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Nakasone MA, Majorek KA, Gabrielsen M, Sibbet GJ, Smith BO, Huang DT. Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension. Nat Chem Biol 2022; 18:422-431. [PMID: 35027744 PMCID: PMC8964413 DOI: 10.1038/s41589-021-00952-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.
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Affiliation(s)
| | | | - Mads Gabrielsen
- Cancer Research UK Beatson Institute, Glasgow, UK
- MVLS Structural Biology and Biophysical Characterisation Facility, University of Glasgow, Glasgow, UK
| | | | - Brian O Smith
- Institute of Molecular Cell and System Biology, University of Glasgow, Glasgow, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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2
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Baumgartner JT, Habeeb Mohammad TS, Czub MP, Majorek KA, Arolli X, Variot C, Anonick M, Minor W, Ballicora MA, Becker DP, Kuhn ML. Gcn5-Related N-Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too. Front Mol Biosci 2021; 8:646046. [PMID: 33912589 PMCID: PMC8072286 DOI: 10.3389/fmolb.2021.646046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Enzymes in the Gcn5-related N-acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead of a general acid/base mechanism. To simplify this enzyme's kinetic characterization, we synthesized a polymyxin B substrate analog and performed molecular docking experiments. We performed site-directed mutagenesis of key active site residues (S148 and E102) and determined the structure of the E102A mutant. We found that the serine residue is essential for catalysis toward the synthetic substrate analog and polymyxin B, but the glutamate residue is more likely important for substrate recognition or stabilization. Our results challenge the current paradigm of GNAT mechanisms and show that this common enzyme scaffold utilizes different active site residues to accomplish a diversity of catalytic reactions.
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Affiliation(s)
- Jackson T. Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | | | - Mateusz P. Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, United States
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, United States
| | - Xhulio Arolli
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Cillian Variot
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Madison Anonick
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, United States
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
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3
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Shabalin IG, Czub MP, Majorek KA, Brzezinski D, Grabowski M, Cooper DR, Panasiuk M, Chruszcz M, Minor W. Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy. IUCrJ 2020; 7:S2052252520012944. [PMID: 33063792 PMCID: PMC7553145 DOI: 10.1107/s2052252520012944] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/22/2020] [Indexed: 05/06/2023]
Abstract
Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Here, the first structure of serum albumin in complex with dexamethasone is reported. Dexamethasone binds to drug site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with an analysis of publicly available clinical data from Wuhan and suggests that an adjustment of the dexamethasone regimen should be further investigated as a strategy for patients affected by two major COVID-19 risk factors: low albumin levels and diabetes.
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Affiliation(s)
- Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz P. Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz Panasiuk
- Department of Clinical Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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4
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Shabalin IG, Czub MP, Majorek KA, Brzezinski D, Grabowski M, Cooper DR, Panasiuk M, Chruszcz M, Minor W. Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy. bioRxiv 2020:2020.07.21.212704. [PMID: 32743572 PMCID: PMC7386489 DOI: 10.1101/2020.07.21.212704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Herein, we report the first structure of serum albumin in complex with dexamethasone. We show that it binds to Drug Site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with our analysis of publicly available clinical data from Wuhan and suggests that an adjustment of dexamethasone regimen should be considered for patients affected by two major COVID-19 risk-factors: low albumin levels and diabetes.
