1
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Liang Y, Li W, Liang H, Lou X, Liu R, Zhang Q, Bartlam M. Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase. Biochem Biophys Res Commun 2021; 560:159-164. [PMID: 33992958 DOI: 10.1016/j.bbrc.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
The Kemp elimination reaction, involving the ring-opening of benzoxazole and its derivatives under the action of natural enzymes or chemical catalysts, has been of interest to researchers since its discovery. Because this reaction does not exist in all currently known metabolic pathways, the computational design of Kemp eliminases has provided valuable insights into principles of enzymatic catalysis. However, it was discovered that the naturally occurring promiscuous enzymes ydbC, xapA and ketosteroid isomerase also can catalyze Kemp elimination. Here, we report the crystal structure of ketosteroid isomerase (KSI) from Mycobacterium smegmatis MC2 155. MsKSI crystallizes in the P212121 space group with two molecules in an asymmetric unit, and ultracentrifugation data confirms that it forms a stable dimer in solution, consistent with the 1.9 Å-resolution structure. Our assays confirm that MsKSI accelerates the Kemp elimination of 5-nitrobenzoxazole (5NBI) with an optimal pH of 5.5. A 2.35 Å resolution crystal structure of the MsKSI-5NBI complex reveals that the substrate 5NBI is bound in the active pocket of the enzyme composed of hydrophobic residues. In addition, the Glu127 residue is proposed to play an important role as a general base in proton transfer and breaking weak O-N bonds to open the five-membered ring. This work provides a starting point for exploring the artificial modification of MsKSI using the natural enzyme as the backbone.
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Affiliation(s)
- Yakun Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Weiping Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Han Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaorui Lou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
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2
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Peng F, Cheng X, Wang H, Song S, Chen T, Li X, He Y, Huang Y, Liu S, Yang F, Su Z. Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ 5-3-ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:821-830. [PMID: 31226491 DOI: 10.1016/j.bbapap.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/25/2022]
Abstract
Protein engineering based on structure homology holds the potential to engineer steroid-transforming enzymes on demand. Based on the genome sequencing analysis of industrial Mycobacterium strain HGMS2 to produce 4-androstene-3,17-dione (4-AD), three hypothetical proteins were predicted as putative Δ5-3-ketosteroid isomerases (KSIs) to catalyze an intramolecular proton transfer involving the transformation of 5-androstene-3,17-dione (5-AD) into 4-AD, which were defined as mKSI228, mKSI291 and mKSI753. Activity assays indicated that mKSI228 and mKSI291 exhibited weak activity, as low as 0.7% and 1.5%, respectively, of a well-studied and highly active KSI from Pseudomonas putida KSI (pKSI), while mKSI753 had no activity similar to Mycobacterium tuberculosis KSI (mtKSI). Although the 3D structures of the putative mKSIs were homologous to pKSI, their amino acid sequences were significantly different from those of pKSI and tKSI. Thus, by use of these two KSIs as homology models, we were able to convert the low-active mKSI291 into a high-active active KSI by site-directed mutagenesis. On the other hand, an X-ray crystallographic structure of mKSI291 identified a water molecule in its active site. This unique water molecule might function as a bridge to connect Ser-OH, Tyr57-OH and C3O of the intermediate form a hydrogen-bonding network that was responsible for its weak activity, compared with that of mtKSI. Our results not only demonstrated the use of a protein engineering approach to understanding KSI catalytic mechanism, but also provided an example for engineering the catalytic active sites and gaining a functional enzyme based on homologous structures.
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Affiliation(s)
- Fei Peng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China; Wuhan Amersino Biodevelop Inc, B1-Building, Biolake Park, Wuhan 430075, China
| | - Hongwei Wang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Shikui Song
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Tian Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Xin Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Yijun He
- Hubei Goto Biotech Inc, No. 1 Baiguoshu Road, Shuidu Industrial Park, Danjiangkou, Hubei 442700, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Fei Yang
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China; Wuhan Amersino Biodevelop Inc, B1-Building, Biolake Park, Wuhan 430075, China.
