1
|
Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
Collapse
Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
2
|
Yang L, Wagner T, Mechaly A, Boyko A, Bruch EM, Megrian D, Gubellini F, Alzari PM, Bellinzoni M. High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun 2023; 14:4851. [PMID: 37563123 PMCID: PMC10415282 DOI: 10.1038/s41467-023-40253-6] [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: 02/23/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.
Collapse
Affiliation(s)
- Lu Yang
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Wuhan Institute of Biological Products Co. Ltd., Wuhan, 430207, PR China
| | - Tristan Wagner
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359, Bremen, Germany
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plateforme de Cristallographie, F-75015, Paris, France
| | - Alexandra Boyko
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- BostonGene, Yerevan, Armenia
| | - Eduardo M Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Sanofi, In vitro Biology, Integrated Drug Discovery, 350 Water St, Cambridge, MA, 02141, USA
| | - Daniela Megrian
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Pedro M Alzari
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France.
| |
Collapse
|
3
|
Liu S, Kormos BL, Knafels JD, Sahasrabudhe PV, Rosado A, Sommese RF, Reyes AR, Ward J, Roth Flach RJ, Wang X, Buzon LM, Reese MR, Bhattacharya SK, Omoto K, Filipski KJ. Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors. J Biol Chem 2023; 299:102959. [PMID: 36717078 PMCID: PMC9976451 DOI: 10.1016/j.jbc.2023.102959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/30/2023] Open
Abstract
The mammalian mitochondrial branched-chain ketoacid dehydrogenase (BCKD) complex is a multienzyme complex involved in the catabolism of branched-chain amino acids. BCKD is regulated by the BCKD kinase, or BCKDK, which binds to the E2 subunit of BCKD, phosphorylates its E1 subunit, and inhibits enzymatic activity. Inhibition of the BCKD complex results in increased levels of branched-chain amino acids and branched-chain ketoacids, and this buildup has been associated with heart failure, type 2 diabetes mellitus, and nonalcoholic fatty liver disease. To find BCKDK inhibitors for potential treatment of these diseases, we performed both NMR and virtual fragment screening and identified tetrazole-bearing fragments that bind BCKDK at multiple sites. Through structure-based virtual screening expanding from these fragments, the angiotensin receptor blocker class antihypertension drugs and angiotensin receptor blocker-like compounds were discovered to be potent BCKDK inhibitors, suggesting potential new avenues for heart failure treatment combining BCKDK inhibition and antihypertension.
Collapse
Affiliation(s)
- Shenping Liu
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA.
| | | | | | | | - Amy Rosado
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA
| | | | - Allan R Reyes
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Jessica Ward
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts, USA
| | | | - Xiaochun Wang
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA
| | | | | | | | - Kiyoyuki Omoto
- Medicine Design, Pfizer Inc, Cambridge, Massachusetts, USA
| | | |
Collapse
|
4
|
Liu S, Xia X, Zhen J, Li Z, Zhou ZH. Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney. Cell Discov 2022; 8:126. [PMID: 36414632 PMCID: PMC9681731 DOI: 10.1038/s41421-022-00487-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/20/2022] [Indexed: 11/23/2022] Open
Abstract
The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
Collapse
Affiliation(s)
- Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - James Zhen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Zihang Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
| |
Collapse
|
5
|
Functional Versatility of the Human 2-Oxoadipate Dehydrogenase in the L-Lysine Degradation Pathway toward Its Non-Cognate Substrate 2-Oxopimelic Acid. Int J Mol Sci 2022; 23:ijms23158213. [PMID: 35897808 PMCID: PMC9367764 DOI: 10.3390/ijms23158213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
The human 2-oxoadipate dehydrogenase complex (OADHc) in L-lysine catabolism is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA and NADH (+H+). Genetic findings have linked the DHTKD1 encoding 2-oxoadipate dehydrogenase (E1a), the first component of the OADHc, to pathogenesis of AMOXAD, eosinophilic esophagitis (EoE), and several neurodegenerative diseases. A multipronged approach, including circular dichroism spectroscopy, Fourier Transform Mass Spectrometry, and computational approaches, was applied to provide novel insight into the mechanism and functional versatility of the OADHc. The results demonstrate that E1a oxidizes a non-cognate substrate 2-oxopimelate (OP) as well as OA through the decarboxylation step, but the OADHc was 100-times less effective in reactions producing adipoyl-CoA and NADH from the dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3). The results revealed that the E2o is capable of producing succinyl-CoA, glutaryl-CoA, and adipoyl-CoA. The important conclusions are the identification of: (i) the functional promiscuity of E1a and (ii) the ability of the E2o to form acyl-CoA products derived from homologous 2-oxo acids with five, six, and even seven carbon atoms. The findings add to our understanding of both the OADHc function in the L-lysine degradative pathway and of the molecular mechanisms leading to the pathogenesis associated with DHTKD1 variants.
Collapse
|
6
|
Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor. mBio 2022; 13:e0039322. [PMID: 35608300 PMCID: PMC9239090 DOI: 10.1128/mbio.00393-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of “rare” actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions.
Collapse
|
7
|
Engineering the 2-Oxoglutarate Dehydrogenase Complex to Understand Catalysis and Alter Substrate Recognition. REACTIONS 2022. [DOI: 10.3390/reactions3010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The E. coli 2-oxoglutarate dehydrogenase complex (OGDHc) is a multienzyme complex in the tricarboxylic acid cycle, consisting of multiple copies of three components, 2-oxoglutarate dehydrogenase (E1o), dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3), which catalyze the formation of succinyl-CoA and NADH (+H+) from 2-oxoglutarate. This review summarizes applications of the site saturation mutagenesis (SSM) to engineer E. coli OGDHc with mechanistic and chemoenzymatic synthetic goals. First, E1o was engineered by creating SSM libraries at positions His260 and His298.Variants were identified that: (a) lead to acceptance of substrate analogues lacking the 5-carboxyl group and (b) performed carboligation reactions producing acetoin-like compounds with good enantioselectivity. Engineering the E2o catalytic (core) domain enabled (a) assignment of roles for pivotal residues involved in catalysis, (b) re-construction of the substrate-binding pocket to accept substrates other than succinyllysyldihydrolipoamide and (c) elucidation of the mechanism of trans-thioesterification to involve stabilization of a tetrahedral oxyanionic intermediate with hydrogen bonds by His375 and Asp374, rather than general acid–base catalysis which has been misunderstood for decades. The E. coli OGDHc is the first example of a 2-oxo acid dehydrogenase complex which was evolved to a 2-oxo aliphatic acid dehydrogenase complex by engineering two consecutive E1o and E2o components.
