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Yang J, Li Y, Qiu Q, Wang R, Yan W, Yu Y, Niu L, Pei H, Wei H, Ouyang L, Ye H, Xu D, Wei Y, Chen Q, Chen L. Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. J Med Chem 2022; 65:9159-9173. [PMID: 35762925 DOI: 10.1021/acs.jmedchem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here, we report a novel mechanism to selectively degrade target proteins. 3-(3-Phenoxybenzyl)amino-β-carboline (PAC), a tubulin inhibitor, promotes selective degradation of αβ-tubulin heterodimers. Biochemical studies have revealed that PAC specifically denatures tubulin, making it prone to aggregation that predisposes it to ubiquitinylation and then degradation. The degradation is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a low-barrier hydrogen bond (LBHB). In contrast, another two tubulin inhibitors that only form normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. We then screened for compounds capable of forming an LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimer degradation through the LBHB. Our study provided a unique example of LBHB function and identified a novel approach to obtain tubulin degraders.
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Affiliation(s)
- Jianhong Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Qiu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Yan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yamei Yu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lu Niu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heying Pei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoche Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoyu Ye
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuquan Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2021; 1869:140557. [PMID: 33148530 PMCID: PMC7736181 DOI: 10.1016/j.bbapap.2020.140557] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023]
Abstract
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States.
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low‐Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology University of Tennessee Knoxville TN 37996 USA
- Present address: Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - Pratul K. Agarwal
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - M. Brett Waddell
- Molecular Interaction Analysis Shared Resource St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Tanja Mittag
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Engin H. Serpersu
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
- National Science Foundation Alexandria VA 22314 USA
| | - Matthew J. Cuneo
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
- Oak Ridge National Laboratory Oak Ridge TN 37830 USA
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Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019; 58:16260-16266. [PMID: 31515870 DOI: 10.1002/anie.201908535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Indexed: 01/14/2023]
Abstract
The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-à-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.
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Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Present address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Engin H Serpersu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.,National Science Foundation, Alexandria, VA, 22314, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Active-site structure of the thermophilic Foc-subunit ring in membranes elucidated by solid-state NMR. Biophys J 2014; 106:390-8. [PMID: 24461014 DOI: 10.1016/j.bpj.2013.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/07/2013] [Accepted: 12/03/2013] [Indexed: 11/20/2022] Open
Abstract
FoF1-ATP synthase uses the electrochemical potential across membranes or ATP hydrolysis to rotate the Foc-subunit ring. To elucidate the underlying mechanism, we carried out a structural analysis focused on the active site of the thermophilic c-subunit (TFoc) ring in membranes with a solid-state NMR method developed for this purpose. We used stereo-array isotope labeling (SAIL) with a cell-free system to highlight the target. TFoc oligomers were purified using a virtual ring His tag. The membrane-reconstituted TFoc oligomer was confirmed to be a ring indistinguishable from that expressed in E. coli on the basis of the H(+)-translocation activity and high-speed atomic force microscopic images. For the analysis of the active site, 2D (13)C-(13)C correlation spectra of TFoc rings labeled with SAIL-Glu and -Asn were recorded. Complete signal assignment could be performed with the aid of the C(α)i+1-C(α)i correlation spectrum of specifically (13)C,(15)N-labeled TFoc rings. The C(δ) chemical shift of Glu-56, which is essential for H(+) translocation, and related crosspeaks revealed that its carboxyl group is protonated in the membrane, forming the H(+)-locked conformation with Asn-23. The chemical shift of Asp-61 C(γ) of the E. coli c ring indicated an involvement of a water molecule in the H(+) locking, in contrast to the involvement of Asn-23 in the TFoc ring, suggesting two different means of proton storage in the c rings.
