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Nguyen K, DeSieno MA, Bae B, Johannes TW, Cobb RE, Zhao H, Nair SK. Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098. Org Biomol Chem 2019; 17:1506-1518. [PMID: 30681110 DOI: 10.1039/c8ob02840k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The latter steps in this biosynthetic pathway for the antimalarial phosphonic acid FR-900098 include the installation of a hydroxamate onto 3-aminopropylphosphonate, which is catalyzed by the consecutive actions of an acetyltransferase and an amine hydroxylase. Here, we present the 1.6 Å resolution co-crystal structure and accompanying biochemical characterization of FrbG, which catalyzes the hydroxylation of aminopropylphosphonate. We show that FrbG is a flavin-dependent N-hydroxylating monooxygenase (NMO), which shares a similar overall structure with flavin-containing monooxygenases (FMOs). Notably, we also show that the cytidine-5'-monophosphate moiety of the substrate is a critical determinant of specificity, distinguishing FrbG from other FMOs in that the nucleotide cofactor-binding domain also serves in conferring substrate recognition. In the FrbG-FAD+-NADPH co-crystal structure, the C4 of the NADPH nicotinamide is situated near the N5 of the FAD isoalloxazine, and is oriented with a distance and stereochemistry to facilitate hydride transfer.
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Affiliation(s)
- Kim Nguyen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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2
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Feklistov A, Bae B, Hauver J, Lass-Napiorkowska A, Kalesse M, Glaus F, Altmann KH, Heyduk T, Landick R, Darst SA. RNA polymerase motions during promoter melting. Science 2017; 356:863-866. [PMID: 28546214 PMCID: PMC5696265 DOI: 10.1126/science.aam7858] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/27/2017] [Indexed: 12/17/2022]
Abstract
All cellular RNA polymerases (RNAPs), from those of bacteria to those of man, possess a clamp that can open and close, and it has been assumed that the open RNAP separates promoter DNA strands and then closes to establish a tight grip on the DNA template. Here, we resolve successive motions of the initiating bacterial RNAP by studying real-time signatures of fluorescent reporters placed on RNAP and DNA in the presence of ligands locking the clamp in distinct conformations. We report evidence for an unexpected and obligatory step early in the initiation involving a transient clamp closure as a prerequisite for DNA melting. We also present a 2.6-angstrom crystal structure of a late-initiation intermediate harboring a rotationally unconstrained downstream DNA duplex within the open RNAP active site cleft. Our findings explain how RNAP thermal motions control the promoter search and drive DNA melting in the absence of external energy sources.
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Affiliation(s)
- Andrey Feklistov
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Brian Bae
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jesse Hauver
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, USA
| | - Markus Kalesse
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Florian Glaus
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10 8093 Zürich, Switzerland
| | - Karl-Heinz Altmann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10 8093 Zürich, Switzerland
| | - Tomasz Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Cobb RE, Bae B, Li Z, DeSieno MA, Nair SK, Zhao H. Structure-guided design and biosynthesis of a novel FR-900098 analogue as a potent Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) inhibitor. Chem Commun (Camb) 2015; 51:2526-8. [PMID: 25567100 DOI: 10.1039/c4cc09181g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the enzymatic biosynthesis of FR-900098 analogues and establish an in vivo platform for the biosynthesis of an N-propionyl derivative FR-900098P. FR-900098P is found to be a significantly more potent inhibitor of Plasmodium falciparum 1-deoxy-D-xylulose 5-phosphate reductoisomerase (PfDxr) than the parent compound, and thus a more promising antimalarial drug candidate.