Collapse
|
8
|
Skalidis I, Kyrilis FL, Tüting C, Hamdi F, Chojnowski G, Kastritis PL. Cryo-EM and artificial intelligence visualize endogenous protein community members. Structure 2022; 30:575-589.e6. [DOI: 10.1016/j.str.2022.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022]
|
9
|
Usey MM, Huet D. Parasite powerhouse: A review of the Toxoplasma gondii mitochondrion. J Eukaryot Microbiol 2022; 69:e12906. [PMID: 35315174 PMCID: PMC9490983 DOI: 10.1111/jeu.12906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Toxoplasma gondii is a member of the apicomplexan phylum, a group of single-celled eukaryotic parasites that cause significant human morbidity and mortality around the world. T. gondii harbors two organelles of endosymbiotic origin: a non-photosynthetic plastid, known as the apicoplast, and a single mitochondrion derived from the ancient engulfment of an α-proteobacterium. Due to excitement surrounding the novelty of the apicoplast, the T. gondii mitochondrion was, to a certain extent, overlooked for about two decades. However, recent work has illustrated that the mitochondrion is an essential hub of apicomplexan-specific biology. Development of novel techniques, such as cryo-electron microscopy, complexome profiling, and next-generation sequencing have led to a renaissance in mitochondrial studies. This review will cover what is currently known about key features of the T. gondii mitochondrion, ranging from its genome to protein import machinery and biochemical pathways. Particular focus will be given to mitochondrial features that diverge significantly from the mammalian host, along with discussion of this important organelle as a drug target.
Collapse
Affiliation(s)
- Madelaine M. Usey
- Department of Cellular BiologyUniversity of GeorgiaAthensGeorgiaUSA,Center for Tropical and Emerging Global DiseasesUniversity of GeorgiaAthensGeorgiaUSA
| | - Diego Huet
- Center for Tropical and Emerging Global DiseasesUniversity of GeorgiaAthensGeorgiaUSA,Department of Pharmaceutical and Biomedical SciencesUniversity of GeorgiaAthensGeorgiaUSA
| |
Collapse
|
10
|
Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex. Proc Natl Acad Sci U S A 2021; 118:2112107118. [PMID: 34819376 DOI: 10.1073/pnas.2112107118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high-molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an odhA gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.
Collapse
|
11
|
Tüting C, Kyrilis FL, Müller J, Sorokina M, Skalidis I, Hamdi F, Sadian Y, Kastritis PL. Cryo-EM snapshots of a native lysate provide structural insights into a metabolon-embedded transacetylase reaction. Nat Commun 2021; 12:6933. [PMID: 34836937 PMCID: PMC8626477 DOI: 10.1038/s41467-021-27287-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Found across all kingdoms of life, 2-keto acid dehydrogenase complexes possess prominent metabolic roles and form major regulatory sites. Although their component structures are known, their higher-order organization is highly heterogeneous, not only across species or tissues but also even within a single cell. Here, we report a cryo-EM structure of the fully active Chaetomium thermophilum pyruvate dehydrogenase complex (PDHc) core scaffold at 3.85 Å resolution (FSC = 0.143) from native cell extracts. By combining cryo-EM with macromolecular docking and molecular dynamics simulations, we resolve all PDHc core scaffold interfaces and dissect the residing transacetylase reaction. Electrostatics attract the lipoyl domain to the transacetylase active site and stabilize the coenzyme A, while apolar interactions position the lipoate in its binding cleft. Our results have direct implications on the structural determinants of the transacetylase reaction and the role of flexible regions in the context of the overall 10 MDa PDHc metabolon architecture.
Collapse
Affiliation(s)
- Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Johannes Müller
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Marija Sorokina
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- RGCC International GmbH, Baarerstrasse 95, Zug, 6300, Switzerland
- BioSolutions GmbH Weinbergweg 22, 06120, Halle/Saale, Germany
| | - Ioannis Skalidis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Yashar Sadian
- Bioimaging Center (cryoGEnic), Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
| |
Collapse
|
12
|
Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nat Commun 2021; 12:5277. [PMID: 34489474 PMCID: PMC8421416 DOI: 10.1038/s41467-021-25570-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site.
Collapse
Affiliation(s)
- Jana Škerlová
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Berndtsson
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hendrik Nolte
- grid.419502.b0000 0004 0373 6590Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Martin Ott
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Pål Stenmark
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden
| |
Collapse
|
13
|
Nemeria NS, Zhang X, Leandro J, Zhou J, Yang L, Houten SM, Jordan F. Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes. Life (Basel) 2021; 11:407. [PMID: 33946784 PMCID: PMC8146983 DOI: 10.3390/life11050407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022] Open
Abstract
The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the tricarboxylic acid (TCA) cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxoacid dehydrogenase complexes, their function and regulation.
Collapse
Affiliation(s)
- Natalia S. Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Xu Zhang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Joao Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.L.); (S.M.H.)
| | - Jieyu Zhou
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Luying Yang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.L.); (S.M.H.)
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| |
Collapse
|
14
|
Nagy B, Polak M, Ozohanics O, Zambo Z, Szabo E, Hubert A, Jordan F, Novaček J, Adam-Vizi V, Ambrus A. Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure. Biochim Biophys Acta Gen Subj 2021; 1865:129889. [PMID: 33684457 DOI: 10.1016/j.bbagen.2021.129889] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/05/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers. METHODS We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling. RESULTS We report the 2.9 Å resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc. CONCLUSIONS The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly. GENERAL SIGNIFICANCE The revealed structural information will support the future pharmacologically targeting of the hKGDHc.