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Affiliation(s)
- Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz P. Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz Panasiuk
- Medical University of Bialystok, Department of Clinical Medicine, 15-089 Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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5
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Czub MP, Venkataramany BS, Majorek KA, Handing KB, Porebski PJ, Beeram SR, Suh K, Woolfork AG, Hage DS, Shabalin IG, Minor W. Testosterone meets albumin - the molecular mechanism of sex hormone transport by serum albumins. Chem Sci 2018; 10:1607-1618. [PMID: 30842823 PMCID: PMC6371759 DOI: 10.1039/c8sc04397c] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/07/2018] [Indexed: 12/23/2022] Open
Abstract
Serum albumin is the most abundant protein in mammalian blood plasma and is responsible for the transport of metals, drugs, and various metabolites, including hormones. We report the first albumin structure in complex with testosterone, the primary male sex hormone. Testosterone is bound in two sites, neither of which overlaps with the previously suggested Sudlow site I. We determined the binding constant of testosterone to equine and human albumins by two different methods: tryptophan fluorescence quenching and ultrafast affinity extraction. The binding studies and similarities between residues comprising the binding sites on serum albumins suggest that testosterone binds to the same sites on both proteins. Our comparative analysis of albumin complexes with hormones, drugs, and other biologically relevant compounds strongly suggests interference between a number of compounds present in blood and testosterone transport by serum albumin. We discuss a possible link between our findings and some phenomena observed in human patients, such as low testosterone levels in diabetic patients.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ; .,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
| | - Barat S Venkataramany
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
| | - Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ; .,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
| | - Sandya R Beeram
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - Kyungah Suh
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - Ashley G Woolfork
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - David S Hage
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ; .,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ; .,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
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6
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Czub MP, Zhang B, Chiarelli MP, Majorek KA, Joe L, Porebski PJ, Revilla A, Wu W, Becker DP, Minor W, Kuhn ML. A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro. Biochemistry 2018; 57:7011-7020. [PMID: 30499668 DOI: 10.1021/acs.biochem.8b00946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deeper exploration of uncharacterized Gcn5-related N-acetyltransferases has the potential to expand our knowledge of the types of molecules that can be acylated by this important superfamily of enzymes and may offer new opportunities for biotechnological applications. While determining native or biologically relevant in vivo functions of uncharacterized proteins is ideal, their alternative or promiscuous in vitro capabilities provide insight into key active site interactions. Additionally, this knowledge can be exploited to selectively modify complex molecules and reduce byproducts when synthetic routes become challenging. During our exploration of uncharacterized Gcn5-related N-acetyltransferases from Pseudomonas aeruginosa, we identified such an example. We found that the PA3944 enzyme acetylates both polymyxin B and colistin on a single diaminobutyric acid residue closest to the macrocyclic ring of the antimicrobial peptide and determined the PA3944 crystal structure. This finding is important for several reasons. (1) To the best of our knowledge, this is the first report of enzymatic acylation of polymyxins and thus reveals a new type of substrate that this enzyme family can use. (2) The enzymatic acetylation offers a controlled method for antibiotic modification compared to classical promiscuous chemical methods. (3) The site of acetylation would reduce the overall positive charge of the molecule, which is important for reducing nephrotoxic effects and may be a salvage strategy for this important class of antibiotics. While the physiological substrate for this enzyme remains unknown, our structural and functional characterization of PA3944 offers insight into its unique noncanonical substrate specificity.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Brian Zhang
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - M Paul Chiarelli
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Layton Joe
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Alina Revilla
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Weiming Wu
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
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7
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Pote S, Pye SE, Sheahan TE, Gawlicka-Chruszcz A, Majorek KA, Chruszcz M. 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog. Biochem Biophys Res Commun 2018; 503:1993-1999. [PMID: 30093108 PMCID: PMC6192261 DOI: 10.1016/j.bbrc.2018.07.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023]
Abstract
Neisseria gonorrhoeae, an obligate human pathogen, is a leading cause of communicable diseases globally. Due to rapid development of drug resistance, the rate of successfully curing gonococcal infections is rapidly decreasing. Hence, research is being directed toward finding alternative drugs or drug targets to help eradicate these infections. 4-Hydroxy-tetrahydrodipicolinate reductase (DapB), an important enzyme in the meso-diaminopimelate pathway, is a promising target for the development of new antibiotics. This manuscript describes the first structure of DapB from N. gonorrhoeae determined at 1.85 Å. This enzyme uses NAD(P)H as cofactor. Details of the interactions of the enzyme with its cofactors and a substrate analog/inhibitor are discussed. A large scale bioinformatics analysis of DapBs' sequences is also described.