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3
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Lamba V, Sanchez E, Fanning LR, Howe K, Alvarez MA, Herschlag D, Forconi M. Kemp Eliminase Activity of Ketosteroid Isomerase. Biochemistry 2017; 56:582-591. [PMID: 28045505 DOI: 10.1021/acs.biochem.6b00762] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kemp eliminases represent the most successful class of computationally designed enzymes, with rate accelerations of up to 109-fold relative to the rate of the same reaction in aqueous solution. Nevertheless, several other systems such as micelles, catalytic antibodies, and cavitands are known to accelerate the Kemp elimination by several orders of magnitude. We found that the naturally occurring enzyme ketosteroid isomerase (KSI) also catalyzes the Kemp elimination. Surprisingly, mutations of D38, the residue that acts as a general base for its natural substrate, produced variants that catalyze the Kemp elimination up to 7000-fold better than wild-type KSI does, and some of these variants accelerate the Kemp elimination more than the computationally designed Kemp eliminases. Analysis of the D38N general base KSI variant suggests that a different active site carboxylate residue, D99, performs the proton abstraction. Docking simulations and analysis of inhibition by active site binders suggest that the Kemp elimination takes place in the active site of KSI and that KSI uses the same catalytic strategies of the computationally designed enzymes. In agreement with prior observations, our results strengthen the conclusion that significant rate accelerations of the Kemp elimination can be achieved with very few, nonspecific interactions with the substrate if a suitable catalytic base is present in a hydrophobic environment. Computational design can fulfill these requirements, and the design of more complex and precise environments represents the next level of challenges for protein design.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States
| | - Enis Sanchez
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| | - Lauren Rose Fanning
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| | - Kathryn Howe
- Palmetto Homeschool Association , Rock Hill, South Carolina 29730, United States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States.,Department of Chemistry, Department of Chemical Engineering, and Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Marcello Forconi
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
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4
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Cha HJ, Jang DS, Jeong JH, Hong BH, Yun YS, Shin EJ, Choi KY. Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1322-7. [PMID: 27375051 DOI: 10.1016/j.bbapap.2016.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Bee Hak Hong
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Young Sung Yun
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Eun Ju Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kwan Yong Choi
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea.
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5
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Jang DS, Choi G, Cha HJ, Shin S, Hong BH, Lee HJ, Lee HC, Choi KY. Contribution of a low-barrier hydrogen bond to catalysis is not significant in ketosteroid isomerase. Mol Cells 2015; 38:409-15. [PMID: 25947291 PMCID: PMC4443282 DOI: 10.14348/molcells.2015.2266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 02/14/2015] [Accepted: 02/16/2015] [Indexed: 11/27/2022] Open
Abstract
Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. Δ(5)-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Δ(5)-3-ketosteroid to its conjugated Δ(4)-isomers at a rate that approaches the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 Oη and C3-O of equilenin, an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 Oη and C3-O of the bound steroid was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI.
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Affiliation(s)
- Do Soo Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Gildon Choi
- Korea Research Institute of Chemical Technology, Daejeon 305-343,
Korea
| | - Hyung Jin Cha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Sejeong Shin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115,
USA
| | - Bee Hak Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Hyeong Ju Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Hee Cheon Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Kwan Yong Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784,
Korea
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6
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Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Sci 2015; 24:762-78. [PMID: 25627867 PMCID: PMC4420525 DOI: 10.1002/pro.2648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/10/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.
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Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Nicholas A DeLateur
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Srinivas Somarowthu
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Walter R Novak
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Dagmar Ringe
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
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7
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Fried SD, Bagchi S, Boxer SG. Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science 2015; 346:1510-4. [PMID: 25525245 DOI: 10.1126/science.1259802] [Citation(s) in RCA: 316] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI's rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme's catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA
| | - Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-1052, USA.
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8
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Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry 2014; 53:2541-55. [PMID: 24597914 PMCID: PMC4004248 DOI: 10.1021/bi401671t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
positioning of catalytic groups within proteins plays an important
role in enzyme catalysis, and here we investigate the positioning
of the general base in the enzyme ketosteroid isomerase (KSI). The
oxygen atoms of Asp38, the general base in KSI, were previously shown
to be involved in anion–aromatic interactions with two neighboring
Phe residues. Here we ask whether those interactions are sufficient,
within the overall protein architecture, to position Asp38 for catalysis
or whether the side chains that pack against Asp38 and/or the residues
of the structured loop that is capped by Asp38 are necessary to achieve
optimal positioning for catalysis. To test positioning, we mutated
each of the aforementioned residues, alone and in combinations, in
a background with the native Asp general base and in a D38E mutant
background, as Glu at position 38 was previously shown to be mispositioned
for general base catalysis. These double-mutant cycles reveal positioning
effects as large as 103-fold, indicating that structural
features in addition to the overall protein architecture and the Phe
residues neighboring the carboxylate oxygen atoms play roles in positioning.
X-ray crystallography and molecular dynamics simulations suggest that
the functional effects arise from both restricting dynamic fluctuations
and disfavoring potential mispositioned states. Whereas it may have
been anticipated that multiple interactions would be necessary for
optimal general base positioning, the energetic contributions from
positioning and the nonadditive nature of these interactions are not
revealed by structural inspection and require functional dissection.
