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Giang PD, Churchman LR, Stok JE, Bell SG, De Voss JJ. Cymredoxin, a [2Fe-2S] ferredoxin, supports catalytic activity of the p-cymene oxidising P450 enzyme CYP108N12. Arch Biochem Biophys 2023; 737:109549. [PMID: 36801262 DOI: 10.1016/j.abb.2023.109549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]
Abstract
Rhodococcus globerulus is a metabolically active organism that has been shown to utilise eucalypt oil as its sole source of carbon and energy. This oil includes 1,8-cineole, p-cymene and limonene. Two identified and characterised cytochromes P450 (P450s) from this organism initiate the biodegradation of the monoterpenes 1,8-cineole (CYP176A1) and p-cymene (CYP108N12). Extensive characterisation has been completed for CYP176A1 and it has been successfully reconstituted with its immediate redox partner, cindoxin, and E. coli flavodoxin reductase. Two putative redox partner genes are encoded in the same operon as CYP108N12 and here the isolation, expression, purification, and characterisation of its specific [2Fe-2S] ferredoxin redox partner, cymredoxin is presented. Reconstitution of CYP108N12 with cymredoxin in place of putidaredoxin, a [2Fe-2S] redox partner of another P450, improves both the rate of electron transfer (from 13 ± 2 to 70 ± 1 μM NADH/min/μM CYP108N12) and the efficiency of NADH utilisation (the so-called coupling efficiency increases from 13% to 90%). Cymredoxin improves the catalytic ability of CYP108N12 in vitro. Aldehyde oxidation products of the previously identified substrates p-cymene (4-isopropylbenzaldehyde) and limonene (perillaldehyde) were observed in addition to major hydroxylation products 4-isopropylbenzyl alcohol and perillyl alcohol respectively. These further oxidation products had not previously been seen with putidaredoxin supported oxidation. Furthermore, when supported by cymredoxin CYP108N12 is able to oxidise a wider range of substrates than previously reported. These include o-xylene, α-terpineol, (-)-carveol and thymol yielding o-tolylmethanol, 7-hydroxyterpineol, (4R)-7-hydroxycarveol and 5-hydroxymethyl-2-isopropylphenol, respectively. Cymredoxin is also capable of supporting CYP108A1 (P450terp) and CYP176A1 activity, allowing them to catalyse the hydroxylation of their native substrates α-terpineol to 7-hydroxyterpineol and 1,8-cineole to 6β-hydroxycineole respectively. These results indicate that cymredoxin not only improves the catalytic capability of CYP108N12 but can also support the activity of other P450s and prove useful for their characterisation.
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Affiliation(s)
- Peter D Giang
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia.
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2
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Lee YS, Ito T, Shimura K, Watanabe T, Bu HB, Hyeon-Deuk K, Kim D. Coupled electronic states in CdTe quantum dot assemblies fabricated by utilizing chemical bonding between ligands. NANOSCALE 2020; 12:7124-7133. [PMID: 32191241 DOI: 10.1039/d0nr00194e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Semiconductor quantum dot superlattices (QDSLs) have attracted much attention as key materials for realizing new optoelectronic devices such as solar cells with high conversion efficiency and thermoelectric elements with high electrical conductivity. To improve the charge transport properties of QDSL-based optoelectronic devices, it is important that the QD structures form minibands, which are the coupled electronic states between QDs. A shorter inter-QD distance and a periodic arrangement of QDs are the essential conditions for the formation of minibands. In this study, we use CdTe QDs capped with short ligands of N-acetyl-l cysteine (NAC) to fabricate three-dimensional QD assemblies by utilizing chemical bonding between NACs. Absorption spectra clearly display the quantum resonance phenomenon originating from the coupling of the wave functions between the adjacent QDs in CdTe QD assemblies. Furthermore, we demonstrate the formation of minibands in CdTe QD assemblies by examining both, the excitation energy dependence of photoluminescence (PL) spectra and the detection energy dependence of PL excitation spectra. The fabrication method of QD assemblies utilizing chemical bonding between NACs can be applied to all QDs capped with NAC as a ligand.
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Affiliation(s)
- Yong-Shin Lee
- Department of Applied Physics, Osaka City University, Osaka 558-8585, Japan.