Collapse
Affiliation(s)
- Balint Nagy
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Martin Polak
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsofia Zambo
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Eszter Szabo
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Agnes Hubert
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Jiří Novaček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vera Adam-Vizi
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
15
|
Kyrilis FL, Semchonok DA, Skalidis I, Tüting C, Hamdi F, O'Reilly FJ, Rappsilber J, Kastritis PL. Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Cell Rep 2021; 34:108727. [PMID: 33567276 DOI: 10.1016/j.celrep.2021.108727] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 12/29/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) is a giant enzymatic assembly involved in pyruvate oxidation. PDHc components have been characterized in isolation, but the complex's quaternary structure has remained elusive due to sheer size, heterogeneity, and plasticity. Here, we identify fully assembled Chaetomium thermophilum α-keto acid dehydrogenase complexes in native cell extracts and characterize their domain arrangements utilizing mass spectrometry, activity assays, crosslinking, electron microscopy (EM), and computational modeling. We report the cryo-EM structure of the PDHc core and observe unique features of the previously unknown native state. The asymmetric reconstruction of the 10-MDa PDHc resolves spatial proximity of its components, agrees with stoichiometric data (60 E2p:12 E3BP:∼20 E1p: ≤ 12 E3), and proposes a minimum reaction path among component enzymes. The PDHc shows the presence of a dynamic pyruvate oxidation compartment, organized by core and peripheral protein species. Our data provide a framework for further understanding PDHc and α-keto acid dehydrogenase complex structure and function.
Collapse
Affiliation(s)
- Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Ioannis Skalidis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany; Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
| |
Collapse
|
16
|
Forsberg BO, Aibara S, Howard RJ, Mortezaei N, Lindahl E. Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex. Nat Commun 2020; 11:4667. [PMID: 32938938 PMCID: PMC7494870 DOI: 10.1038/s41467-020-18401-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/20/2020] [Indexed: 11/21/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC. The pyruvate dehydrogenase complex (PDC) is a multienzyme complex connecting glycolysis to mitochondrial oxidation of pyruvate. Cryo-EM analysis of PDC from Neurospora crassa reveals localization of fungi-specific protein X (PX) and confirms that it functions like the mammalian E3BP, recruiting the E3 component of PDC.
Collapse
Affiliation(s)
- B O Forsberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165, Solna, Sweden
| | - S Aibara
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165, Solna, Sweden.,Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - R J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165, Solna, Sweden
| | - N Mortezaei
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165, Solna, Sweden.,Vironova AB, 11330, Stockholm, Sweden
| | - E Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165, Solna, Sweden. .,Department of Applied Physics, Swedish eScience Research Center, KTH Royal Institute of Technology, 17168, Solna, Sweden.
| |
Collapse
|
17
|
Sun WH, Wu BB, Wang YQ, Wu MY, Dong XR, Zhang YP, Lu W, Zhang P, Yang B, Zhang M, Wu HJ, Zhou WH. Identification of eight novel mutations in 11 Chinese patients with maple syrup urine disease. World J Pediatr 2020; 16:401-410. [PMID: 32193832 DOI: 10.1007/s12519-020-00349-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/18/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Maple syrup urine disease (MSUD) is an autosomal recessive inherited disorder that affects the degradation of branched-chain amino acids and is associated with acute and chronic brain dysfunction. This study presents 11 new patients with MSUD and describes the clinical characteristics and gene mutations reported in Chinese individuals. METHODS During 2011-2018, 11 pedaitric patients with MSUD from 11 Chinese families were analyzed based on clinical characteristics and mass spectrometry, with confirmation via gene sequencing. Novel mutations affecting protein function were predicted with Mutation-Taster, PolyPhen-2, CADD and SIFT software. 3D models of the mutated proteins were generated by using the SWISS-MODEL online server, and the models were visualized in PyMOL. The characteristics and gene mutations in patients with MSUD were analyzed retrospectively. RESULTS Seventeen mutations in the BCKDHA, BCKDHB and DBT genes were found, 8 of which are novel: c.55C>/T, c.349C>T, c.565C>T, c.808G>A, c.859C>G, and c.1270dupC in BCKDHA; c.275-2A>G in BCKDHB; and c.1291C>T in DBT. Eight patients died. Two patients had severe mental retardation and were physically handicapped. One patient with the intermediate type had relatively good prognosis, with mild psychomotor retardation and adiposity. Four mothers underwent amniocentesis for prenatal diagnosis during their second pregnancy; two fetuses were wild type, and two were carriers of one heterozygous mutation. CONCLUSIONS Eight novel mutations were associated with MSUD in Chinese patients. Prenatal diagnosis was successfully performed by genetic analysis. Mutations in the BCKDHB gene were found in the majority of Chinese patients with MSUD.
Collapse
Affiliation(s)
- Wei-Hua Sun
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
| | - Bing-Bing Wu
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ya-Qiong Wang
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
| | - Meng-Yuan Wu
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
| | - Xin-Ran Dong
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
| | - Yue-Ping Zhang
- Shanghai Ji-ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Wei Lu
- Department of Endocrinology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ping Zhang
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
| | - Bin Yang
- Department of Radiology, Children's Hospital of Shanghai, Shanghai, 201102, China
| | - Min Zhang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Hong-Jiang Wu
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China
| | - Wen-Hao Zhou
- Institute of Pediatrics, Shanghai Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Wanyuan Road 399, Shanghai, 201102, China.
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, 201102, China.
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, Shanghai, 201102, China.
| |
Collapse
|
18
|
Bezerra GA, Foster WR, Bailey HJ, Hicks KG, Sauer SW, Dimitrov B, McCorvie TJ, Okun JG, Rutter J, Kölker S, Yue WW. Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. IUCRJ 2020; 7:693-706. [PMID: 32695416 PMCID: PMC7340257 DOI: 10.1107/s205225252000696x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/22/2020] [Indexed: 05/05/2023]
Abstract
DHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de-hydrogenases. In complex with E2 (di-hydro-lipo-amide succinyltransferase, DLST) and E3 (dihydrolipo-amide de-hydrogenase, DLD) components, DHTKD1 is involved in lysine and tryptophan catabolism by catalysing the oxidative de-carboxyl-ation of 2-oxoadipate (2OA) in mitochondria. Here, the 1.9 Å resolution crystal structure of human DHTKD1 is solved in complex with the thi-amine diphosphate co-factor. The structure reveals how the DHTKD1 active site is modelled upon the well characterized homologue 2-oxoglutarate (2OG) de-hydrogenase but engineered specifically to accommodate its preference for the longer substrate of 2OA over 2OG. A 4.7 Å resolution reconstruction of the human DLST catalytic core is also generated by single-particle electron microscopy, revealing a 24-mer cubic scaffold for assembling DHTKD1 and DLD protomers into a megacomplex. It is further demonstrated that missense DHTKD1 variants causing the inborn error of 2-amino-adipic and 2-oxoadipic aciduria impact on the complex formation, either directly by disrupting the interaction with DLST, or indirectly through destabilizing the DHTKD1 protein. This study provides the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism.