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Affiliation(s)
- Swanandi Pote
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sarah E. Pye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Tyler E. Sheahan
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Anna Gawlicka-Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
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8
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Booth WT, Morris TL, Mysona DP, Shah MJ, Taylor LK, Karlin TW, Clary K, Majorek KA, Offermann LR, Chruszcz M. Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH 3 -dependent NAD + synthetase. FEBS J 2017; 284:2425-2441. [PMID: 28618168 PMCID: PMC5551413 DOI: 10.1111/febs.14136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/08/2017] [Accepted: 06/12/2017] [Indexed: 11/27/2022]
Abstract
Streptococcus pyogenes, also known as Group A Strep (GAS), is an obligate human pathogen that is responsible for millions of infections and numerous deaths per year. Infection manifestations can range from simple, acute pharyngitis to more complex, necrotizing fasciitis. To date, most treatments for GAS infections involve the use of common antibiotics including tetracycline and clindamycin. Unfortunately, new strains have been identified that are resistant to these drugs, therefore, new targets must be identified to treat drug-resistant strains. This work is focused on the structural and functional characterization of three proteins: spNadC, spNadD, and spNadE. These enzymes are involved in the biosynthesis of nicotinamide adenine dinucleotide (NAD+ ). The structures of spNadC and spNadE were determined. SpNadC is suggested to play a role in GAS virulence, while spNadE, functions as an NAD synthetase and is considered to be a new drug target. Determination of the spNadE structure uncovered a putative, NH3 channel, which may provide insight into the mechanistic details of NH3 -dependent NAD+ synthetases in prokaryotes. ENZYMES Quinolinate phosphoribosyltransferase: EC2.4.2.19 and NAD synthetase: EC6.3.1.5. DATABASE Protein structures for spNadC, spNadCΔ69A , and spNadE are deposited into Protein Data Bank under the accession codes 5HUL, 5HUO & 5HUP, and 5HUH & 5HUJ, respectively.
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Affiliation(s)
- William T. Booth
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Trevor L. Morris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - David P. Mysona
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Milan J. Shah
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Linda K. Taylor
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Taylor W. Karlin
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Kathryn Clary
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908
| | - Lesa R. Offermann
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
- Department of Chemistry, Davidson College, Davidson, NC 28035
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
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9
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Reidl C, Majorek KA, Dang J, Tran D, Jew K, Law M, Payne Y, Minor W, Becker DP, Kuhn ML. Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases. FEBS Lett 2017; 591:2348-2361. [PMID: 28703494 PMCID: PMC5578807 DOI: 10.1002/1873-3468.12753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 01/07/2023]
Abstract
Gcn5-related N-acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor-bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X-ray induced radical-mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely applicable across the GNAT superfamily and can be used to improve the success rate of obtaining liganded structures of other acyltransferases.
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Affiliation(s)
- Cory Reidl
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Joseph Dang
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - David Tran
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Kristen Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Yasmine Payne
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Daniel P. Becker
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA,To whom correspondence may be addressed: Either Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, Tel.: 773-508-3089;
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA,To whom correspondence may be addressed: Either Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, Tel.: 773-508-3089;
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10
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Majorek KA, Osinski T, Tran DT, Revilla A, Anderson WF, Minor W, Kuhn ML. Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria. Biochim Biophys Acta Proteins Proteom 2017; 1865:55-64. [PMID: 27783928 PMCID: PMC5127773 DOI: 10.1016/j.bbapap.2016.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 09/26/2016] [Accepted: 10/20/2016] [Indexed: 01/07/2023]
Abstract
Members of the Gcn5-related N-acetyltransferase (GNAT) superfamily catalyze the acetylation of a wide range of small molecule and protein substrates. Due to their abundance in all kingdoms of life and diversity of their functions, they are implicated in many aspects of eukaryotic and prokaryotic physiology. Although numerous GNATs have been identified thus far, many remain structurally and functionally uncharacterized. The elucidation of their structures and functions is critical for broadening our knowledge of this diverse and important superfamily. In this work, we present the structural and kinetic analyses of two previously uncharacterized bacterial acetyltransferases - SACOL1063 from Staphylococcus aureus strain COL and CD1211 from Clostridium difficile strain 630. Our structures of SACOL1063 show substantial flexibility of a loop that is likely responsible for substrate recognition and binding compared to structures of other homologs. In the CoA complex structure, we found two CoA molecules bound in both the canonical AcCoA/CoA-binding site and the acceptor-substrate-binding site. Our work also provides initial clues regarding the substrate specificity of these two enzymes; however, their native function(s) remain unknown. We found both proteins act as N- rather than O-acetyltransferases and preferentially acetylate l-threonine. The combination of structural and kinetic analyses of these two previously uncharacterized GNATs provides fundamental knowledge and a framework on which future studies can be built to elucidate their native functions.