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3
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Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. Nat Commun 2017; 8:955. [PMID: 29038582 PMCID: PMC5643538 DOI: 10.1038/s41467-017-01060-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/15/2017] [Indexed: 11/13/2022] Open
Abstract
Enzymes dependent on pyridoxal 5′-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase. Pyridoxal 5’-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.
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4
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Dajnowicz S, Parks JM, Hu X, Gesler K, Kovalevsky AY, Mueser TC. Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5'-phosphate in aspartate aminotransferase. J Biol Chem 2017; 292:5970-5980. [PMID: 28232482 DOI: 10.1074/jbc.m116.774588] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is a fundamental, multifunctional enzyme cofactor used to catalyze a wide variety of chemical reactions involved in amino acid metabolism. PLP-dependent enzymes optimize specific chemical reactions by modulating the electronic states of PLP through distinct active site environments. In aspartate aminotransferase (AAT), an extended hydrogen bond network is coupled to the pyridinyl nitrogen of the PLP, influencing the electrophilicity of the cofactor. This network, which involves residues Asp-222, His-143, Thr-139, His-189, and structural waters, is located at the edge of PLP opposite the reactive Schiff base. We demonstrate that this hydrogen bond network directly influences the protonation state of the pyridine nitrogen of PLP, which affects the rates of catalysis. We analyzed perturbations caused by single- and double-mutant variants using steady-state kinetics, high resolution X-ray crystallography, and quantum chemical calculations. Protonation of the pyridinyl nitrogen to form a pyridinium cation induces electronic delocalization in the PLP, which correlates with the enhancement in catalytic rate in AAT. Thus, PLP activation is controlled by the proximity of the pyridinyl nitrogen to the hydrogen bond microenvironment. Quantum chemical calculations indicate that Asp-222, which is directly coupled to the pyridinyl nitrogen, increases the pKa of the pyridine nitrogen and stabilizes the pyridinium cation. His-143 and His-189 also increase the pKa of the pyridine nitrogen but, more significantly, influence the position of the proton that resides between Asp-222 and the pyridinyl nitrogen. These findings indicate that the second shell residues directly enhance the rate of catalysis in AAT.
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Affiliation(s)
- Steven Dajnowicz
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606.,the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Jerry M Parks
- the University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Xiche Hu
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606
| | - Korie Gesler
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606
| | - Andrey Y Kovalevsky
- the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Timothy C Mueser
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606,
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5
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Chan-Huot M, Dos A, Zander R, Sharif S, Tolstoy PM, Compton S, Fogle E, Toney MD, Shenderovich I, Denisov GS, Limbach HH. NMR Studies of Protonation and Hydrogen Bond States of Internal Aldimines of Pyridoxal 5′-Phosphate Acid–Base in Alanine Racemase, Aspartate Aminotransferase, and Poly-l-lysine. J Am Chem Soc 2013; 135:18160-75. [DOI: 10.1021/ja408988z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monique Chan-Huot
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- Ecole Normale Supérieure, Laboratoire des BioMolécules, 24 rue Lhomond, 75231 Cedex 05, Paris, France
| | - Alexandra Dos
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Reinhard Zander
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Shasad Sharif
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Peter M. Tolstoy
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- Department
of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russian Federation
| | - Shara Compton
- Department
of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, Widener University, One University Place, Chester, Pennsylvania 19013, United States
| | - Emily Fogle
- Department
of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Chemistry & Biochemistry, CalPoly, San Luis Obispo, California 93407, United States
| | - Michael D. Toney
- Department
of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ilya Shenderovich
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- University of Regensburg, Universitätsstr.