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Emenike BU, Liu AT, Naveo EP, Roberts JD. Substituent Effects on Energetics of Peptide-Carboxylate Hydrogen Bonds as Studied by 1H NMR Spectroscopy: Implications for Enzyme Catalysis. J Org Chem 2013; 78:11765-71. [DOI: 10.1021/jo401762m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bright U. Emenike
- Gates and Crellin Laboratories
of Chemistry, California Institute of Technology, Pasadena, California 91125
| | - Albert Tianxiang Liu
- Gates and Crellin Laboratories
of Chemistry, California Institute of Technology, Pasadena, California 91125
| | - Elsy P. Naveo
- Gates and Crellin Laboratories
of Chemistry, California Institute of Technology, Pasadena, California 91125
| | - John D. Roberts
- Gates and Crellin Laboratories
of Chemistry, California Institute of Technology, Pasadena, California 91125
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Clawson JS, Kennedy-Gabb S, Lee AY, Copley RCB. One-phase crystal disorder in pharmaceutical solids and its implication for solid-state stability. J Pharm Sci 2011; 100:4302-16. [PMID: 21590691 DOI: 10.1002/jps.22621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 03/08/2011] [Accepted: 04/21/2011] [Indexed: 01/13/2023]
Abstract
Solid-state disorders of active pharmaceutical ingredients have been characterized by means of X-ray diffraction techniques and solid-state nuclear magnetic resonance spectroscopy. The results determined that the pleuromutilin-derivative, I, displays a unique continuous conformational disorder while retaining its long-range crystalline structure. The propionic acid (PA) version of this compound displayed partial crystalline order and site disorder of PA, depending on the quantity of PA incorporated in the structure. Thus, I is a unique example of one-phase crystalline-amorphous model. Physical and chemical stability data was acquired on these disordered systems and discussed in relation with the characterized disorder present in the crystal systems. Analysis of the results showed that in contrast to phase-separated amorphous, restrained disorders do not influence the stability.
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Affiliation(s)
- Jacalyn S Clawson
- Product Development, GlaxoSmithKline plc., King of Prussia, Pennsylvania 19406.
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Schmidt HLF, Shah GJ, Sperling LJ, Rienstra CM. NMR Determination of Protein pK(a) Values in the Solid State. J Phys Chem Lett 2010; 1:1623-1628. [PMID: 20563223 PMCID: PMC2885713 DOI: 10.1021/jz1004413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Charged residues play an important role in defining key mechanistic features in many biomolecules. Determining the pK(a) values of large, membrane or fibrillar proteins can be challenging with traditional methods. In this study we show how solid-state NMR is used to monitor chemical shift changes during a pH titration for the small soluble β1 immunoglobulin binding domain of protein G. The chemical shifts of all the amino acids with charged side-chains throughout the uniformly-(13)C,(15)N-labeled protein were monitored over several samples varying in pH; pK(a) values were determined from these shifts for E27, D36, and E42, and the bounds for the pK(a) of other acidic side-chain resonances were determined. Additionally, this study shows how the calculated pK(a) values give insights into the crystal packing of the protein.
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Cleland W. The low-barrier hydrogen bond in enzymic catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44001-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kurz LC, Constantine CZ, Jiang H, Kappock TJ. The partial substrate dethiaacetyl-coenzyme A mimics all critical carbon acid reactions in the condensation half-reaction catalyzed by Thermoplasma acidophilum citrate synthase. Biochemistry 2009; 48:7878-91. [PMID: 19645419 DOI: 10.1021/bi9006447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Citrate synthase (CS) performs two half-reactions: the mechanistically intriguing condensation of acetyl-CoA with oxaloacetate (OAA) to form citryl-CoA and the subsequent, slower hydrolysis of citryl-CoA that generally dominates steady-state kinetics. The condensation reaction requires the abstraction of a proton from the methyl carbon of acetyl-CoA to generate a reactive enolate intermediate. The carbanion of that intermediate then attacks the OAA carbonyl to furnish citryl-CoA, the initial product. Using stopped-flow and steady-state fluorescence methods, kinetic substrate isotope effects, and mutagenesis of active site residues, we show that all of the processes that occur in the condensation half-reaction performed by Thermoplasma acidophilum citrate synthase (TpCS) with the natural thioester substrate, acetyl-CoA, also occur with the ketone inhibitor dethiaacetyl-CoA. Free energy profiles demonstrate that the nonhydrolyzable product of the condensation reaction, dethiacitryl-CoA, forms a particularly stable complex with TpCS but not pig heart CS.