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Affiliation(s)
- Ryan E Cobb
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA
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Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. eLife 2015; 4. [PMID: 26349034 PMCID: PMC4593161 DOI: 10.7554/elife.08505] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/04/2015] [Indexed: 01/25/2023] Open
Abstract
A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD. DOI:http://dx.doi.org/10.7554/eLife.08505.001 Inside cells, molecules of double-stranded DNA encode the instructions needed to make proteins. To make a protein, the two strands of DNA that make up a gene are separated and one strand acts as a template to make molecules of messenger ribonucleic acid (or mRNA for short). This process is called transcription. The mRNA is then used as a template to assemble the protein. An enzyme called RNA polymerase carries out transcription and is found in all cells ranging from bacteria to humans and other animals. Bacteria have the simplest form of RNA polymerase and provide an excellent system to study how it controls transcription. It is made up of several proteins that work together to make RNA using DNA as a template. However, it requires the help of another protein called sigma factor to direct it to regions of DNA called promoters, which are just before the start of the gene. When RNA polymerase and the sigma factor interact the resulting group of proteins is known as the RNA polymerase ‘holoenzyme’. Transcription takes place in several stages. To start with, the RNA polymerase holoenzyme locates and binds to promoter DNA. Next, it separates the two strands of DNA and exposes a portion of the template strand. At this point, the DNA and the holoenzyme are said to be in an ‘open promoter complex’ and the section of promoter DNA that is within it is known as a ‘transcription bubble’. Another protein called CarD helps to speed up transcription but it is not clear how this stage of the process works. Bae et al. have now used X-ray crystallography to reveal the structure of CarD bound to the RNA polymerase holoenyzme and a DNA promoter. The structures show that one part of CarD interacts with the DNA at the start of the transcription bubble, and another part binds to the RNA polymerase. CarD fits between the two strands of DNA in the promoter, like a wedge, to keep the strands apart. Therefore, CarD stabilizes the open promoter complex and prevents the transcription bubble from collapsing. These findings reveal a previously unseen mechanism involved in activating transcription and will guide further experiments probing the role of CarD in living cells. Another study by Bae, Feklistov et al.—which involves some of the same researchers as this study—reveals that the sigma factor also binds to DNA at the start of the transcription bubble. The general principles outlined by these studies may help to identify other proteins that regulate transcription. DOI:http://dx.doi.org/10.7554/eLife.08505.002
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Affiliation(s)
- Brian Bae
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - James Chen
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Elizabeth Davis
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Katherine Leon
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Seth A Darst
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Elizabeth A Campbell
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
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Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 2015; 4. [PMID: 26349032 PMCID: PMC4593229 DOI: 10.7554/elife.08504] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/03/2015] [Indexed: 01/17/2023] Open
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the −10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the −10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation. DOI:http://dx.doi.org/10.7554/eLife.08504.001 Inside cells, molecules of double-stranded DNA encode the instructions needed to make proteins. To make a protein, the two strands of DNA that make up a gene are separated and one strand acts as a template to make molecules of messenger ribonucleic acid (or mRNA for short). This process is called transcription. The mRNA is then used as a template to assemble the protein. An enzyme called RNA polymerase carries out transcription and is found in all cells ranging from bacteria to humans and other animals. Bacteria have the simplest form of RNA polymerase and provide an excellent system to study how it controls transcription. It is made up of several proteins that work together to make RNA using DNA as a template. However, it requires the help of another protein called sigma factor to direct it to regions of DNA called promoters, which are just before the start of the gene. When RNA polymerase and the sigma factor interact the resulting group of proteins is known as the RNA polymerase ‘holoenzyme’. Transcription takes place in several stages. To start with, the RNA polymerase holoenzyme locates and binds to promoter DNA. Next, it separates the two strands of DNA and exposes a portion of the template strand. At this point, the DNA and the holoenzyme are said to be in an ‘open promoter complex’ and the section of promoter DNA that is within it is known as a ‘transcription bubble’. However, it is not clear how RNA polymerase holoenzyme interacts with DNA in the open promoter complex. Bae, Feklistov et al. have now used X-ray crystallography to reveal the three-dimensional structure of the open promoter complex with an entire transcription bubble from a bacterium called Thermus aquaticus. The experiments show that there are several important interactions between RNA polymerase holoenzyme and promoter DNA. In particular, the sigma factor inserts into a region of the DNA at the start of the transcription bubble. This rearranges the DNA in a manner that allows the DNA to be exposed and contact the main part of the RNA polymerase. If the holoenyzyme fails to contact the DNA in this way, the holoenzyme does not bind properly to the promoter and transcription does not start. These findings build on previous work to provide a detailed structural framework for understanding how the RNA polymerase holoenzyme and DNA interact to form the open promoter complex. Another study by Bae et al.—which involved some of the same researchers as this study—reveals how another protein called CarD also binds to DNA at the start of the transcription bubble to stabilize the open promoter complex. DOI:http://dx.doi.org/10.7554/eLife.08504.002
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Affiliation(s)
- Brian Bae
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Andrey Feklistov
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-madison, Madison, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
| | - Seth A Darst
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
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6
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Han Y, Agarwal V, Dodd D, Kim J, Bae B, Mackie RI, Nair SK, Cann IKO. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus. J Biol Chem 2012; 287:34946-34960. [PMID: 22918832 DOI: 10.1074/jbc.m112.391532] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.