31, 93040 Regensburg, Germany
| | - Gleb S. Denisov
- Institute
of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Hans-Heinrich Limbach
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
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Cooper AJL, Bruschi SA, Conway M, Hutson SM. Human mitochondrial and cytosolic branched-chain aminotransferases are cysteine S-conjugate beta-lyases, but turnover leads to inactivation. Biochem Pharmacol 2003; 65:181-92. [PMID: 12504794 DOI: 10.1016/s0006-2952(02)01513-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The mitochondrial and cytosolic branched-chain aminotransferases (BCAT(m) and BCAT(c)) are homodimers in the fold type IV class of pyridoxal 5'-phosphate-containing enzymes that also contains D-amino acid aminotransferase and 4-amino-4-deoxychorismate lyase (a beta-lyase). Recombinant human BCAT(m) and BCAT(c) were shown to have beta-lyase activity toward three toxic cysteine S-conjugates [S-(1,1,2,2-tetrafluoroethyl)-L-cysteine, S-(1,2-dichlorovinyl)-L-cysteine, and S-(2-chloro-1,1,2-trifluoroethyl)-L-cysteine] and toward beta-chloro-L-alanine. Human BCAT(m) is a much more effective beta-chloro-L-alanine beta-lyase than two aminotransferases (cytosolic and mitochondrial isozymes of aspartate aminotransferase) previously shown to possess this activity. BCAT(m), but not BCAT(c), also exhibits measurable beta-lyase activity toward a relatively bulky cysteine S-conjugate [benzothiazolyl-L-cysteine]. Benzothiazolyl-L-cysteine, however, inhibits the L-leucine-alpha-ketoglutarate transamination reaction catalyzed by both enzymes. Inhibition was more pronounced with BCAT(m). In the presence of beta-lyase substrates and alpha-ketoisocaproate (the alpha-keto acid analogue of leucine), no transamination could be detected. Therefore, with an amino acid containing a good leaving group in the beta position, beta-elimination is greatly preferred over transamination. Both BCAT isozymes are rapidly inactivated by the beta-lyase substrates. The ratio of turnover to inactivation per monomer in the presence of toxic halogenated cysteine S-conjugates is approximately 170-280 for BCAT(m) and approximately 40-50 for BCAT(c). Mitochondrial enzymes of energy metabolism are especially vulnerable to thioacylation and inactivation by the reactive fragment released from toxic, halogenated cysteine S-conjugates such as S-(1,1,2,2-tetrafluoroethyl)-L-cysteine. The present results suggest that BCAT isozymes may contribute to the mitochondrial toxicity of these compounds by providing thioacylating fragments, but inactivation of the BCAT isozymes might also block essential metabolic pathways.
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Affiliation(s)
- Arthur J L Cooper
- Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA.
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7
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Metzler DE, Metzler CM, Sauke DJ. Determining Structures and Analyzing Cells. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50006-4] [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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8
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Mildvan AS, Harris TK, Abeygunawardana C. Nuclear magnetic resonance methods for the detection and study of low-barrier hydrogen bonds on enzymes. Methods Enzymol 1999; 308:219-45. [PMID: 10507007 DOI: 10.1016/s0076-6879(99)08012-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- A S Mildvan
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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9
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Kahyaoglu A, Haghjoo K, Guo F, Jordan F, Kettner C, Felföldi F, Polgár L. Low barrier hydrogen bond is absent in the catalytic triads in the ground state but Is present in a transition-state complex in the prolyl oligopeptidase family of serine proteases. J Biol Chem 1997; 272:25547-54. [PMID: 9325271 DOI: 10.1074/jbc.272.41.25547] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
High frequency proton NMR spectra for two members of the prolyl oligopeptidase class of serine proteases, prolyl oligopeptidase and oligopeptidase B, showed that resonances corresponding to the active center histidine Ndelta1H and Nepsilon2H generally observed in this region, are absent in these enzymes. However, for both enzymes, as well as with the H652A and H652Q active center variants of oligopeptidase B, there are two resonances observed in this region that could be assigned to two protonated histidines with a noncatalytic function. The results indicate that these two histidines participate in strong hydrogen bonds. The absence of resonances pertinent to the active center histidine resonances suggests the absence of a low barrier hydrogen bond between the Asp and His in these two enzymes in their ground states. Addition of the peptide boronic acid t-butoxycarbonyl-(D)Val-Leu-(L)boroArg to oligopeptidase B resulted in potent, slow binding inhibition of the enzyme and the appearance of a new resonance at 15.8 ppm, whose chemical shift is appropriate for a tetrahedral boronate complex and a low barrier hydrogen bond. The results demonstrate important dissimilarities between the active centers of the prolyl oligopeptidase class of serine proteases and the pancreatic and subtilisin classes both in the ground state and in the transition-state analog complexes.
