1
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Schaff H, Dey P, Heiss C, Keiser G, Moro TR, Azadi P, Patel P, Free SJ. Characterization of the need for galactofuranose during the Neurospora crassa life cycle. Fungal Genet Biol 2023; 168:103826. [PMID: 37541569 DOI: 10.1016/j.fgb.2023.103826] [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] [Received: 06/14/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Galactofuranose is a constituent of the cell walls of filamentous fungi. The galactofuranose can be found as a component of N-linked oligosaccharides, in O-linked oligosaccharides, in GPI-anchored galactomannan, and in free galactomannan. The Neurospora genome contains a single UDP-galactose mutase gene (ugm-1/NCU01824) and two UDP-galactofuranose translocases used to import UDP-galactofuranose into the lumen of the Golgi apparatus (ugt-1/NCU01826 and ugt-2/NCU01456). Our results demonstrate that loss of galactofuranose synthesis or its translocation into the lumen of the secretory pathway affects the morphology and growth rate of the vegetative hyphae, the production of conidia (asexual spores), and dramatically affects the sexual stages of the life cycle. In mutants that are unable to make galactofuranose or transport it into the lumen of the Golgi apparatus, ascospore development is aborted soon after fertilization and perithecium maturation is aborted prior to the formation of the neck and ostiole. The Neurospora genome contains three genes encoding possible galactofuranosyltransferases from the GT31 family of glycosyltransferases (gfs-1/NCU05878, gfs-2/NCU07762, and gfs-3/NCU02213) which might be involved in generating galactofuranose-containing oligosaccharide structures. Analysis of triple KO mutants in GT31 glycosyltransferases shows that these mutants have normal morphology, suggesting that these genes do not encode vital galactofuranosyltransferases.
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Affiliation(s)
- Hayden Schaff
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States
| | - Protyusha Dey
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States
| | - Christian Heiss
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Griffin Keiser
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Tatiana Rojo Moro
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Pavan Patel
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States
| | - Stephen J Free
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States.
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2
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Dozova N, Lacombat F, Lombard M, Hamdane D, Plaza P. Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX. Phys Chem Chem Phys 2021; 23:22692-22702. [PMID: 34605505 DOI: 10.1039/d1cp03379d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH-) as prosthetic group and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH- in ThyX is only mildly more constrained than that of free FADH- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH- photophysics to the constraints exerted by its immediate surroundings.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Pascal Plaza
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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3
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Gaber A, Pavšič M. Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches. Int J Mol Sci 2021; 22:9081. [PMID: 34445785 PMCID: PMC8396596 DOI: 10.3390/ijms22169081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
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4
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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5
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Valentino H, Campbell AC, Schuermann JP, Sultana N, Nam HG, LeBlanc S, Tanner JJ, Sobrado P. Structure and function of a flavin-dependent S-monooxygenase from garlic ( Allium sativum). J Biol Chem 2020; 295:11042-11055. [PMID: 32527723 DOI: 10.1074/jbc.ra120.014484] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/07/2020] [Indexed: 12/26/2022] Open
Abstract
Allicin is a component of the characteristic smell and flavor of garlic (Allium sativum). A flavin-containing monooxygenase (FMO) produced by A. sativum (AsFMO) was previously proposed to oxidize S-allyl-l-cysteine (SAC) to alliin, an allicin precursor. Here, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC; however, the enzyme was highly active with l-cysteine, N-acetyl-l-cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly (KD of ∼2 μm) to AsFMO and that the hydride transfer occurs with pro-R stereospecificity. We detected the formation of a long-wavelength band when AsFMO was reduced by NADPH, probably representing the formation of a charge-transfer complex. In the absence of substrate, the reduced enzyme, in complex with NADP+, reacted with oxygen and formed an intermediate with a spectrum characteristic of C4a-hydroperoxyflavin, which decays several orders of magnitude more slowly than the k cat The presence of substrate enhanced C4a-hydroperoxyflavin formation and, upon hydroxylation, oxidation occurred with a rate constant similar to the k cat The structure of AsFMO complexed with FAD at 2.08-Å resolution features two domains for binding of FAD and NADPH, representative of class B flavin monooxygenases. These biochemical and structural results are consistent with AsFMO being an S-monooxygenase involved in allicin biosynthesis through direct formation of sulfenic acid and not SAC oxidation.
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Affiliation(s)
- Hannah Valentino
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA.,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, USA
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jonathan P Schuermann
- Northeastern Collaborative Access Team, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Nazneen Sultana
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Han G Nam
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Sophie LeBlanc
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA .,Department of Chemistry, University of Missouri, Columbia, Missouri, USA
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA .,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, USA
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6
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Cossio-Pérez R, Pierdominici-Sottile G, Sobrado P, Palma J. Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. J Chem Inf Model 2019; 59:809-817. [PMID: 30608160 DOI: 10.1021/acs.jcim.8b00675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes that both substrate and enzyme undergo during the process. It was determined that the galactopyranose portion of the substrate is highly mobile and that the opening/closing of the active site occurs in stages. Previously uncharacterized interactions with highly conserved residues were also identified. These findings provide new pieces of information that contribute to the rational design of drugs against T. cruzi.