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Affiliation(s)
- Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Vinayak Agarwal
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801
| | - Jason Kim
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801
| | - Brian Bae
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Satish K Nair
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.
| | - Isaac K O Cann
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801.
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Bae B, Cobb RE, DeSieno MA, Zhao H, Nair SK. New N-acetyltransferase fold in the structure and mechanism of the phosphonate biosynthetic enzyme FrbF. J Biol Chem 2011; 286:36132-36141. [PMID: 21865168 DOI: 10.1074/jbc.m111.263533] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The enzyme catalyzes acetyl transfer onto the hydroxamate of the FR-900098 precursors cytidine 5'-monophosphate-3-aminopropylphosphonate and cytidine 5'-monophosphate-N-hydroxy-3-aminopropylphosphonate. Despite the established function as a bona fide N-acetyltransferase, FrbF shows no sequence similarity to any member of the GCN5-like N-acetyltransferase (GNAT) superfamily. Here, we present the 2.0 Å resolution crystal structure of FrbF in complex with acetyl-CoA, which demonstrates a unique architecture that is distinct from those of canonical GNAT-like acetyltransferases. We also utilized the co-crystal structure to guide structure-function studies that identified the roles of putative active site residues in the acetyltransferase mechanism. The combined biochemical and structural analyses of FrbF provide insights into this previously uncharacterized family of N-acetyltransferases and also provide a molecular framework toward the production of novel N-acyl derivatives of FR-900098.
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Affiliation(s)
- Brian Bae
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Matthew A DeSieno
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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Yoshida S, Park DS, Bae B, Mackie R, Cann IKO, Nair SK. Structural and Functional Analyses of a Glycoside Hydrolase Family 5 Enzyme with an Unexpected β-Fucosidase Activity. Biochemistry 2011; 50:3369-75. [DOI: 10.1021/bi200222u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shosuke Yoshida
- Department of Biochemistry, ‡Energy Biosciences Institute, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Department of Microbiology, and &Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - David S. Park
- Department of Biochemistry, ‡Energy Biosciences Institute, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Department of Microbiology, and &Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Brian Bae
- Department of Biochemistry, ‡Energy Biosciences Institute, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Department of Microbiology, and &Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Roderick Mackie
- Department of Biochemistry, ‡Energy Biosciences Institute, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Department of Microbiology, and &Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Isaac K. O. Cann
- Department of Biochemistry, ‡Energy Biosciences Institute, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Department of Microbiology, and &Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, ‡Energy Biosciences Institute, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Department of Microbiology, and &Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States
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9