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Affiliation(s)
- Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA, Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Tomasz Osinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA, Center for Structural Genomics of Infectious Diseases (CSGID)
| | - David T. Tran
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Alina Revilla
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Wayne F. Anderson
- Northwestern University Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL 60611, USA, Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA, Center for Structural Genomics of Infectious Diseases (CSGID), To whom correspondence may be addressed: Dept. of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Dept. of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. Tel.: 434-243-6865; Fax: 434-982-1616;
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA, To whom correspondence may be addressed: Dept. of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Dept. of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. Tel.: 434-243-6865; Fax: 434-982-1616;
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11
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Offermann LR, Schlachter CR, Perdue ML, Majorek KA, He JZ, Booth WT, Garrett J, Kowal K, Chruszcz M. Structural, Functional, and Immunological Characterization of Profilin Panallergens Amb a 8, Art v 4, and Bet v 2. J Biol Chem 2016; 291:15447-59. [PMID: 27231348 DOI: 10.1074/jbc.m116.733659] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 11/06/2022] Open
Abstract
Ragweed allergens affect several million people in the United States and Canada. To date, only two ragweed allergens, Amb t 5 and Amb a 11, have their structures determined and deposited to the Protein Data Bank. Here, we present structures of methylated ragweed allergen Amb a 8, Amb a 8 in the presence of poly(l-proline), and Art v 4 (mugwort allergen). Amb a 8 and Art v 4 are panallergens belonging to the profilin family of proteins. They share significant sequence and structural similarities, which results in cross-recognition by IgE antibodies. Molecular and immunological properties of Amb a 8 and Art v 4 are compared with those of Bet v 2 (birch pollen allergen) as well as with other allergenic profilins. We purified recombinant allergens that are recognized by patient IgE and are highly cross-reactive. It was determined that the analyzed allergens are relatively unstable. Structures of Amb a 8 in complex with poly(l-proline)10 or poly(l-proline)14 are the first structures of the plant profilin in complex with proline-rich peptides. Amb a 8 binds the poly(l-proline) in a mode similar to that observed in human, mouse, and P. falciparum profilin·peptide complexes. However, only some of the residues that form the peptide binding site are conserved.
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Affiliation(s)
- Lesa R Offermann
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, the Department of Chemistry, Davidson College, Davidson, North Carolina 28035
| | - Caleb R Schlachter
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Makenzie L Perdue
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Karolina A Majorek
- the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, and
| | - John Z He
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - William T Booth
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Jessica Garrett
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Krzysztof Kowal
- the Departments of Allergology and Internal Medicine and Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok 15-276, Poland
| | - Maksymilian Chruszcz
- From the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208,
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12
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Handing KB, Shabalin IG, Szlachta K, Majorek KA, Minor W. Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site. Mol Immunol 2016; 71:143-151. [PMID: 26896718 DOI: 10.1016/j.molimm.2016.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 01/08/2023]
Abstract
Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1Å. Cetirizine is bound in two sites--a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizine binding sites. We show that the residues forming the binding pockets in ESA are highly conserved in human serum albumin (HSA), and suggest that binding of cetirizine to HSA will be similar. In support of that hypothesis, we show that the dissociation constants for cetirizine binding to CBS2 in ESA and HSA are identical using tryptophan fluorescence quenching. Presence of lysine and arginine residues that have been previously reported to undergo nonenzymatic glycosylation in CBS1 and CBS2 suggests that cetirizine transport in patients with diabetes could be altered. A review of all available SA structures from the PDB shows that in addition to the novel drug binding site we present here (CBS1), there are two pockets on SA capable of binding drugs that do not overlap with fatty acid binding sites and have not been discussed in published reviews.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Karol Szlachta
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; Faculty of Physics, Warsaw University of Technology, 00-662 Warszawa, Poland
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA; New York Structural Genomics Research Consortium (NYSGRC), USA.