Collapse
Affiliation(s)
- Gustavo A. Bezerra
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - William R. Foster
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Henry J. Bailey
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Kevin G. Hicks
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Sven W. Sauer
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Bianca Dimitrov
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Thomas J. McCorvie
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Jürgen G. Okun
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Wyatt W. Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| |
Collapse
|
19
|
Yang C, Linpeng S, Cao Y, Wu L. Identification of six novel mutations in five infants with suspected maple syrup urine disease based on blood and urine metabolism screening. Gene 2019; 710:9-16. [PMID: 31112740 DOI: 10.1016/j.gene.2019.04.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/09/2019] [Accepted: 04/30/2019] [Indexed: 11/18/2022]
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive genetic metabolic disease, with a high incidence rate in infants. We analyzed the data of molecular genetic analysis of five infants whose metabolism screening suspected MSUD and described their clinical symptoms. Further, we performed next-generation sequencing and Sanger sequencing to determine the genetic causes of the disease. Bioinformatics tools were used to predict the pathogenicity of novel mutations by performing structural modeling. All the five infants showed symptoms before one year of age and had elevated plasma leucine and valine levels. Among them, four infants presented an obvious increase in the urine lactic acid level. We identified the genetic cause of the disease in four infants and analyzed the pathogenicity of six novel mutations, viz., two mutations in BCKDHA (p.Gly180Asp and p.Arg265Gln), three in BCKDHB (p.Tyr169Cys, p.Ala331Thr, and p.Gly336Ser), and one in DBT (p.Leu69Arg), using in silico analysis. We also reviewed previously reported mutations in Chinese patients and summarized their genotypic and phenotypic characteristics. Our study has confirmed or corrected the clinical diagnosis and enriched the mutation spectrum of BCKDHA, BCKDHB, and DBT. We suggest blood and urine metabolism screening combined with next generation sequencing to diagnose MSUD, especially in infants, to achieve early diagnosis and early treatment.
Collapse
Affiliation(s)
- Chenxi Yang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Siyuan Linpeng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yingxi Cao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lingqian Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
| |
Collapse
|
20
|
Prajapati S, Haselbach D, Wittig S, Patel MS, Chari A, Schmidt C, Stark H, Tittmann K. Structural and Functional Analyses of the Human PDH Complex Suggest a "Division-of-Labor" Mechanism by Local E1 and E3 Clusters. Structure 2019; 27:1124-1136.e4. [PMID: 31130485 DOI: 10.1016/j.str.2019.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 01/17/2019] [Accepted: 04/11/2019] [Indexed: 11/27/2022]
Abstract
The pseudo-atomic structural model of human pyruvate dehydrogenase complex (PDHc) core composed of full-length E2 and E3BP components, calculated from our cryoelectron microscopy-derived density maps at 6-Å resolution, is similar to those of prokaryotic E2 structures. The spatial organization of human PDHc components as evidenced by negative-staining electron microscopy and native mass spectrometry is not homogeneous, and entails the unanticipated formation of local clusters of E1:E2 and E3BP:E3 complexes. Such uneven, clustered organization translates into specific duties for E1-E2 clusters (oxidative decarboxylation and acetyl transfer) and E3BP-E3 clusters (regeneration of reduced lipoamide) corresponding to half-reactions of the PDHc catalytic cycle. The addition of substrate coenzyme A modulates the conformational landscape of PDHc, in particular of the lipoyl domains, extending the postulated multiple random coupling mechanism. The conformational and associated chemical landscapes of PDHc are thus not determined entirely stochastically, but are restrained and channeled through an asymmetric architecture and further modulated by substrate binding.
Collapse
Affiliation(s)
- Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany; Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Haselbach
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sabine Wittig
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany
| | - Mulchand S Patel
- Jacobs School of Medicine and Biomedical Sciences, Department of Biochemistry, University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany.
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany; Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany.
| |
Collapse
|
21
|
Ali EZ, Ngu LH. Fourteen new mutations of BCKDHA, BCKDHB and DBT genes associated with maple syrup urine disease (MSUD) in Malaysian population. Mol Genet Metab Rep 2018; 17:22-30. [PMID: 30228974 PMCID: PMC6140420 DOI: 10.1016/j.ymgmr.2018.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022] Open
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive metabolic disorder. This disorder is usually caused by mutations in any one of the genes; BCKDHA, BCKDHB and DBT, which represent E1α, E1β and E2 subunits of the branched-chain α-keto acid dehydrogenase (BCKDH) complex, respectively. This study presents the molecular characterization of 31 MSUD patients. Twenty one mutations including 14 new mutations were identified. The BCKDHB gene was the most commonly affected (45.2%) compared to BCKDHA gene (16.1%) and DBT gene (38.7%). In silico webservers predicted all mutations were disease-causing. In addition, structural evaluation disclosed that all new missenses in BCKDHA, BCKDHB and DBT genes affected stability and formation of E1 and E2 subunits. Majority of the patients had neonatal onset MSUD (26 of 31). Meanwhile, the new mutation; c.1196C > G (p.S399C) in DBT gene was noted to be recurrent and found in 9 patients. Conclusion: Our findings have expanded the mutational spectrum of the MSUD and revealed the genetic heterogeneity among Malaysian MSUD patients. We also discovered the p.S399C from DBT gene was noted as a recurrent mutation in Malay community and it suggested the existence of common and unique mutation in Malay population.