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Su X, Agarwal V, Dodd D, Bae B, Mackie RI, Nair SK, Cann IKO. Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules. J Biol Chem 2010; 285:34665-76. [PMID: 20739280 DOI: 10.1074/jbc.m110.168302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate binding modules (CBMs) are specialized proteins that bind to polysaccharides and oligosaccharides. Caldanaerobius polysaccharolyticus Man5ACBM16-1/CBM16-2 bind to glucose-, mannose-, and glucose/mannose-configured substrates. The crystal structures of the two proteins represent the only examples in CBM family 16, and studies that evaluate the roles of amino acid residues in ligand binding in this family are lacking. In this study, we probed the roles of amino acids (selected based on CBM16-1/ligand co-crystal structures) on substrate binding. Two tryptophan (Trp-20 and Trp-125) and two glutamine (Gln-81 and Gln-93) residues are shown to be critical in ligand binding. Additionally, several polar residues that flank the critical residues also contribute to ligand binding. The CBM16-1 Q121E mutation increased affinity for all substrates tested, whereas the Q21G and N97R mutants exhibited decreased substrate affinity. We solved CBM/substrate co-crystal structures to elucidate the molecular basis of the increased substrate binding by CBM16-1 Q121E. The Gln-121, Gln-21, and Asn-97 residues can be manipulated to fine-tune ligand binding by the Man5A CBMs. Surprisingly, none of the eight residues investigated was absolutely conserved in CBM family 16. Thus, the critical residues in the Man5A CBMs are either not essential for substrate binding in the other members of this family or the two CBMs are evolutionarily distinct from the members available in the current protein database. Man5A is dependent on its CBMs for robust activity, and insights from this study should serve to enhance our understanding of the interdependence of its catalytic and substrate binding modules.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
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Bae B, Dodd D, Mackie R, Cann I, Nair S. Structure and Function of a Novel Bi‐Functional Xylanase‐Esterase. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.lb213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Dylan Dodd
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL
- Institute of Genomic BiologyUrbanaIL
| | - Roderick Mackie
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL
- Institute of Genomic BiologyUrbanaIL
| | - Isaac Cann
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL
- Institute of Genomic BiologyUrbanaIL
| | - Satish Nair
- Department of Biochemsitry
- Institute of Genomic BiologyUrbanaIL
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Bae B, Chen YH, Costa A, Onesti S, Brunzelle JS, Lin Y, Cann IK, Nair SK. Insights into the Architecture of the Replicative Helicase from the Structure of an Archaeal MCM Homolog. Structure 2009; 17:211-22. [DOI: 10.1016/j.str.2008.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 11/13/2008] [Accepted: 11/13/2008] [Indexed: 10/21/2022]
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13
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Bae B, Ohene-Adjei S, Kocherginskaya S, Mackie RI, Spies MA, Cann IK, Nair SK. Molecular Basis for the Selectivity and Specificity of Ligand Recognition by the Family 16 Carbohydrate-binding Modules from Thermoanaerobacterium polysaccharolyticum ManA. J Biol Chem 2008; 283:12415-25. [DOI: 10.1074/jbc.m706513200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Yeom J, Oh I, Field C, Radadia A, Ni Z, Bae B, Han J, Masel R, Shannon M. Enhanced toxic gas detection using a MEMS preconcentrator coated with the metal organic framework absorber. ACTA ACUST UNITED AC 2008. [DOI: 10.1109/memsys.2008.4443635] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Local zones of easily unwound DNA are characteristic of prokaryotic and eukaryotic replication origins. The DNA-unwinding element of the human c-myc replication origin is essential for replicator activity and is a target of the DNA-unwinding element-binding protein DUE-B in vivo. We present here the 2.0A crystal structure of DUE-B and complementary biochemical characterization of its biological activity. The structure corresponds to a dimer of the N-terminal domain of the full-length protein and contains many of the structural elements of the nucleotide binding fold. A single magnesium ion resides in the putative active site cavity, which could serve to facilitate ATP hydrolytic activity of this protein. The structure also demonstrates a notable similarity to those of tRNA-editing enzymes. Consistent with this structural homology, the N-terminal core of DUE-B is shown to display both D-aminoacyl-tRNA deacylase activity and ATPase activity. We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA.