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Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Juliana Palma
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
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7
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Pierdominici-Sottile G, Cossio-Pérez R, Da Fonseca I, Kizjakina K, Tanner JJ, Sobrado P. Steric Control of the Rate-Limiting Step of UDP-Galactopyranose Mutase. Biochemistry 2018; 57:3713-3721. [PMID: 29757624 DOI: 10.1021/acs.biochem.8b00323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Galactose is an abundant monosaccharide found exclusively in mammals as galactopyranose (Gal p), the six-membered ring form of this sugar. In contrast, galactose appears in many pathogenic microorganisms as the five-membered ring form, galactofuranose (Gal f). Gal f biosynthesis begins with the conversion of UDP-Gal p to UDP-Gal f catalyzed by the flavoenzyme UDP-galactopyranose mutase (UGM). Because UGM is essential for the survival and proliferation of several pathogens, there is interest in understanding the catalytic mechanism to aid inhibitor development. Herein, we have used kinetic measurements and molecular dynamics simulations to explore the features of UGM that control the rate-limiting step (RLS). We show that UGM from the pathogenic fungus Aspergillus fumigatus also catalyzes the isomerization of UDP-arabinopyranose (UDP-Ara p), which differs from UDP-Gal p by lacking a -CH2-OH substituent at the C5 position of the hexose ring. Unexpectedly, the RLS changed from a chemical step for the natural substrate to product release with UDP-Ara p. This result implicated residues that contact the -CH2-OH of UDP-Gal p in controlling the mechanistic path. The mutation of one of these residues, Trp315, to Ala changed the RLS of the natural substrate to product release, similar to the wild-type enzyme with UDP-Ara p. Molecular dynamics simulations suggest that steric complementarity in the Michaelis complex is responsible for this distinct behavior. These results provide new insight into the UGM mechanism and, more generally, how steric factors in the enzyme active site control the free energy barriers along the reaction path.
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Affiliation(s)
| | - Rodrigo Cossio-Pérez
- Sci-prot. Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , Bernal B1876BXD , Argentina
| | - Isabel Da Fonseca
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Karina Kizjakina
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry , University of Missouri-Columbia , Columbia , Missouri 65211 , United States
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
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8
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Korasick DA, Tanner JJ. Determination of protein oligomeric structure from small-angle X-ray scattering. Protein Sci 2018; 27:814-824. [PMID: 29352739 DOI: 10.1002/pro.3376] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 11/09/2022]
Abstract
Small-angle X-ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer. This approach is especially robust when the crystal structure of the target protein is known, and the candidate oligomer models are derived from the crystal lattice. When SAXS data are obtained at multiple protein concentrations, this analysis can provide insight into dynamic self-association equilibria. Herein, we summarize the computational methods that are used to determine protein molecular mass and quaternary structure from SAXS data. These methods are organized into a workflow and demonstrated with four case studies using experimental SAXS data from the published literature.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211.,Department of Chemistry, University of Missouri, Columbia, Missouri, 65211
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9
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Wangkanont K, Winton VJ, Forest KT, Kiessling LL. Conformational Control of UDP-Galactopyranose Mutase Inhibition. Biochemistry 2017; 56:3983-3992. [PMID: 28608671 PMCID: PMC5739916 DOI: 10.1021/acs.biochem.7b00189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
UDP-galactopyranose mutase (Glf or UGM) catalyzes the formation of uridine 5'-diphosphate-α-d-galactofuranose (UDP-Galf) from UDP-galactopyranose (UDP-Galp). The enzyme is required for the production of Galf-containing glycans. UGM is absent in mammals, but members of the Corynebacterineae suborder require UGM for cell envelope biosynthesis. The need for UGM in some pathogens has prompted the search for inhibitors that could serve as antibiotic leads. Optimizing inhibitor potency, however, has been challenging. The UGM from Klebsiella pneumoniae (KpUGM), which is not required for viability, is more effectively impeded by small-molecule inhibitors than are essential UGMs from species such as Mycobacterium tuberculosis or Corynebacterium diphtheriae. Why KpUGM is more susceptible to inhibition than other orthologs is not clear. One potential source of difference is UGM ortholog conformation. We previously determined a structure of CdUGM bound to a triazolothiadiazine inhibitor in the open form, but it was unclear whether the small-molecule inhibitor bound this form or to the closed form. By varying the terminal tag (CdUGM-His6 and GSG-CdUGM), we crystallized CdUGM to capture the enzyme in different conformations. These structures reveal a pocket in the active site that can be exploited to augment inhibitor affinity. Moreover, they suggest the inhibitor binds the open form of most prokaryotic UGMs but can bind the closed form of KpUGM. This model and the structures suggest strategies for optimizing inhibitor potency by exploiting UGM conformational flexibility.