Collapse
Affiliation(s)
- Ernie Zuraida Ali
- Molecular Diagnostics and Protein Unit, Specialized Diagnostics Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Lock-Hock Ngu
- Medical Genetics Department, Kuala Lumpur Hospital, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| |
Collapse
|
22
|
Chakraborty J, Nemeria NS, Farinas E, Jordan F. Catalysis of transthiolacylation in the active centers of dihydrolipoamide acyltransacetylase components of 2-oxo acid dehydrogenase complexes. FEBS Open Bio 2018; 8:880-896. [PMID: 29928569 PMCID: PMC5986005 DOI: 10.1002/2211-5463.12431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli 2‐oxoglutarate dehydrogenase complex (OGDHc) comprises multiple copies of three enzymes—E1o, E2o, and E3—and transthioesterification takes place within the catalytic domain of E2o. The succinyl group from the thiol ester of S8‐succinyldihydrolipoyl‐E2o is transferred to the thiol group of coenzyme A (CoA), forming the all‐important succinyl‐CoA. Here, we report mechanistic studies of enzymatic transthioesterification on OGDHc. Evidence is provided for the importance of His375 and Asp374 in E2o for the succinyl transfer reaction. The magnitude of the rate acceleration provided by these residues (54‐fold from each with alanine substitution) suggests a role in stabilization of the symmetrical tetrahedral oxyanionic intermediate by formation of two hydrogen bonds, rather than in acid–base catalysis. Further evidence ruling out a role in acid–base catalysis is provided by site‐saturation mutagenesis studies at His375 (His375Trp substitution with little penalty) and substitutions to other potential hydrogen bond participants at Asp374. Taking into account that the rate constant for reductive succinylation of the E2o lipoyl domain (LDo) by E1o and 2‐oxoglutarate (99 s−1) was approximately twofold larger than the rate constant for kcat of 48 s−1 for the overall reaction (NADH production), it could be concluded that succinyl transfer to CoA and release of succinyl‐CoA, rather than reductive succinylation, is the rate‐limiting step. The results suggest a revised mechanism of catalysis for acyl transfer in the superfamily of 2‐oxo acid dehydrogenase complexes, thus provide fundamental information regarding acyl‐CoA formation, so important for several biological processes including post‐translational succinylation of protein lysines. Enzymes 2‐oxoglutarate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/4/2.html); dihydrolipoamide succinyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/61.html); dihydrolipoamide dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/8/1/4.html); pyruvate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/4/1.html); dihydrolipoamide acetyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/12.html).
Collapse
Affiliation(s)
- Joydeep Chakraborty
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark NJ USA
| | | | - Edgardo Farinas
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark NJ USA
| | - Frank Jordan
- Department of Chemistry Rutgers University Newark NJ USA
| |
Collapse
|
23
|
Jiang J, Baiesc FL, Hiromasa Y, Yu X, Hui WH, Dai X, Roche TE, Zhou ZH. Atomic Structure of the E2 Inner Core of Human Pyruvate Dehydrogenase Complex. Biochemistry 2018; 57:2325-2334. [PMID: 29608861 DOI: 10.1021/acs.biochem.8b00357] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pyruvate dehydrogenase complex (PDC) is a large multienzyme complex that catalyzes the irreversible conversion of pyruvate to acetyl-coenzyme A with reduction of NAD+. Distinctive from PDCs in lower forms of life, in mammalian PDC, dihydrolipoyl acetyltransferase (E2; E2p in PDC) and dihydrolipoamide dehydrogenase binding protein (E3BP) combine to form a complex that plays a central role in the organization, regulation, and integration of catalytic reactions of PDC. However, the atomic structure and organization of the mammalian E2p/E3BP heterocomplex are unknown. Here, we report the structure of the recombinant dodecahedral core formed by the C-terminal inner-core/catalytic (IC) domain of human E2p determined at 3.1 Å resolution by cryo electron microscopy (cryoEM). The structure of the N-terminal fragment and four other surface areas of the human E2p IC domain exhibit significant differences from those of the other E2 crystal structures, which may have implications for the integration of E3BP in mammals. This structure also allowed us to obtain a homology model for the highly homologous IC domain of E3BP. Analysis of the interactions of human E2p or E3BP with their adjacent IC domains in the dodecahedron provides new insights into the organization of the E2p/E3BP heterocomplex and suggests a potential contribution by E3BP to catalysis in mammalian PDC.
Collapse
Affiliation(s)
- Jiansen Jiang
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Flavius L Baiesc
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Yasuaki Hiromasa
- Faculty of Agriculture, Attached Promotive Center for International Education and Research of Agriculture , Kyushu University , Fukuoka 812-8581 , Japan.,Department of Biochemistry and Molecular Biophysics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Wong Hoi Hui
- California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Xinghong Dai
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Thomas E Roche
- Department of Biochemistry and Molecular Biophysics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| |
Collapse
|
24
|
Solmonson A, DeBerardinis RJ. Lipoic acid metabolism and mitochondrial redox regulation. J Biol Chem 2017; 293:7522-7530. [PMID: 29191830 DOI: 10.1074/jbc.tm117.000259] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Lipoic acid is an essential cofactor for mitochondrial metabolism and is synthesized de novo using intermediates from mitochondrial fatty-acid synthesis type II, S-adenosylmethionine and iron-sulfur clusters. This cofactor is required for catalysis by multiple mitochondrial 2-ketoacid dehydrogenase complexes, including pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and branched-chain ketoacid dehydrogenase. Lipoic acid also plays a critical role in stabilizing and regulating these multienzyme complexes. Many of these dehydrogenases are regulated by reactive oxygen species, mediated through the disulfide bond of the prosthetic lipoyl moiety. Collectively, its functions explain why lipoic acid is required for cell growth, mitochondrial activity, and coordination of fuel metabolism.
Collapse
Affiliation(s)
- Ashley Solmonson
- From the Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Ralph J DeBerardinis
- From the Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| |
Collapse
|
25
|
|
26
|
Smith CA, Toth M, Weiss TM, Frase H, Vakulenko SB. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2754-64. [PMID: 25286858 PMCID: PMC4188014 DOI: 10.1107/s1399004714017635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/31/2014] [Indexed: 11/11/2022]
Abstract
Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and enterococcal pathogens is primarily conferred by the bifunctional enzyme AAC(6')-Ie-APH(2'')-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6')-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2'')-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2'')-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6')-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6')-Ie enzyme is joined to APH(2'')-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2'')-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6')-Ie-APH(2'')-Ia enzyme.