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Affiliation(s)
- Michael Kemp
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA
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Nair SK, Bae B, Lin K, Cann IK. Crystal Structure of an Archaeal Replication Protein A Homolog. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.lb56-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Satish K. Nair
- BiochemistryUniversity of Illinois at Urbana‐Champaign427 RAL/600 S. Mathews AveUrbanaIL61801
| | - Brian Bae
- BiochemistryUniversity of Illinois at Urbana‐Champaign427 RAL/600 S. Mathews AveUrbanaIL61801
| | - Kent Lin
- Animal SciencesUniversity of Illinois at Urbana‐Champaign456 ASL/1207 W Gregory Dr.UrbanaIL61801
| | - Isaac K. Cann
- Animal SciencesUniversity of Illinois at Urbana‐Champaign456 ASL/1207 W Gregory Dr.UrbanaIL61801
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Bae B, Jeong JH, Lee SJ. The quantification and characterization of endocrine disruptor bisphenol-A leaching from epoxy resin. Water Sci Technol 2002; 46:381-387. [PMID: 12523782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bisphenol-A (BPA), a known endocrine disruptor, is a main building block of epoxy resin which has been widely used as a surface coating agent on residential water storage tanks. Therefore, BPA leaching from the epoxy resin can adversely affect human health. In this study, BPA leaching from three epoxy resins were quantified at 20, 50, 75 and 100 degrees C both in deionized water and the specified test water, respectively. BPA leached to the test water was identified using GC-MS and quantified with GC-FID after a sequential extraction and concentration. The results showed that BPA leaching has occurred in all three samples tested. The quantity of BPA from unit area of epoxy resin coating was in the range of 01.68-273. 12 microg/m2 for sample A, 29.74-1734.05 microg/m2 for sample B and 52.86-548.78 microg/m2 for sample C depending on the test temperature, respectively. In general, the amount of BPA leashing increased as the water temperature increases. This result implies a higher risk of BPA leaching to drinking water during a summer season. In addition, microbial growth, measured by colony forming units, in epoxy coated water tanks was higher than that in a stainless steel tank. The results suggest that compounds leaching from epoxy resin may support the growth of microorganisms in a residential water holding tank.
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Affiliation(s)
- B Bae
- Department of Civil & Environmental Engineering, Kyungwon University, Sungnam, Kyunggi, Korea
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Abstract
The objective of this study was to determine how copper influences the ability of HL-60 cells to differentiate into cells of the granulocytic lineage. We hypothesized that granulopoiesis requires copper because copper-deficient humans become neutropenic. Differentiation of HL-60 cells along the granulocytic lineage with retinoic acid was enhanced by copper. The results showed a greater number of cells were more differentiated when copper was added to the medium for 96 h. The respiratory burst activity of retinoic acid-induced cells was increased by copper supplementation, but intracellular superoxide anion generation was not affected. Supplementation with copper resulted in more cell-associated copper in both noninduced and induced cells; however, the induced cells accumulated three times more copper than the noninduced cells. Even though the amount of copper associated with retinoic acid-treated cells was greater than in untreated cells, the activity of a copper-requiring enzyme, copper/zinc superoxide dismutase, was significantly lower. Copper supplementation increased the activity of this enzyme in both retinoic acid-treated and untreated cells. Cytochrome c oxidase activity was not affected by retinoic acid treatment or by copper supplementation. Copper seems to play a specific role during the early stages of granulocyte differentiation.
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Affiliation(s)
- B Bae
- Food Science and Human Nutrition Department, University of Florida, Gainesville 32611
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Percival SS, Bae B, Patrice M. Copper is required to maintain Cu/Zn-superoxide dismutase activity during HL-60 cell differentiation. Proc Soc Exp Biol Med 1993; 203:78-83. [PMID: 7682718 DOI: 10.3181/00379727-203-43576] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The objective of these studies was to characterize the relationship between copper levels and Cu/Zn superoxide dismutase (Cu/Zn-SOD) during cellular differentiation. It was hypothesized that the decrease in Cu/Zn-SOD activity that accompanied differentiation would be reversed by supplementing the culture medium with copper. HL-60 cells, a human promyelocytic cell line, were induced to differentiate with retinoic acid and were concurrently supplemented with copper or a copper chelator, tetraethylenepentamine. The results showed that retinoic acid-treated cells contained more copper after differentiation. When the medium was supplemented with copper during retinoic acid treatment, the differentiating cells accumulated more copper than the nondifferentiating cells. Differentiation was accompanied by a significant reduction in Cu/Zn-SOD activity and a slight reduction in Cu/Zn-SOD protein. Activity returned to control values when an extracellular source of copper was provided. Incubation of retinoic acid-treated cells with the chelator showed that they lost proportionally less copper than the noninduced controls. Levels of Cu/Zn-SOD protein were not affected by the copper or chelator treatments. It was concluded that the requirement of differentiating HL-60 cells for copper is not related to providing copper for Cu/Zn-SOD activity. If a supplemental source is not supplied in the medium, then the cells may acquire copper from an intracellular source, namely Cu/Zn-SOD.
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Affiliation(s)
- S S Percival
- Food Science and Human Nutrition Department, University of Florida, Gainesville 32611
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