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13
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Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W. Protein purification and crystallization artifacts: The tale usually not told. Protein Sci 2016; 25:720-33. [PMID: 26660914 DOI: 10.1002/pro.2861] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 01/07/2023]
Abstract
The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow, 30-239, Poland.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439
| | - Olga Gasiorowska
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439
| | - Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439.,Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, 60611
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439.,Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, 60611.,New York Structural Genomics Research Consortium (NYSGRC), Bronx, New York, 10461
| | - Ewelina Zasadzinska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 6044, Charlottesville, Virginia, 22908
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, Virginia, 22908.,Midwest Center for Structural Genomics (MCSG), Argonne, Illinois, 60439.,Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, 60611.,New York Structural Genomics Research Consortium (NYSGRC), Bronx, New York, 10461
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14
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Osinski T, Pomés A, Majorek KA, Glesner J, Offermann LR, Vailes LD, Chapman MD, Minor W, Chruszcz M. Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies. J Immunol 2015; 195:307-16. [PMID: 26026055 DOI: 10.4049/jimmunol.1402199] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 04/20/2015] [Indexed: 12/22/2022]
Abstract
Der p 1 is a major allergen from the house dust mite, Dermatophagoides pteronyssinus, that belongs to the papain-like cysteine protease family. To investigate the antigenic determinants of Der p 1, we determined two crystal structures of Der p 1 in complex with the Fab fragments of mAbs 5H8 or 10B9. Epitopes for these two Der p 1-specific Abs are located in different, nonoverlapping parts of the Der p 1 molecule. Nevertheless, surface area and identity of the amino acid residues involved in hydrogen bonds between allergen and Ab are similar. The epitope for mAb 10B9 only showed a partial overlap with the previously reported epitope for mAb 4C1, a cross-reactive mAb that binds Der p 1 and its homolog Der f 1 from Dermatophagoides farinae. Upon binding to Der p 1, the Fab fragment of mAb 10B9 was found to form a very rare α helix in its third CDR of the H chain. To provide an overview of the surface properties of the interfaces formed by the complexes of Der p 1-10B9 and Der p 1-5H8, along with the complexes of 4C1 with Der p 1 and Der f 1, a broad analysis of the surfaces and hydrogen bonds of all complexes of Fab-protein or Fab-peptide was performed. This work provides detailed insight into the cross-reactive and specific allergen-Ab interactions in group 1 mite allergens. The surface data of Fab-protein and Fab-peptide interfaces can be used in the design of conformational epitopes with reduced Ab binding for immunotherapy.
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Affiliation(s)
- Tomasz Osinski
- University of Virginia, Charlottesville, VA 22908; Adam Mickiewicz University, 61-712 Poznan, Poland
| | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903; and
| | - Karolina A Majorek
- University of Virginia, Charlottesville, VA 22908; Adam Mickiewicz University, 61-712 Poznan, Poland
| | - Jill Glesner
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903; and
| | | | - Lisa D Vailes
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903; and
| | | | - Wladek Minor
- University of Virginia, Charlottesville, VA 22908
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15
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Majorek KA, Kuhn ML, Chruszcz M, Anderson WF, Minor W. Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments. Protein Sci 2014; 23:1359-68. [PMID: 25044180 PMCID: PMC4286991 DOI: 10.1002/pro.2520] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/06/2014] [Accepted: 07/11/2014] [Indexed: 01/07/2023]
Abstract
The availability of purified and active protein is the starting point for the majority of in vitro biomedical, biochemical, and drug discovery experiments. The use of polyhistidine affinity tags has resulted in great increases of the efficiency of the protein purification process, but can negatively affect structure and/or activity measurements. Similarly, buffer molecules may perturb the conformational stability of a protein or its activity. During the determination of the structure of a Gcn5-related N-acetyltransferase (GNAT) from Pseudomonas aeruginosa (PA4794), we found that both HEPES and the polyhistidine affinity tag bind (separately) in the substrate-binding site. In the case of HEPES, the molecule induces conformational changes in the active site, but does not significantly affect enzyme activity. In contrast, the uncleaved His-tag does not induce major conformational changes but acts as a weak competitive inhibitor of peptide substrate. In two other GNAT enzymes, we observed that the presence of the His-tag had a strong influence on the activity of these proteins. The influence of protein preparation on functional studies may affect the reproducibility of experiments in other laboratories, even when changes between protocols seem at first glance to be insignificant. Moreover, the results presented here show how critical it is to adjust the experimental conditions for each protein or family of proteins, and investigate the influence of these factors on protein activity and structure, as they may significantly alter the effectiveness of functional characterization and screening methods. Thus, we show that a polyhistidine tag and the buffer molecule HEPES bind in the substrate-binding site and influence the conformation of the active site and the activity of GNAT acetyltransferases. We believe that such discrepancies can influence the reproducibility of some experiments and therefore could have a significant "ripple effect" on subsequent studies.