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Affiliation(s)
- Linda C Kurz
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Hu YY, Schmidt-Rohr K. Effects of L-spin longitudinal quadrupolar relaxation in S[L] heteronuclear recoupling and S-spin magic-angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 197:193-207. [PMID: 19217811 DOI: 10.1016/j.jmr.2008.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 12/19/2008] [Accepted: 12/22/2008] [Indexed: 05/27/2023]
Abstract
In experiments on S-L heteronuclear spin systems with evolution of the S-spin magnetization under the influence of a quadrupolar nucleus (L-spin), effects of longitudinal quadrupolar (T(1Q)) relaxation of the L-spin coherence on the sub-millisecond time scale have been documented and explored, and methods for minimizing their effect have been demonstrated. The longitudinal relaxation results in heteronuclear dephasing even in the reference signal S(0) of S[L] REDOR, REAPDOR, RIDER, or SPIDER experiments, due to T(1Q)-relaxation of the transiently generated S(y)L(z) coherence, reducing or even eliminating the observable dephasing DeltaS. Pulse sequences for measuring an improved reference signal S(00) with minimal heteronuclear recoupling but the same number of pulses as for S(0) and S have been demonstrated. From the observed intensity DeltaS(0)=S(00)-S(0) and the SPIDER signal DeltaS/S(0), T(1Q) can be estimated. Accelerated decays analogous to the dipolar S(0) curves will occur in T(2) measurements for J-coupled S-L spin pairs. Even in the absence of recoupling pulses, fast T(1Q) relaxation of the unobserved nucleus shortens the transverse relaxation time T(2S,MAS) of the observed nucleus, in particular at low spinning frequencies, due to unavoidable heteronuclear dipolar evolution during a rotation period. The observed spinning-frequency dependence of T(2S,MAS) matches the theoretical prediction and may be used to estimate T(1Q). The effects are demonstrated on several (13)C[(14)N] spin systems, including an arginine derivative, the natural N-acetylated polysaccharide chitin, and a model peptide, (POG)(10).
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Affiliation(s)
- Y-Y Hu
- Ames Laboratory, Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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Yang J, Parkanzky PD, Bodner ML, Duskin CA, Weliky DP. Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 159:101-110. [PMID: 12482688 DOI: 10.1016/s1090-7807(02)00033-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clean MAS observation of 13C-labeled carbons in membrane-bound HIV-1 and influenza fusion peptides was made by using a rotational-echo double-resonance spectroscopy (REDOR) filter of directly bonded 13C-15N pairs. The clean filtering achieved with the REDOR approach is superior to filtering done with sample difference spectroscopy. In one labeling approach, the peptide had labels at a single 13C carbonyl and its directly bonded 15N. The resulting chemical shift distribution of the filtered signal is used to assess the distribution of local secondary structures at the labeled carbonyl. For the influenza peptide, the Leu-2 carbonyl chemical shift distribution is shown to vary markedly with lipid and detergent composition, as well as peptide:lipid ratio, suggesting that the local peptide structure also has a strong dependence on these factors. Because most carboxylic- and amino-labeled amino acids are commercially available, this REDOR approach should have broad applicability to chemically synthesized peptides as well as bacterially synthesized proteins. In a second labeling approach, the HIV-1 fusion peptide had U-13C, 15N labeling over three sequential residues. When a 1.6 ms REDOR dephasing time is used, only backbone 13C signals are observed. The resulting spectra are used to determine spectral linewidths and to assess feasibility of assignment of uniformly labeled peptide.
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Affiliation(s)
- Jun Yang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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Abstract
Coenzyme A (I) and enzyme-bound phosphopantetheine (II) function as acyl carriers and as carbonyl activating groups for Claisen reactions as well as for amide-, ester-, and thioester-forming reactions in the cell. In so doing, these cofactors play a key role in the biosynthesis and breakdown of fatty acids and in the biosynthesis of polyketides and nonribosomal peptides. Coenzyme A is biosynthesized in bacteria in nine steps. The biosynthesis begins with the decarboxylation of aspartate to give beta-alanine. Pantoic acid is formed by the hydroxymethylation of alpha-ketoisovalerate followed by reduction. These intermediates are then condensed to give pantothenic acid. Phosphorylation of pantothenic acid followed by condensation with cysteine and decarboxylation gives 4'-phosphopantetheine. Adenylation and phosphorylation of 4'-phosphopantetheine completes the biosynthesis of coenzyme A. This review will focus on the mechanistic enzymology of coenzyme A biosynthesis in bacteria.
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Affiliation(s)
- T P Begley
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
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Metzler DE, Metzler CM, Sauke DJ. Enzymatic Addition, Elimination, Condensation, and Isomerization. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Sanders CR, Oxenoid K. Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1508:129-45. [PMID: 11090822 DOI: 10.1016/s0005-2736(00)00308-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.
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Affiliation(s)
- C R Sanders
- Department of Physiology and Biophysics, Case Western Reserve University, 44106-4970, Cleveland, OH, USA.
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Scheiner S, Gu Y, Kar T. Evaluation of the H-bonding properties of CH⋯O interactions based upon NMR spectra. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00375-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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