Recognizing the extent, type, and energetic interconnectivity of interactions
that contribute to positioning catalytic groups has implications for
enzyme evolution and may help reveal the nature and extent of interactions
required to design enzymes that rival those found in biology.
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Affiliation(s)
- Jason P Schwans
- Department of Biochemistry, Stanford University , B400 Beckman Center, 279 Campus Drive, Stanford, California 94305, United States
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9
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Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site. Proc Natl Acad Sci U S A 2013; 110:11308-13. [PMID: 23798413 DOI: 10.1073/pnas.1206710110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the cation-pi pair, formed between a side chain or substrate cation and the negative electrostatic potential of a pi system on the face of an aromatic ring, has been widely discussed and has been shown to be important in protein structure and protein-ligand interactions, there has been little discussion of the potential structural and functional importance in proteins of the related anion-aromatic pair (i.e., interaction of a negatively charged group with the positive electrostatic potential on the ring edge of an aromatic group). We posited, based on prior structural information, that anion-aromatic interactions between the anionic Asp general base and Phe54 and Phe116 might be used instead of a hydrogen-bond network to position the general base in the active site of ketosteroid isomerase from Comamonas testosteroni as there are no neighboring hydrogen-bonding groups. We have tested the role of the Phe residues using site-directed mutagenesis, double-mutant cycles, and high-resolution X-ray crystallography. These results indicate a catalytic role of these Phe residues. Extensive analysis of the Protein Data Bank provides strong support for a catalytic role of these and other Phe residues in providing anion-aromatic interactions that position anionic general bases within enzyme active sites. Our results further reveal a potential selective advantage of Phe in certain situations, relative to more traditional hydrogen-bonding groups, because it can simultaneously aid in the binding of hydrophobic substrates and positioning of a neighboring general base.
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10
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Hanoian P, Hammes-Schiffer S. Water in the active site of ketosteroid isomerase. Biochemistry 2011; 50:6689-700. [PMID: 21710970 DOI: 10.1021/bi200703y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable in WT KSI.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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11
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Childs W, Boxer SG. Proton affinity of the oxyanion hole in the active site of ketosteroid isomerase. Biochemistry 2010; 49:2725-31. [PMID: 20143849 DOI: 10.1021/bi100074s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The absorption spectra of a series of inhibitors bound at the active site of Delta(5)-3-ketosteroid isomerase from Pseudomonas putida were found to exhibit substantial variations in the contributions of the protonated and deprotonated forms. Systematic variation of the inhibitor solution pK(a) combined with a method of quantifying the contributions of each protonation state showed the oxyanion hole in the active site of wild-type Delta(5)-3-ketosteroid isomerase to have a proton affinity equal to a solution pK(a) of 10.05 +/- 0.03, which is similar to the measured pK(a) (10.0) of the reaction intermediate. This observation supports the prediction of Cleland, Kreevoy, Frey, Gassman, and Gerlt that an enzyme utilizing a strong hydrogen bond for catalysis matches the proton affinity of the protein to the intermediate [Cleland, W. W., and Kreevoy, M. M. (1994) Science 264, 1887-1890; Frey, P. A., Whitt, S., and Tobin, J. (1994) Science 264, 1927-1930; Gerlt, J. A., and Gassman, P. G. (1993) Biochemistry 32, 11934-11952]. As the difference in proton affinity decreases, the strength of the hydrogen bond increases, and the closely matched proton affinity between the active site and the reaction intermediate supports the possibility that a short, strong hydrogen bond is catalytically relevant in Delta(5)-3-ketosteroid isomerase.
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Affiliation(s)
- William Childs
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase. Proc Natl Acad Sci U S A 2009; 106:14271-5. [PMID: 19706511 DOI: 10.1073/pnas.0901032106] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fundamental difference between enzymes and small chemical catalysts is the ability of enzymes to use binding interactions with nonreactive portions of substrates to accelerate chemical reactions. Remote binding interactions can localize substrates to the active site, position substrates relative to enzymatic functional groups and other substrates, trigger conformational changes, induce local destabilization, and modulate an active site environment by solvent exclusion. We investigated the role of remote substrate binding interactions in the reaction catalyzed by the enzyme ketosteroid isomerase (KSI), which catalyzes a double bond migration of steroid substrates through a dienolate intermediate that is stabilized in an oxyanion hole. Comparison of a single-ring and multiple-ring substrate allowed the catalytic contribution of binding interactions with the distal substrate rings to be determined. The value of k(cat)/K(M) for a single-ring substrate is reduced 27,000-fold relative to a multiple-ring steroid substrate, suggesting that remote binding interactions with the steroid substrate contribute substantially to the KSI reaction. Nevertheless, the reaction rates for KSI-bound single- and multiple-ring substrates (k(cat)) are within 2-fold. Further, oxyanion hole mutations have the same effect on reactions of the single- and multiple-ring substrates. These results suggest that remote binding interactions contribute >5 kcal/mol to catalysis by KSI but that local rather than remote interactions dictate the catalytic contributions from KSI's general base and oxyanion hole.