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Affiliation(s)
- Kittikhun Wangkanont
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Valerie J. Winton
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katrina T. Forest
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA,Department of Bacteriology University of Wisconsin-Madison, Madison, WI, 53706, USA,Corresponding authors: Katrina T. Forest (Tel. 608-265-3566, ) and Laura L. Kiessling (Tel. 608-262-0541, )
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA,Corresponding authors: Katrina T. Forest (Tel. 608-265-3566, ) and Laura L. Kiessling (Tel. 608-262-0541, )
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10
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Villaume SA, Fu J, N'Go I, Liang H, Lou H, Kremer L, Pan W, Vincent SP. Natural and Synthetic Flavonoids as Potent
Mycobacterium tuberculosis
UGM Inhibitors. Chemistry 2017; 23:10423-10429. [DOI: 10.1002/chem.201701812] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Sydney A. Villaume
- Department of ChemistryUniversity of Namur Rue de Bruxelles 61 5000 Namur Belgium
| | - Jian Fu
- Department of ChemistryUniversity of Namur Rue de Bruxelles 61 5000 Namur Belgium
| | - Inès N'Go
- Department of ChemistryUniversity of Namur Rue de Bruxelles 61 5000 Namur Belgium
| | - Hui Liang
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical University 3491 Baijin Road Guiyang 550014 P. R. China
| | - Huayong Lou
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical University 3491 Baijin Road Guiyang 550014 P. R. China
| | - Laurent Kremer
- IRIM (ex-CPBS)-UMR 9004Infectious Disease Research Institute of Montpellier (IDRIM)Université de Montpellier, CNRS 34293 Montpellier France
- INSERMIRIM 34293 Montpellier France
| | - Weidong Pan
- State Key Laboratory of Functions and Applications of Medicinal PlantsGuizhou Medical University 3491 Baijin Road Guiyang 550014 P. R. China
| | - Stéphane P. Vincent
- Department of ChemistryUniversity of Namur Rue de Bruxelles 61 5000 Namur Belgium
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11
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Sobrado P, Tanner JJ. Multiple functionalities of reduced flavin in the non-redox reaction catalyzed by UDP-galactopyranose mutase. Arch Biochem Biophys 2017; 632:59-65. [PMID: 28652025 DOI: 10.1016/j.abb.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/29/2022]
Abstract
Flavin cofactors are widely used by enzymes to catalyze a broad range of chemical reactions. Traditionally, flavins in enzymes are regarded as redox centers, which enable enzymes to catalyze the oxidation or reduction of substrates. However, a new class of flavoenzyme has emerged over the past quarter century in which the flavin functions as a catalytic center in a non-redox reaction. Here we introduce the unifying concept of flavin hot spots to understand and categorize the mechanisms and reactivities of both traditional and noncanonical flavoenzymes. The major hot spots of reactivity include the N5, C4a, and C4O atoms of the isoalloxazine, and the 2' hydroxyl of the ribityl chain. The role of hot spots in traditional flavoenzymes, such as monooxygenases, is briefly reviewed. A more detailed description of flavin hot spots in noncanonical flavoenzymes is provided, with a focus on UDP-galactopyranose mutase, where the N5 functions as a nucleophile that attacks the anomeric carbon atom of the substrate. Recent results from mechanistic enzymology, kinetic crystallography, and computational chemistry provide a complete picture of the chemical mechanism of UDP-galactopyranose mutase.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO 65211, USA.
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12
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Tanner JJ. Empirical power laws for the radii of gyration of protein oligomers. Acta Crystallogr D Struct Biol 2016; 72:1119-1129. [PMID: 27710933 PMCID: PMC5053138 DOI: 10.1107/s2059798316013218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 08/16/2016] [Indexed: 11/10/2022] Open
Abstract
The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2-6 and 8. The power-law exponents for oligomers span a narrow range of 0.38-0.41, which is close to the value of 0.40 obtained for monomers. This result shows that protein oligomers exhibit essentially the same power-law behavior as monomers. A simple power-law formula is provided for estimating the oligomeric state from an experimental measurement of the radius of gyration. Several proteins in the Protein Data Bank are found to deviate substantially from power-law behavior by having an atypically large radius of gyration. Some of the outliers have highly elongated structures, such as coiled coils. For coiled coils, the radius of gyration does not follow a power law and instead scales linearly with the number of residues in the oligomer. Other outliers are proteins whose oligomeric state or quaternary structure is incorrectly annotated in the Protein Data Bank. The power laws could be used to identify such errors and help prevent them in future depositions.