Collapse
Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
27
|
Wang J, Nemeria NS, Chandrasekhar K, Kumaran S, Arjunan P, Reynolds S, Calero G, Brukh R, Kakalis L, Furey W, Jordan F. Structure and function of the catalytic domain of the dihydrolipoyl acetyltransferase component in Escherichia coli pyruvate dehydrogenase complex. J Biol Chem 2014; 289:15215-30. [PMID: 24742683 DOI: 10.1074/jbc.m113.544080] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The Escherichia coli pyruvate dehydrogenase complex (PDHc) catalyzing conversion of pyruvate to acetyl-CoA comprises three components: E1p, E2p, and E3. The E2p is the five-domain core component, consisting of three tandem lipoyl domains (LDs), a peripheral subunit binding domain (PSBD), and a catalytic domain (E2pCD). Herein are reported the following. 1) The x-ray structure of E2pCD revealed both intra- and intertrimer interactions, similar to those reported for other E2pCDs. 2) Reconstitution of recombinant LD and E2pCD with E1p and E3p into PDHc could maintain at least 6.4% activity (NADH production), confirming the functional competence of the E2pCD and active center coupling among E1p, LD, E2pCD, and E3 even in the absence of PSBD and of a covalent link between domains within E2p. 3) Direct acetyl transfer between LD and coenzyme A catalyzed by E2pCD was observed with a rate constant of 199 s(-1), comparable with the rate of NADH production in the PDHc reaction. Hence, neither reductive acetylation of E2p nor acetyl transfer within E2p is rate-limiting. 4) An unprecedented finding is that although no interaction could be detected between E1p and E2pCD by itself, a domain-induced interaction was identified on E1p active centers upon assembly with E2p and C-terminally truncated E2p proteins by hydrogen/deuterium exchange mass spectrometry. The inclusion of each additional domain of E2p strengthened the interaction with E1p, and the interaction was strongest with intact E2p. E2p domain-induced changes at the E1p active site were also manifested by the appearance of a circular dichroism band characteristic of the canonical 4'-aminopyrimidine tautomer of bound thiamin diphosphate (AP).
Collapse
Affiliation(s)
- Junjie Wang
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Natalia S Nemeria
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Krishnamoorthy Chandrasekhar
- the Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Sowmini Kumaran
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Palaniappa Arjunan
- the Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Shelley Reynolds
- the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Guillermo Calero
- the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Roman Brukh
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Lazaros Kakalis
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - William Furey
- the Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, the Veterans Affairs Medical Center, Pittsburgh, Pennsylvania 15240, and
| | - Frank Jordan
- From the Department of Chemistry, Rutgers University, Newark, New Jersey 07102,
| |
Collapse
|
28
|
Jaafar N, Moleirinho A, Kerkeni E, Monastiri K, Seboui H, Amorim A, Prata MJ, Quental S. Molecular characterization of maple syrup urine disease patients from Tunisia. Gene 2013; 517:116-9. [PMID: 23313820 DOI: 10.1016/j.gene.2012.12.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 11/30/2012] [Accepted: 12/14/2012] [Indexed: 11/30/2022]
Abstract
Maple syrup urine disease (MSUD) is a rare disorder of branched-chain amino acids (BCAA) metabolism caused by the defective function of branched-chain α-ketoacid dehydrogenase complex (BCKD). The disease causal mutations can occur either in BCKDHA, BCKDHB or DBT genes encoding respectively the E1α, E1β and E2 subunits of the complex. In this study we report the molecular characterization of 3 Tunisian patients with the classic form of MSUD. Two novel putative mutations have been identified: the alteration c.716A>G (p.Glu239Gly) in BCKDHB and a small deletion (c.1333_1336delAATG; p.Asn445X) detected in DBT gene.
Collapse
Affiliation(s)
- N Jaafar
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Zhang T, Jia X, Zhuo Y, Liu M, Gao H, Liu J, Zhang L. Cloning and characterization of a novel 2-ketoisovalerate reductase from the beauvericin producer Fusarium proliferatum LF061. BMC Biotechnol 2012; 12:55. [PMID: 22916830 PMCID: PMC3478992 DOI: 10.1186/1472-6750-12-55] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/15/2012] [Indexed: 11/21/2022] Open
Abstract
Background The ketoisovalerate reductase (EC 1.2.7.7 ) is required for the formation of beauvericin via the nonribosomal peptide synthetase biosynthetic pathway. It catalyzes the NADPH-specific reduction of ketoisovaleric acid to hydroxyisovalerate. However, little is known about the bioinformatics’ data about the 2-Kiv reductase in Fusarium. To date, heterologous production of the gene KivRFp from Fusarium has not been achieved. Results The KivRFp gene was subcloned and expressed in Escherichia coli BL21 using the pET expression system. The gene KivRFp contained a 1,359 bp open reading frame (ORF) encoding a polypeptide of 452 amino acids with a molecular mass of 52 kDa. Sequence analysis indicated that it showed 61% and 52% amino acid identities to ketoisovalerate reductase from Beauveria bassiana ATCC 7159 (ACI30654) and Metarhizium acridum CQMa 102 (EFY89891), respectively; and several conserved regions were identified, including the putative nucleotide-binding signature site, GXGXXG, a catalytic triad (Glu405, Asn184, and Lys285). The KivRFp exhibited the highest activity at 35°C and pH 7.5 respectively, by reduction of ketoisovalerate. It also exhibited the high level of stability over wide temperature and pH spectra and in the presence of metal ions or detergents. Conclusions A new ketoisovalerate reductase KivRFp was identified and characterized from the depsipeptide-producing fungus F. proliferatum. KivRFp has been shown to have useful properties, such as moderate thermal stability and broad pH optima, and may serve as the starting points for future protein engineering and directed evolution, towards the goal of developing efficient enzyme for downstream biotechnological applications.