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Yun YS, Nam GH, Kim YG, Oh BH, Choi KY. Small exterior hydrophobic cluster contributes to conformational stability and steroid binding in ketosteroid isomerase from Pseudomonas putida biotype B. FEBS J 2005; 272:1999-2011. [PMID: 15819891 DOI: 10.1111/j.1742-4658.2005.04627.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A structural motif called the small exterior hydrophobic cluster (SEHC) has been proposed to explain the stabilizing effect mediated by solvent-exposed hydrophobic residues; however, little is known about its biological roles. Unusually, in Delta(5)-3-ketosteroid isomerase from Pseudomonas putida biotype B (KSI-PI) Trp92 is exposed to solvent on the protein surface, forming a SEHC with the side-chains of Leu125 and Val127. In order to identify the role of the SEHC in KSI-PI, mutants of those amino acids associated with the SEHC were prepared. The W92A, L125A/V127A, and W92A/L125A/V127A mutations largely decreased the conformational stability, while the L125F/V127F mutation slightly increased the stability, indicating that hydrophobic packing by the SEHC is important in maintaining stability. The crystal structure of W92A revealed that the decreased stability caused by the removal of the bulky side-chain of Trp92 could be attributed to the destabilization of the surface hydrophobic layer consisting of a solvent-exposed beta-sheet. Consistent with the structural data, the binding affinities for three different steroids showed that the surface hydrophobic layer stabilized by SEHC is required for KSI-PI to efficiently recognize hydrophobic steroids. Unfolding kinetics based on analysis of the Phi(U) value also indicated that the SEHC in the native state was resistant to the unfolding process, despite its solvent-exposed site. Taken together, our results demonstrate that the SEHC plays a key role in the structural integrity that is needed for KSI-PI to stabilize the hydrophobic surface conformation and thereby contributes both to the overall conformational stability and to the binding of hydrophobic steroids in water solution.
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Affiliation(s)
- Young S Yun
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, South Korea
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Nam GH, Cha SS, Yun YS, Oh YH, Hong BH, Lee HS, Choi KY. The conserved cis-Pro39 residue plays a crucial role in the proper positioning of the catalytic base Asp38 in ketosteroid isomerase from Comamonas testosteroni. Biochem J 2003; 375:297-305. [PMID: 12852789 PMCID: PMC1223686 DOI: 10.1042/bj20030263] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Revised: 06/27/2003] [Accepted: 07/10/2003] [Indexed: 11/17/2022]
Abstract
KSI (ketosteroid isomerase) from Comamonas testosteroni is a homodimeric enzyme that catalyses the allylic isomerization of Delta5-3-ketosteroids to their conjugated Delta4-isomers at a reaction rate equivalent to the diffusion-controlled limit. Based on the structural analysis of KSI at a high resolution, the conserved cis-Pro39 residue was proposed to be involved in the proper positioning of Asp38, a critical catalytic residue, since the residue was found not only to be structurally associated with Asp38, but also to confer a structural rigidity on the local active-site geometry consisting of Asp38, Pro39, Val40, Gly41 and Ser42 at the flexible loop between b-strands B1 and B2. In order to investigate the structural role of the conserved cis-Pro39 residue near the active site of KSI, Pro39 was replaced with alanine or glycine. The free energy of activation for the P39A and P39G mutants increased by 10.5 and 16.7 kJ/mol (2.5 and 4.0 kcal/mol) respectively, while DG(U)H2O (the free-energy change for unfolding in the absence of urea at 25.00+/-0.02 degrees C) decreased by 31.0 and 35.6 kJ/mol (7.4 and 8.5 kcal/mol) respectively, compared with the wild-type enzyme. The crystal structure of the P39A mutant in complex with d-equilenin [d-1,3,5(10),6,8-estrapentaen-3-ol-17-one], a reaction intermediate analogue, determined at 2.3 A (0.23 nm) resolution revealed that the P39A mutation significantly disrupted the proper orientations of both d-equilenin and Asp38, as well as the local active-site geometry near Asp38, which resulted in substantial decreases in the activity and stability of KSI. Upon binding 1-anilinonaphthalene-8-sulphonic acid, the fluorescence intensities of the P39A and P39G mutants were increased drastically, with maximum wavelengths blue-shifted upon binding, indicating that the mutations might alter the hydrophobic active site of KSI. Taken together, our results demonstrate that the conserved cis-Pro39 residue plays a crucial role in the proper positioning of the critical catalytic base Asp38 and in the structural integrity of the active site in KSI.