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Affiliation(s)
- John J. Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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13
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Misra S, Valicherla GR, Mohd Shahab, Gupta J, Gayen JR, Misra-Bhattacharya S. UDP-galactopyranose mutase, a potential drug target against human pathogenic nematodeBrugia malayi. Pathog Dis 2016; 74:ftw072. [DOI: 10.1093/femspd/ftw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/02/2023] Open
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14
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Mehra-Chaudhary R, Dai Y, Sobrado P, Tanner JJ. In Crystallo Capture of a Covalent Intermediate in the UDP-Galactopyranose Mutase Reaction. Biochemistry 2016; 55:833-6. [PMID: 26836146 PMCID: PMC4819441 DOI: 10.1021/acs.biochem.6b00035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
UDP-galactopyranose mutase (UGM)
plays an essential role in galactofuranose
biosynthesis in pathogens by catalyzing the conversion of UDP-galactopyranose
to UDP-galactofuranose. Here we report the first crystal structure
of a covalent intermediate in the UGM reaction. The 2.3 Å resolution
structure reveals UDP bound in the active site and galactopyranose
linked to the FAD through a covalent bond between the anomeric C of
galactopyranose and N5 of the FAD. The structure confirms the role
of the flavin as nucleophile and supports the hypothesis that the
proton destined for O5 of galactofuranose is shuttled from N5 of the
FAD via O4 of the FAD.
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Affiliation(s)
- Ritcha Mehra-Chaudhary
- Structural Biology Core, University of Missouri-Columbia , Columbia, Missouri 65211, United States
| | - Yumin Dai
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia , Columbia, Missouri 65211, United States
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15
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Oka T, Goto M. Biosynthesis of Galactofuranose-containing Glycans in Filamentous Fungi. TRENDS GLYCOSCI GLYC 2016. [DOI: 10.4052/tigg.1428.1j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Takuji Oka
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo, University
| | - Masatoshi Goto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University
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16
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Oka T, Goto M. Biosynthesis of Galactofuranose-containing Glycans in Filamentous Fungi. TRENDS GLYCOSCI GLYC 2016. [DOI: 10.4052/tigg.1428.1e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Takuji Oka
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo, University
| | - Masatoshi Goto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University
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17
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Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL. Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents. ACS Chem Biol 2015. [PMID: 26214585 DOI: 10.1021/acschembio.5b00370] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Galactofuranose (Galf) is present in glycans critical for the virulence and viability of several pathogenic microbes, including Mycobacterium tuberculosis, yet the monosaccharide is absent from mammalian glycans. Uridine 5'-diphosphate-galactopyranose mutase (UGM) catalyzes the formation of UDP-Galf, which is required to produce Galf-containing glycoconjugates. Inhibitors of UGM have therefore been sought, both as antimicrobial leads and as tools to delineate the roles of Galf in cells. Obtaining cell permeable UGM probes by either design or high throughput screens has been difficult, as has elucidating how UGM binds small molecule, noncarbohydrate inhibitors. To address these issues, we employed structure-based virtual screening to uncover new inhibitor chemotypes, including a triazolothiadiazine series. These compounds are among the most potent antimycobacterial UGM inhibitors described. They also facilitated determination of a UGM-small molecule inhibitor structure, which can guide optimization. A comparison of results from the computational screen and a high-throughput fluorescence polarization (FP) screen indicated that the scaffold hits from the former had been evaluated in the FP screen but missed. By focusing on promising compounds, the virtual screen rescued false negatives, providing a blueprint for generating new UGM probes and therapeutic leads.
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Affiliation(s)
- Virginia A. Kincaid
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Nir London
- Department
of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, California 94158, United States
| | - Kittikhun Wangkanont
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Darryl A. Wesener
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Sarah A. Marcus
- Department
of Pathobiological Sciences, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Annie Héroux
- Photon
Sciences Directorate, Brookhaven National Laboratories, Upton, New York 11973, United States
| | - Lyudmila Nedyalkova
- Ontario Institute
of Cancer Research and Faculty of Pharmacy, University of Toronto, Toronto, Canada
| | - Adel M. Talaat
- Department
of Pathobiological Sciences, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Katrina T. Forest
- Department
of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, California 94158, United States
- Ontario Institute
of Cancer Research and Faculty of Pharmacy, University of Toronto, Toronto, Canada
| | - Laura L. Kiessling
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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18
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Eppe G, El Bkassiny S, Vincent SP. Galactofuranose Biosynthesis: Discovery, Mechanisms and Therapeutic Relevance. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Galactofuranose, the atypical and thermodynamically disfavored form of d-galactose, has in reality a very old history in chemistry and biochemistry. The purpose of this book chapter is to give an overview on the fundamental aspects of the galactofuranose biosynthesis, from the biological occurrence to the search of inhibitors.