Collapse
Affiliation(s)
- Tao Zhang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Bei'er Tiao Road, Zhongguancun Haidian District, Beijing 100190, China
| | | | | | | | | | | | | |
Collapse
|
30
|
Yang N, Han L, Gu X, Ye J, Qiu W, Zhang H, Gong Z, Zhang Y. Analysis of gene mutations in Chinese patients with maple syrup urine disease. Mol Genet Metab 2012; 106:412-8. [PMID: 22727569 DOI: 10.1016/j.ymgme.2012.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 05/29/2012] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Maple syrup urine disease (MSUD) is predominantly caused by mutations in the BCKDHA, BCKDHB and DBT genes, which encode for the E1α, E1β and E2 subunits of the branched-chain α-keto acid dehydrogenase complex, respectively. The aim of this study was to screen DNA samples from 16 Chinese MSUD patients and assess a potential correlation between genotype and phenotype. METHODS BCKDHA, BCKDHB and DBT genes were analyzed by polymerase chain reaction (PCR) and direct sequencing. Segments bearing novel mutations were identified by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. RESULTS Within the variant alleles, 28 mutations (28/32, 87.5%), were detected in 15 patients, while one patient displayed no mutations. Mutations were comprised of 20 different: 6 BCKDHA gene mutations in 4 cases, 10 BCKDHB gene mutations in 8 cases and 4 DBT gene mutations in 3 cases. From these, 14 were novel, which included 3 mutations in the BCKDHA gene, 7 in the BCKDHB gene and 4 in the DBT gene. Only two patients with mutations in the BCKDHB and DBT genes were thiamine-responsive and presented a better clinical outcome. CONCLUSION We identified 20 different mutations within the BCKDHA, BCKDHB and DBT genes among 16 Chinese MSUD patients, including 14 novel mutations. The majority were non-responsive to thiamine, associating with a worse clinical outcome. Our data provide the basis for further genotype-phenotype correlation studies in these patients, which will be beneficial for early diagnosis and in directing the approach to clinical intervention.
Collapse
Affiliation(s)
- Nan Yang
- Department of Pediatric Endocrinology, Genetic and Metabolic Disease, Shanghai Institute of Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Wynn RM, Li J, Brautigam CA, Chuang JL, Chuang DT. Structural and biochemical characterization of human mitochondrial branched-chain α-ketoacid dehydrogenase phosphatase. J Biol Chem 2012; 287:9178-92. [PMID: 22291014 DOI: 10.1074/jbc.m111.314963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The branched-chain α-ketoacid dehydrogenase phosphatase (BDP) component of the human branched-chain α-ketoacid dehydrogenase complex (BCKDC) has been expressed in Escherichia coli and purified in the soluble form. The monomeric BDP shows a strict dependence on Mn(2+) ions for phosphatase activity, whereas Mg(2+) and Ca(2+) ions do not support catalysis. Metal binding constants for BDP, determined by competition isothermal titration calorimetry, are 2.4 nm and 10 μm for Mn(2+) and Mg(2+) ions, respectively. Using the phosphorylated decarboxylase component (p-E1b) of BCKDC as a substrate, BDP shows a specific activity of 68 nmol/min/mg. The Ca(2+)-independent binding of BDP to the 24-meric transacylase (dihydrolipoyl transacylase; E2b) core of BCKDC results in a 3-fold increase in the dephosphorylation rate of p-E1b. However, the lipoyl prosthetic group on E2b is not essential for BDP binding or E2b-stimulated phosphatase activity. Acidic residues in the C-terminal linker of the E2b lipoyl domain are essential for the interaction between BDP and E2b. The BDP structure was determined by x-ray crystallography to 2.4 Å resolution. The BDP structure is dominated by a central β-sandwich. There are two protrusions forming a narrow cleft ∼10 Å wide, which constitutes the active site. The carboxylate moieties of acidic residues Asp-109, Asp-207, Asp-298, and Asp-337 in the active-site cleft participate in binding two metal ions. Substitutions of these residues with alanine nullify BDP phosphatase activity. Alteration of the nearby Arg-104 increases the K(m) for p-E1b peptide by 60-fold, suggesting that this residue is critical for the recognition of the native p-E1b protein.
Collapse
Affiliation(s)
- R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9038, USA.
| | | | | | | | | |
Collapse
|
32
|
Brunetti-Pierri N, Lanpher B, Erez A, Ananieva EA, Islam M, Marini JC, Sun Q, Yu C, Hegde M, Li J, Wynn RM, Chuang DT, Hutson S, Lee B. Phenylbutyrate therapy for maple syrup urine disease. Hum Mol Genet 2010; 20:631-40. [PMID: 21098507 DOI: 10.1093/hmg/ddq507] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Therapy with sodium phenylacetate/benzoate or sodium phenylbutyrate in urea cycle disorder patients has been associated with a selective reduction in branched-chain amino acids (BCAA) in spite of adequate dietary protein intake. Based on this clinical observation, we investigated the potential of phenylbutyrate treatment to lower BCAA and their corresponding α-keto acids (BCKA) in patients with classic and variant late-onset forms of maple syrup urine disease (MSUD). We also performed in vitro and in vivo experiments to elucidate the mechanism for this effect. We found that BCAA and BCKA are both significantly reduced following phenylbutyrate therapy in control subjects and in patients with late-onset, intermediate MSUD. In vitro treatment with phenylbutyrate of control fibroblasts and lymphoblasts resulted in an increase in the residual enzyme activity, while treatment of MSUD cells resulted in the variable response which did not simply predict the biochemical response in the patients. In vivo phenylbutyrate increases the proportion of active hepatic enzyme and unphosphorylated form over the inactive phosphorylated form of the E1α subunit of the branched-chain α-keto acid dehydrogenase complex (BCKDC). Using recombinant enzymes, we show that phenylbutyrate prevents phosphorylation of E1α by inhibition of the BCKDC kinase to activate BCKDC overall activity, providing a molecular explanation for the effect of phenylbutyrate in a subset of MSUD patients. Phenylbutyrate treatment may be a valuable treatment for reducing the plasma levels of neurotoxic BCAA and their corresponding BCKA in a subset of MSUD patients and studies of its long-term efficacy are indicated.
Collapse
Affiliation(s)
- Nicola Brunetti-Pierri
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Brodtkorb E, Strand J, Backe PH, Lund AM, Bjørås M, Rootwelt T, Rootwelt H, Woldseth B, Eide L. Four novel mutations identified in Norwegian patients result in intermittent maple syrup urine disease when combined with the R301C mutation. Mol Genet Metab 2010; 100:324-32. [PMID: 20570198 DOI: 10.1016/j.ymgme.2010.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 04/26/2010] [Indexed: 01/03/2023]
Abstract
Maple syrup urine disease (MSUD) is caused by a defect in branched chain alpha-ketoacid dehydrogenase complex (BCKD), an essential metabolon for the catabolism of the branched chain amino acids. Here, we report four novel mutations in the DBT gene, encoding the transacylase subunit (E2) of BCKD, resulting in intermittent MSUD in seven Norwegian patients. The patients had episodes with neurological symptoms including lethargy and/or ataxia during childhood infections. All seven patients were heterozygous for the annotated R301C mutation. The second allelic mutations were identified in five patients; one nonsense mutation (G62X), two missense mutations (W84C and R376C) and a mutation in the 3' untranslated region (UTR; c. *358A>C) in two patients. These four novel mutations result in near depletion of E2 protein, and the common R301C protein contributes predominantly to the residual (14%) cellular BCKD activity. Structural analyses of the mutations implied that the W84C and R376C mutations affect stability of intramolecular domains in E2, while the R301C mutation likely disturbs E2 trimer assembly as previously reported. The UTR mutated allele coincided with a strong reduction in mRNA levels, as did the non-R301C specific allele in two patients where the second mutation could not be identified. In summary, the pathogenic effect of the novel mutations is depletion of cellular protein, and the intermittent form of MSUD appears to be attributed to the residual R301C mutant protein in these patients.
