System I pathway intermediates allowed the determination of heme redox potentials. The data support a model whereby heme is oxidized to form holoCcmE and subsequently reduced by CcmF/H for thioether formation, with Fe(2+) being required for attachment to CXXCH. Results provide insight into mechanisms for the oxidation and reduction of heme in vivo.
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Affiliation(s)
- Molly C Sutherland
- Department of Biology, Washington University , St. Louis, Missouri 63130, United States
| | - Joel A Rankin
- Department of Biology, Washington University , St. Louis, Missouri 63130, United States
| | - Robert G Kranz
- Department of Biology, Washington University , St. Louis, Missouri 63130, United States
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Khalfaoui-Hassani B, Verissimo AF, Shroff NP, Ekici S, Trasnea PI, Utz M, Koch HG, Daldal F. Biogenesis of Cytochrome c Complexes: From Insertion of Redox Cofactors to Assembly of Different Subunits. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK. Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231. BMC Microbiol 2015; 15:135. [PMID: 26141380 PMCID: PMC4491210 DOI: 10.1186/s12866-015-0471-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/23/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In the genome of H. pylori 26695, 149 proteins containing the CXXC motif characteristic of thioldisulfide oxidoreductases have been identified to date. However, only two of these proteins have a thioredoxin-like fold (i.e., HP0377 and HP0231) and are periplasm-located. We have previously shown that HP0231 is a dimeric oxidoreductase that catalyzes disulfide bond formation in the periplasm. Although HP0377 was originally described as DsbC homologue, its resolved structure and location of the hp0377 gene in the genome indicate that it is a counterpart of CcmG/DsbE. RESULTS The present work shows that HP0377 is present in H. pylori cells only in a reduced form and that absence of the main periplasmic oxidase HP0231 influences its redox state. Our biochemical analysis indicates that HP0377 is a specific reductase, as it does not reduce insulin. However, it possesses disulfide isomerase activity, as it catalyzes the refolding of scrambled RNase. Additionally, although its standard redox potential is -176 mV, it is the first described CcmG protein having an acidic pKa of the N-terminal cysteine of the CXXC motif, similar to E. coli DsbA or E. coli DsbC. The CcmG proteins that play a role in a cytochrome c-maturation, both in system I and system II, are kept in the reduced form by an integral membrane protein DsbD or its analogue, CcdA. In H. pylori HP0377 is re-reduced by CcdA (HP0265); however in E. coli it remains in the oxidized state as it does not interact with E. coli DsbD. Our in vivo work also suggests that both HP0377, which plays a role in apocytochrome reduction, and HP0378, which is involved in heme transport and its ligation into apocytochrome, provide essential functions in H. pylori. CONCLUSIONS The present data, in combination with the resolved three-dimensional structure of the HP0377, suggest that HP0377 is an unusual, multifunctional CcmG protein.
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Affiliation(s)
- Paula Roszczenko
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland. .,Present address: Department of Cell Biology, Nencki Institute of Experimental Biology, PAS, Warsaw, Poland.
| | - Magdalena Grzeszczuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Patrycja Kobierecka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Ewa Wywial
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
| | - Paweł Urbanowicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Piotr Wincek
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Elzbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
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Watkins DW, Armstrong CT, Anderson JLR. De novo protein components for oxidoreductase assembly and biological integration. Curr Opin Chem Biol 2014; 19:90-8. [DOI: 10.1016/j.cbpa.2014.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/23/2014] [Accepted: 01/29/2014] [Indexed: 01/03/2023]
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Verissimo AF, Daldal F. Cytochrome c biogenesis System I: an intricate process catalyzed by a maturase supercomplex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:989-98. [PMID: 24631867 DOI: 10.1016/j.bbabio.2014.03.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/16/2022]
Abstract
Cytochromes c are ubiquitous heme proteins that are found in most living organisms and are essential for various energy production pathways as well as other cellular processes. Their biosynthesis relies on a complex post-translational process, called cytochrome c biogenesis, responsible for the formation of stereo-specific thioether bonds between the vinyl groups of heme b (protoporphyrin IX-Fe) and the thiol groups of apocytochromes c heme-binding site (C1XXC2H) cysteine residues. In some organisms this process involves up to nine (CcmABCDEFGHI) membrane proteins working together to achieve heme ligation, designated the Cytochrome c maturation (Ccm)-System I. Here, we review recent findings related to the Ccm-System I found in bacteria, archaea and plant mitochondria, with an emphasis on protein interactions between the Ccm components and their substrates (apocytochrome c and heme). We discuss the possibility that the Ccm proteins may form a multi subunit supercomplex (dubbed "Ccm machine"), and based on the currently available data, we present an updated version of a mechanistic model for Ccm. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA.
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