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Affiliation(s)
- Guillaume Eppe
- University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique rue de Bruxelles 61 B-5000 Namur Belgium
| | - Sandy El Bkassiny
- University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique rue de Bruxelles 61 B-5000 Namur Belgium
| | - Stéphane P. Vincent
- University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique rue de Bruxelles 61 B-5000 Namur Belgium
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19
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Chai AF, Bulloch EMM, Evans GL, Lott JS, Baker EN, Johnston JM. A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket. ACTA ACUST UNITED AC 2015; 71:862-72. [PMID: 25849397 DOI: 10.1107/s1399004715001650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/25/2015] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis. Access to iron in host macrophages depends on iron-chelating siderophores called mycobactins and is strongly correlated with Mtb virulence. Here, the crystal structure of an Mtb enzyme involved in mycobactin biosynthesis, MbtN, in complex with its FAD cofactor is presented at 2.30 Å resolution. The polypeptide fold of MbtN conforms to that of the acyl-CoA dehydrogenase (ACAD) family, consistent with its predicted role of introducing a double bond into the acyl chain of mycobactin. Structural comparisons and the presence of an acyl carrier protein, MbtL, in the same gene locus suggest that MbtN acts on an acyl-(acyl carrier protein) rather than an acyl-CoA. A notable feature of the crystal structure is the tubular density projecting from N(5) of FAD. This was interpreted as a covalently bound polyethylene glycol (PEG) fragment and resides in a hydrophobic pocket where the substrate acyl group is likely to bind. The pocket could accommodate an acyl chain of 14-21 C atoms, consistent with the expected length of the mycobactin acyl chain. Supporting this, steady-state kinetics show that MbtN has ACAD activity, preferring acyl chains of at least 16 C atoms. The acyl-binding pocket adopts a different orientation (relative to the FAD) to other structurally characterized ACADs. This difference may be correlated with the apparent ability of MbtN to catalyse the formation of an unusual cis double bond in the mycobactin acyl chain.
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Affiliation(s)
- Ai-Fen Chai
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Esther M M Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Genevieve L Evans
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J Shaun Lott
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jodie M Johnston
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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20
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Da Fonseca I, Qureshi IA, Mehra-Chaudhary R, Kizjakina K, Tanner JJ, Sobrado P. Contributions of unique active site residues of eukaryotic UDP-galactopyranose mutases to substrate recognition and active site dynamics. Biochemistry 2014; 53:7794-804. [PMID: 25412209 PMCID: PMC4270374 DOI: 10.1021/bi501008z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
UDP-galactopyranose mutase (UGM)
catalyzes the interconversion
between UDP-galactopyranose and UDP-galactofuranose. Absent in humans,
galactofuranose is found in bacterial and fungal cell walls and is
a cell surface virulence factor in protozoan parasites. For these
reasons, UGMs are targets for drug discovery. Here, we report a mutagenesis
and structural study of the UGMs from Aspergillus fumigatus and Trypanosoma cruzi focused on
active site residues that are conserved in eukaryotic UGMs but are
absent or different in bacterial UGMs. Kinetic analysis of the variants
F66A, Y104A, Q107A, N207A, and Y317A (A. fumigatus numbering) show decreases in kcat/KM values of 200–1000-fold for the mutase
reaction. In contrast, none of the mutations significantly affect
the kinetics of enzyme activation by NADPH. These results indicate
that the targeted residues are important for promoting the transition
state conformation for UDP-galactofuranose formation. Crystal structures
of the A. fumigatus mutant enzymes
were determined in the presence and absence of UDP to understand the
structural consequences of the mutations. The structures suggest important
roles for Asn207 in stabilizing the closed active site, and Tyr317
in positioning of the uridine ring. Phe66 and the corresponding residue
in Mycobacterium tuberculosis UGM (His68)
play a role as the backstop, stabilizing the galactopyranose group
for nucleophilic attack. Together, these results provide insight into
the essentiality of the targeted residues for realizing maximal catalytic
activity and a proposal for how conformational changes that close
the active site are temporally related and coupled together.
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Affiliation(s)
- Isabel Da Fonseca
- Department of Biochemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
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21
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Pierdominici-Sottile G, Cossio Pérez R, Galindo JF, Palma J. QM/MM molecular dynamics study of the galactopyranose → galactofuranose reaction catalysed by Trypanosoma cruzi UDP-galactopyranose mutase. PLoS One 2014; 9:e109559. [PMID: 25299056 PMCID: PMC4192007 DOI: 10.1371/journal.pone.0109559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/25/2014] [Indexed: 12/18/2022] Open
Abstract
The enzyme UDP-Galactopyranose Mutase (UGM) catalyses the conversion of galactopyranose into galactofuranose. It is known to be critical for the survival and proliferation of several pathogenic agents, both prokaryotic and eukaryotic. Among them is Trypanosoma cruzi, the parasite responsible for Chagas' disease. Since the enzyme is not present in mammals, it appears as a promising target for the design of drugs to treat this illness. A precise knowledge of the mechanism of the catalysed reaction would be crucial to assist in such design. In this article we present a detailed study of all the putative steps of the mechanism. The study is based on QM/MM free energy calculations along properly selected reaction coordinates, and on the analysis of the main structural changes and interactions taking place at every step. The results are discussed in connection with the experimental evidence and previous theoretical studies.