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Affiliation(s)
- Gyu Hyun Nam
- National Research Laboratory of Protein Folding and Engineering, Pohang 790-784, Republic of Korea
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Yun YS, Lee TH, Nam GH, Jang DS, Shin S, Oh BH, Choi KY. Origin of the different pH activity profile in two homologous ketosteroid isomerases. J Biol Chem 2003; 278:28229-36. [PMID: 12734184 DOI: 10.1074/jbc.m302166200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two homologous Delta5-3-ketosteroid isomerases from Comamonas testosteroni (TI-WT) and Pseudomonas putida biotype B (PI-WT) exhibit different pH activity profiles. TI-WT loses activity below pH 5.0 due to the protonation of the conserved catalytic base, Asp-38, while PI-WT does not. Based on the structural analysis of PI-WT, the critical catalytic base, Asp-38, was found to form a hydrogen bond with the indole ring NH of Trp-116, which is homologously replaced with Phe-116 in TI-WT. To investigate the role of Trp-116, we prepared the F116W mutant of TI-WT (TI-F116W) and the W116F mutant of PI-WT (PI-W116F) and compared kinetic parameters of those mutants at different pH levels. PI-W116F exhibited significantly decreased catalytic activity at acidic pH like TI-WT, whereas TI-F116W maintained catalytic activity at acidic pH like PI-WT and increased the kcat/Km value by 2.5- to 4.7-fold compared with TI-WT at pH 3.8. The crystal structure of TI-F116W clearly showed that the indole ring NH of Trp-116 could form a hydrogen bond with the carboxyl oxygen of Asp-38 like that of PI-WT. The present results demonstrate that the activities of both PI-WT and TI-F116W at low pH were maintained by a tryptophan, which was able not only to lower the pKa value of the catalytic base but also to increase the substrate affinity. This is one example of the strategy nature can adopt to evolve the diversity of the catalytic function in the enzymes. Our results provide insight into deciphering the molecular evolution of the enzyme and creating novel enzymes by protein engineering.
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Affiliation(s)
- Young Sung Yun
- Division of Molecular and Life Sciences, the National Research Laboratory of Protein Folding and Engineering, Pohang University of Science and Technology, Pohang 790-784, South Korea
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Kim DH, Nam GH, Jang DS, Yun S, Choi G, Lee HC, Choi KY. Roles of dimerization in folding and stability of ketosteroid isomerase from Pseudomonas putida biotype B. Protein Sci 2001; 10:741-52. [PMID: 11274465 PMCID: PMC2373975 DOI: 10.1110/ps.18501] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Equilibrium and kinetic analyses have been performed to elucidate the roles of dimerization in folding and stability of KSI from Pseudomonas putida biotype B. Folding was reversible in secondary and tertiary structures as well as in activity. Equilibrium unfolding transition, as monitored by fluorescence and ellipticity measurements, could be modeled by a two-state mechanism without thermodynamically stable intermediates. Consistent with the two-state model, one dimensional (1D) NMR spectra and gel-filtration chromatography analysis did not show any evidence for a folded monomeric intermediate. Interestingly enough, Cys 81 located at the dimeric interface was modified by DTNB before unfolding. This inconsistent result might be explained by increased dynamic motion of the interface residues in the presence of urea to expose Cys 81 more frequently without the dimer dissociation. The refolding process, as monitored by fluorescence change, could best be described by five kinetic phases, in which the second phase was a bimolecular step. Because <30% of the total fluorescence change occurred during the first step, most of the native tertiary structure may be driven to form by the bimolecular step. During the refolding process, negative ellipticity at 225 nm increased very fast within 80 msec to account for >80% of the total amplitude. This result suggests that the protein folds into a monomer containing most of the alpha-helical structures before dimerization. Monitoring the enzyme activity during the refolding process could estimate the activity of the monomer that is not fully active. Together, these results stress the importance of dimerization in the formation and maintenance of the functional native tertiary structure.
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Affiliation(s)
- D H Kim
- Division of Molecular Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
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