Collapse
Affiliation(s)
- Else Brodtkorb
- Institute of Clinical Biochemistry, Institute of Clinical Medicine, University of Oslo, Centre of Molecular Biology and Neuroscience, Sognsvannsveien 20, Oslo, Norway
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Xin Y, Gadda G, Hamelberg D. The Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase. Biochemistry 2009; 48:9599-605. [DOI: 10.1021/bi901295a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Giovanni Gadda
- Department of Chemistry
- Department of Biology
- The Center for Biotechnology and Drug Design
| | - Donald Hamelberg
- Department of Chemistry
- The Center for Biotechnology and Drug Design
| |
Collapse
|
35
|
Quental S, Macedo-Ribeiro S, Matos R, Vilarinho L, Martins E, Teles EL, Rodrigues E, Diogo L, Garcia P, Eusébio F, Gaspar A, Sequeira S, Furtado F, Lança I, Amorim A, Prata MJ. Molecular and structural analyses of maple syrup urine disease and identification of a founder mutation in a Portuguese Gypsy community. Mol Genet Metab 2008; 94:148-56. [PMID: 18378174 DOI: 10.1016/j.ymgme.2008.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 02/14/2008] [Indexed: 11/23/2022]
Abstract
Maple syrup urine disease (MSUD) is an autosomal recessive disorder, caused by the defective function of the branched-chain alpha-ketoacid dehydrogenase complex (BCKD). BCKD is a mitochondrial complex, encoded by four nuclear genes (BCKDHA, BCKDHB, DBT and DLD), involved in the metabolism of branched-chain amino acids (BCAAs). Since the MSUD mutational spectrum has not been previously assessed in Portugal, in this study we present the molecular characterization of 30 MSUD Portuguese patients. Seventeen putative mutations have been identified (six in BCKDHA, five in BCKDHB and six in DBT); seven of them are here described for the first time. The most common mutation identified was a C deletion in BCKDHA gene (c.117delC; p.R40GfsX23), already reported in the Spanish population. Interestingly, it was found in all patients of a Gypsy community from South of the country, so a founder effect is probably responsible for the high incidence of the disease in this community. Structural models of MSUD missense mutations have been performed to understand their pathogenic effect, in order to elucidate and often to predict the severity of a mutation clinical consequence.
Collapse
Affiliation(s)
- Sofia Quental
- IPATIMUP-Institute of Pathology and Molecular Immunology of University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Structures of the human pyruvate dehydrogenase complex cores: a highly conserved catalytic center with flexible N-terminal domains. Structure 2008; 16:104-14. [PMID: 18184588 DOI: 10.1016/j.str.2007.10.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2007] [Revised: 10/09/2007] [Accepted: 10/27/2007] [Indexed: 11/21/2022]
Abstract
Dihydrolipoyl acetyltransferase (E2) is the central component of pyruvate dehydrogenase complex (PDC), which converts pyruvate to acetyl-CoA. Structural comparison by cryo-electron microscopy (cryo-EM) of the human full-length and truncated E2 (tE2) cores revealed flexible linkers emanating from the edges of trimers of the internal catalytic domains. Using the secondary structure constraints revealed in our 8 A cryo-EM reconstruction and the prokaryotic tE2 atomic structure as a template, we derived a pseudo atomic model of human tE2. The active sites are conserved between prokaryotic tE2 and human tE2. However, marked structural differences are apparent in the hairpin domain and in the N-terminal helix connected to the flexible linker. These permutations away from the catalytic center likely impart structures needed to integrate a second component into the inner core and provide a sturdy base for the linker that holds the pyruvate dehydrogenase for access by the E2-bound regulatory kinase/phosphatase components in humans.
Collapse
|
37
|
Islam MM, Wallin R, Wynn RM, Conway M, Fujii H, Mobley JA, Chuang DT, Hutson SM. A novel branched-chain amino acid metabolon. Protein-protein interactions in a supramolecular complex. J Biol Chem 2007; 282:11893-903. [PMID: 17314104 DOI: 10.1074/jbc.m700198200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The catabolic pathways of branched-chain amino acids have two common steps. The first step is deamination catalyzed by the vitamin B(6)-dependent branched-chain aminotransferase isozymes (BCATs) to produce branched-chain alpha-keto acids (BCKAs). The second step is oxidative decarboxylation of the BCKAs mediated by the branched-chain alpha-keto acid dehydrogenase enzyme complex (BCKD complex). The BCKD complex is organized around a cubic core consisting of 24 lipoate-bearing dihydrolipoyl transacylase (E2) subunits, associated with the branched-chain alpha-keto acid decarboxylase/dehydrogenase (E1), dihydrolipoamide dehydrogenase (E3), BCKD kinase, and BCKD phosphatase. In this study, we provide evidence that human mitochondrial BCAT (hBCATm) associates with the E1 decarboxylase component of the rat or human BCKD complex with a K(D) of 2.8 microM. NADH dissociates the complex. The E2 and E3 components do not interact with hBCATm. In the presence of hBCATm, k(cat) values for E1-catalyzed decarboxylation of the BCKAs are enhanced 12-fold. Mutations of hBCATm proteins in the catalytically important CXXC center or E1 proteins in the phosphorylation loop residues prevent complex formation, indicating that these regions are important for the interaction between hBCATm and E1. Our results provide evidence for substrate channeling between hBCATm and BCKD complex and formation of a metabolic unit (termed branched-chain amino acid metabolon) that can be influenced by the redox state in mitochondria.
Collapse
Affiliation(s)
- Mohammad Mainul Islam
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
| | | | | | | | | | | | | | | |
Collapse
|