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Affiliation(s)
| | - Rodrigo Cossio Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Johan F. Galindo
- Quantum and Computational Chemistry Group, Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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22
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El Bkassiny S, N'Go I, Sevrain CM, Tikad A, Vincent SP. Synthesis of a novel UDP-carbasugar as UDP-galactopyranose mutase inhibitor. Org Lett 2014; 16:2462-5. [PMID: 24746099 DOI: 10.1021/ol500848q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The multistep synthesis of a novel UDP-C-cyclohexene, designed as a high energy intermediate analogue of the UDP-galactopyranose mutase (UGM) catalyzed isomerization reaction, is reported. The synthesis of the central carbasugar involved the preparation of a galactitol derivative bearing two olefins necessary for the construction of the cyclohexene ring by a ring-closing metathesis as a key step. Further successive phosphonylation, deprotection, and UMP coupling provided the target molecule. The final molecule was assayed against UGM and compared with UDP-C-Galf, the C-glycosidic UGM substrate analogue.
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Affiliation(s)
- Sandy El Bkassiny
- University of Namur , Département de Chimie, Laboratoire de Chimie Bio-Organique, rue de Bruxelles 61, B-5000 Namur, Belgium
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23
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Tanner JJ, Boechi L, Andrew McCammon J, Sobrado P. Structure, mechanism, and dynamics of UDP-galactopyranose mutase. Arch Biochem Biophys 2014; 544:128-41. [PMID: 24096172 PMCID: PMC3946560 DOI: 10.1016/j.abb.2013.09.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 11/16/2022]
Abstract
The flavoenzyme UDP-galactopyranose mutase (UGM) is a key enzyme in galactofuranose biosynthesis. The enzyme catalyzes the 6-to-5 ring contraction of UDP-galactopyranose to UDP-galactofuranose. Galactofuranose is absent in humans yet is an essential component of bacterial and fungal cell walls and a cell surface virulence factor in protozoan parasites. Thus, inhibition of galactofuranose biosynthesis is a valid strategy for developing new antimicrobials. UGM is an excellent target in this effort because the product of the UGM reaction represents the first appearance of galactofuranose in the biosynthetic pathway. The UGM reaction is redox neutral, which is atypical for flavoenzymes, motivating intense examination of the chemical mechanism and structural features that tune the flavin for its unique role in catalysis. These studies show that the flavin functions as nucleophile, forming a flavin-sugar adduct that facilitates galactose-ring opening and contraction. The 3-dimensional fold is novel and conserved among all UGMs, however the larger eukaryotic enzymes have additional secondary structure elements that lead to significant differences in quaternary structure, substrate conformation, and conformational flexibility. Here we present a comprehensive review of UGM three-dimensional structure, provide an update on recent developments in understanding the mechanism of the enzyme, and summarize computational studies of active site flexibility.
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Affiliation(s)
- John J Tanner
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, MO, United States.
| | - Leonardo Boechi
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States
| | - J Andrew McCammon
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States; Howard Hughes Medical Institute, Department of Pharmacology, University of California San Diego, La Jolla, CA, United States
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States; Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.
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24
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Kizjakina K, Tanner JJ, Sobrado P. Targeting UDP-galactopyranose mutases from eukaryotic human pathogens. Curr Pharm Des 2013; 19:2561-73. [PMID: 23116395 PMCID: PMC3624792 DOI: 10.2174/1381612811319140007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 12/19/2022]
Abstract
UDP-Galactopyranose mutase (UGM) is a unique flavin-dependent enzyme that catalyzes the conversion of UDP-galactopyranose(UDP-Galp) to UDP-galactofuranose (UDP-Galf). The product of this reaction is the precursor to Galf, a major component of the cell wall and of cell surface glycoproteins and glycolipids in many eukaryotic and prokaryotic human pathogens. The function of UGM is important in the virulence of fungi, parasites, and bacteria. Its role in virulence and its absence in humans suggest that UGM is an ideal drug target. Significant structural and mechanistic information has been accumulated on the prokaryotic UGMs; however, in the past few years the research interest has shifted to UGMs from eukaryotic human pathogens such as fungi and protozoan parasites. It has become clear that UGMs from prokaryotic and eukaryotic organisms have different structural and mechanistic features. The amino acid sequence identity between these two classes of enzymes is low, resulting in differences in oligomeric states, substrate binding, active site flexibility, and interaction with redox partners. However, the unique role of the flavin cofactor in catalysis is conserved among this enzyme family. In this review, recent findings on eukaryotic UGMs are discussed and presented in comparison with prokaryotic UGMs.