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Affiliation(s)
- A Kahyaoglu
- Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102, USA
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10
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Metzler DE. Nuclear magnetic resonance in study of active sites of pyridoxal-dependent enzymes. Methods Enzymol 1997; 280:30-40. [PMID: 9211302 DOI: 10.1016/s0076-6879(97)80098-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- D E Metzler
- Department of Biochemistry and Biophysics, Iowa State University, Ames 50011, USA
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11
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Ahmed SA, McPhie P, Miles EW. Mechanism of activation of the tryptophan synthase alpha2beta2 complex. Solvent effects of the co-substrate beta-mercaptoethanol. J Biol Chem 1996; 271:29100-6. [PMID: 8910565 DOI: 10.1074/jbc.271.46.29100] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
To characterize the conformational transitions that lead to activation of catalysis by the tryptophan synthase alpha2beta2 complex, we have determined the solvent effects of a co-substrate, beta-mercaptoethanol, and of a model nonsubstrate, ethanol, on the catalytic and spectroscopic properties of the enzyme. Our results show that ethanol and beta-mercaptoethanol both alter the equilibrium distribution of pyridoxal 5'-phosphate intermediates formed in the reactions of L-serine at the beta site in the alpha2beta2 complex. Addition of increasing concentrations of ethanol increases the proportion of the external aldimine of L-serine and decreases the proportion of the external aldimine of aminoacrylate. Low concentrations of the co-substrate beta-mercaptoethanol (Kd = approximately 13 mM) decrease the proportion of the external aldimine of aminoacrylate and induce formation of the quinonoid of S-hydroxyethyl-L-cysteine. Higher concentrations of beta-mercaptoethanol decrease the concentration of the quinonoid intermediate and increase the proportion of the external aldimine of L-serine. Data analysis shows that beta-mercaptoethanol and ethanol both interact or bind preferentially with the conformer of the enzyme that predominates when the aldimine of L-serine is formed and shift the equilibrium in favor of this conformer. We propose that a nonpolar region of the beta subunit, possibly the hydrophobic indole tunnel, becomes less exposed to solvent in the conformational transition that activates the alpha2beta2 complex.
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Affiliation(s)
- S A Ahmed
- Laboratory of Biochemical Pharmacology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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Tong H, Davis L. 2-Amino-3-ketobutyrate-CoA ligase from beef liver mitochondria: an NMR spectroscopic study of low-barrier hydrogen bonds of a pyridoxal 5'-phosphate-dependent enzyme. Biochemistry 1995; 34:3362-7. [PMID: 7880831 DOI: 10.1021/bi00010a027] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A study of protons associated with low-barrier hydrogen bonds in 2-amino-3-ketobutyrate-CoA ligase (AKB-ligase, EC 2.3.1.29) by NMR is reported. Three resonances are observed in the range of delta H = 15-20 ppm when the NMR spectrum of AKB-ligase is recorded at 600 MHz. These low-barrier hydrogen bonds are associated respectively with a side chain proton, the PLP pyridinium ring nitrogen proton, and the PLP Schiff base proton at the active site of the ligase. The pyridinium proton has been assigned a chemical shift of 19.10 ppm and the Schiff base proton 14.90 ppm. The third low-barrier hydrogen bond associated proton resonating at 16.20 ppm is assigned to a proton of a side chain group. All three resonances disappear when pyridoxal phosphate is removed from the ligase. Consistent with NOE coupling, the side chain group proton should be close to the proton of the Schiff base nitrogen of the pyridoxal 5'-phosphate. The effects of temperature, pH, substrate, and NOE on the three resonances are also studied, in order to assign the protons. The three low-barrier hydrogen bonds described in this report may serve to anchor the cofactor in the active site of 2-amino-3-ketobutyrate-CoA ligase.
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Affiliation(s)
- H Tong
- Department of Chemistry, University of Iowa, Iowa City 52242
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Metzler DE, Metzler CM, Scott RD, Mollova ET, Kagamiyama H, Yano T, Kuramitsu S, Hayashi H, Hirotsu K, Miyahara I. NMR studies of 1H resonances in the 10-18-ppm range for aspartate aminotransferase from Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)46890-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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