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Affiliation(s)
- Karina Kizjakina
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
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25
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Boechi L, de Oliveira CAF, Da Fonseca I, Kizjakina K, Sobrado P, Tanner JJ, McCammon JA. Substrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design. Protein Sci 2013; 22:1490-501. [PMID: 23934860 DOI: 10.1002/pro.2332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 02/04/2023]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected tropical disease that represents one of the major health challenges of the Latin American countries. Successful efforts were made during the last few decades to control the transmission of this disease, but there is still no treatment for the 10 million adults in the chronic phase of the disease. In T. cruzi, as well as in other pathogens, the flavoenzyme UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, a precursor of the cell surface β-galactofuranose that is involved in the virulence of the pathogen. The fact that UGM is not present in humans makes inhibition of this enzyme a good approach in the design of new Chagas therapeutics. By performing a series of computer simulations of T. cruzi UGM in the presence or absence of an active site ligand, we address the molecular details of the mechanism that controls the uptake and retention of the substrate. The simulations suggest a modular mechanism in which each moiety of the substrate controls the flexibility of a different protein loop. Furthermore, the calculations indicate that interactions with the substrate diphosphate moiety are especially important for stabilizing the closed active site. This hypothesis is supported with kinetics measurements of site-directed mutants of T. cruzi UGM. Our results extend our knowledge of UGM dynamics and offer new alternatives for the prospective design of drugs.
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Affiliation(s)
- Leonardo Boechi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
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26
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Fonseca IO, Kizjakina K, Sobrado P. UDP-galactopyranose mutases from Leishmania species that cause visceral and cutaneous leishmaniasis. Arch Biochem Biophys 2013; 538:103-10. [PMID: 24012809 DOI: 10.1016/j.abb.2013.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/21/2013] [Accepted: 08/24/2013] [Indexed: 01/18/2023]
Abstract
Leishmaniasis is a vector-borne, neglected tropical disease caused by parasites from the genus Leishmania. Galactofuranose (Galf) is found on the cell surface of Leishmania parasites and is important for virulence. The flavoenzyme that catalyzes the isomerization of UDP-galactopyranose to UDP-Galf, UDP-galactopyranose mutase (UGM), is a validated drug target in protozoan parasites. UGMs from L. mexicana and L. infantum were recombinantly expressed, purified, and characterized. The isolated enzymes contained tightly bound flavin cofactor and were active only in the reduced form. NADPH is the preferred redox partner for both enzymes. A kcat value of 6 ± 0.4s(-1) and a Km value of 252 ± 42 μM were determined for L. infantum UGM. For L. mexicana UGM, these values were ∼4-times lower. Binding of UDP-Galp is enhanced 10-20 fold in the reduced form of the enzymes. Changes in the spectra of the reduced flavin upon interaction with the substrate are consistent with formation of a flavin-iminium ion intermediate.
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Affiliation(s)
- Isabel O Fonseca
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, United States
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27
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Abstract
Nematodes represent a diverse phylum of both free living and parasitic species. While the species Caenorhabditis elegans is a valuable model organism, parasitic nematodes or helminths pose a serious threat to human health. Indeed, helminths cause many neglected tropical diseases that afflict humans. Nematode glycoconjugates have been implicated in evasive immunomodulation, a hallmark of nematode infections. One monosaccharide residue present in the glycoconjugates of several human pathogens is galactofuranose (Galf). This five-membered ring isomer of galactose has not been detected in mammals, making Galf metabolic enzymes attractive therapeutic targets. The only known pathway for biosynthetic incorporation of Galf into glycoconjugates depends upon generation of the glycosyl donor UDP-Galf by the flavoenzyme uridine 5'-diphosphate (UDP) galactopyranose mutase (UGM or Glf). A putative UGM encoding gene (glf-1) was recently identified in C. elegans. We sought to assess the catalytic activity of the corresponding gene product (CeUGM). CeUGM catalyzes the isomerization of UDP-Galf and UDP-galactopyranose (UDP-Galp). In the presence of enzyme, substrate, and a hydride source, a galactose-N5-FAD adduct was isolated, suggesting the CeUGM flavin adenine dinucleotide (FAD) cofactor serves as a nucleophile in covalent catalysis. Homology modeling and protein variants indicate that CeUGM possesses an active site similar to that of prokaryotic enzymes, despite the low sequence identity (∼15%) between eukaryotic and prokaryotic UGM proteins. Even with the primary sequence differences, heterocyclic UGM inhibitors developed against prokaryotic proteins also inhibit CeUGM activity. We postulate that inhibitors of CeUGM can serve as chemical probes of Galf in nematodes and as anthelmintic leads. The available data suggest that CeUGM facilitates the biosynthetic incorporation of Galf into nematode glycoconjugates through generation of the glycosyl donor UDP-Galf.
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Affiliation(s)
- Darryl A. Wesener
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 USA
| | - John F. May
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 USA
| | - Elizabeth M. Huffman
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 USA
| | - Laura L. Kiessling
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 USA
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 USA
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28
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Huang W, Gauld JW. Tautomerization in the UDP-galactopyranose mutase mechanism: a DFT-cluster and QM/MM investigation. J Phys Chem B 2012; 116:14040-50. [PMID: 23148701 DOI: 10.1021/jp310952c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-galactopyranose mutase (UGM) is a key flavoenzyme involved in cell wall biosynthesis of a variety of pathogenic bacteria and hence, integral to their survival. It catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf); interconversion of the galactose moieties six- and five-membered ring forms. We have synergistically applied both density functional theory (DFT)-cluster and ONIOM quantum mechanics/molecular mechanics (QM/MM) hybrid calculations to elucidate the mechanism of this important enzyme and to provide insight into its uncommon mechanism. It is shown that the flavin must initially be in its fully reduced form. Furthermore, it requires an N5(FAD)-H proton, which, through a series of tautomerizations, is transferred onto the ring oxygen of the substrate's Galp moiety to facilitate ring-opening with concomitant Schiff base formation. Conversely, Galf formation is achieved via a series of tautomerizations involving proton transfer from the galactose's -O4(Gal)H group ultimately onto the flavin's N5(FAD) center. With the DFT-cluster model, the overall rate-limiting step with a barrier of 120.0 kJ mol(-1) is the interconversion of two Galf-flavin tautomers: one containing a C4(FAD)-OH group and the other a tetrahedral protonated-N5(FAD) center. In contrast, in the QM/MM model a considerably more extensive chemical model was used that included all of the residues surrounding the active site, and modeled both their steric and electrostatic effects. In this approach, the overall rate-limiting step with a barrier of 99.2 kJ mol(-1) occurs during conformational rearrangement of the Schiff base linear galactose-flavin complex. This appears due to the lack of suitable functional groups to facilitate the rearrangement.
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Affiliation(s)
- WenJuan Huang
- Department of Chemistry and Biochemistry, University of Windsor, Ontario, Canada
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29
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Abstract
Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a "molecular scaffold" in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
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30
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Dhatwalia R, Singh H, Solano LM, Oppenheimer M, Robinson RM, Ellerbrock JF, Sobrado P, Tanner JJ. Identification of the NAD(P)H binding site of eukaryotic UDP-galactopyranose mutase. J Am Chem Soc 2012; 134:18132-8. [PMID: 23036087 PMCID: PMC3493617 DOI: 10.1021/ja308188z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UDP-galactopyranose mutase (UGM) plays an essential role in galactofuranose biosynthesis in microorganisms by catalyzing the conversion of UDP-galactopyranose to UDP-galactofuranose. The enzyme has gained attention recently as a promising target for the design of new antifungal, antitrypanosomal, and antileishmanial agents. Here we report the first crystal structure of UGM complexed with its redox partner NAD(P)H. Kinetic protein crystallography was used to obtain structures of oxidized Aspergillus fumigatus UGM (AfUGM) complexed with NADPH and NADH, as well as reduced AfUGM after dissociation of NADP(+). NAD(P)H binds with the nicotinamide near the FAD isoalloxazine and the ADP moiety extending toward the mobile 200s active site flap. The nicotinamide riboside binding site overlaps that of the substrate galactopyranose moiety, and thus NADPH and substrate binding are mutually exclusive. On the other hand, the pockets for the adenine of NADPH and uracil of the substrate are distinct and separated by only 6 Å, which raises the possibility of designing novel inhibitors that bind both sites. All 12 residues that contact NADP(H) are conserved among eukaryotic UGMs. Residues that form the AMP pocket are absent in bacterial UGMs, which suggests that eukaryotic and bacterial UGMs have different NADP(H) binding sites. The structures address the longstanding question of how UGM binds NAD(P)H and provide new opportunities for drug discovery.
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Affiliation(s)
- Richa Dhatwalia
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Luis M. Solano
- Department of Biology, Costa Rica Institute of Technology, Cartago, Costa Rica
| | | | | | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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Ansiaux C, N'Go I, Vincent SP. Reversible and Efficient Inhibition of UDP-Galactopyranose Mutase by Electrophilic, Constrained and Unsaturated UDP-Galactitol Analogues. Chemistry 2012; 18:14860-6. [DOI: 10.1002/chem.201202302] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Indexed: 11/09/2022]
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Dhatwalia R, Singh H, Oppenheimer M, Sobrado P, Tanner JJ. Crystal structures of Trypanosoma cruzi UDP-galactopyranose mutase implicate flexibility of the histidine loop in enzyme activation. Biochemistry 2012; 51:4968-79. [PMID: 22646091 PMCID: PMC3426654 DOI: 10.1021/bi300498c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 Å movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k(cat). Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.
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Affiliation(s)
- Richa Dhatwalia
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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