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Affiliation(s)
- Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia, 22908,Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University61–614, Poznan, Poland,Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases (CSGID)USA,Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of MedicineChicago, Illinois, 60611
| | - Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia, 22908,Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA,Department of Chemistry and Biochemistry, University of South CarolinaColumbia, South Carolina, 29208
| | - Wayne F Anderson
- Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA,Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of MedicineChicago, Illinois, 60611
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia, 22908,Midwest Center for Structural GenomicsUSA,Center for Structural Genomics of Infectious Diseases (CSGID)USA,*Correspondence to: Wladek Minor, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. E-mail:
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16
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Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM. The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. Nucleic Acids Res 2014; 42:4160-79. [PMID: 24464998 PMCID: PMC3985635 DOI: 10.1093/nar/gkt1414] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/12/2013] [Accepted: 12/26/2013] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease H-like (RNHL) superfamily, also called the retroviral integrase superfamily, groups together numerous enzymes involved in nucleic acid metabolism and implicated in many biological processes, including replication, homologous recombination, DNA repair, transposition and RNA interference. The RNHL superfamily proteins show extensive divergence of sequences and structures. We conducted database searches to identify members of the RNHL superfamily (including those previously unknown), yielding >60 000 unique domain sequences. Our analysis led to the identification of new RNHL superfamily members, such as RRXRR (PF14239), DUF460 (PF04312, COG2433), DUF3010 (PF11215), DUF429 (PF04250 and COG2410, COG4328, COG4923), DUF1092 (PF06485), COG5558, OrfB_IS605 (PF01385, COG0675) and Peptidase_A17 (PF05380). Based on the clustering analysis we grouped all identified RNHL domain sequences into 152 families. Phylogenetic studies revealed relationships between these families, and suggested a possible history of the evolution of RNHL fold and its active site. Our results revealed clear division of the RNHL superfamily into exonucleases and endonucleases. Structural analyses of features characteristic for particular groups revealed a correlation between the orientation of the C-terminal helix with the exonuclease/endonuclease function and the architecture of the active site. Our analysis provides a comprehensive picture of sequence-structure-function relationships in the RNHL superfamily that may guide functional studies of the previously uncharacterized protein families.
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Affiliation(s)
- Karolina A. Majorek
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Anna Muszewska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA-22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL-02-089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL-02-106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
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17
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Chruszcz M, Ciardiello MA, Osinski T, Majorek KA, Giangrieco I, Font J, Breiteneder H, Thalassinos K, Minor W. Structural and bioinformatic analysis of the kiwifruit allergen Act d 11, a member of the family of ripening-related proteins. Mol Immunol 2013; 56:794-803. [PMID: 23969108 PMCID: PMC3783527 DOI: 10.1016/j.molimm.2013.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 06/28/2013] [Accepted: 07/04/2013] [Indexed: 01/07/2023]
Abstract
The allergen Act d 11, also known as kirola, is a 17 kDa protein expressed in large amounts in ripe green and yellow-fleshed kiwifruit. Ten percent of all kiwifruit-allergic individuals produce IgE specific for the protein. Using X-ray crystallography, we determined the first three-dimensional structures of Act d 11, produced from both recombinant expression in Escherichia coli and from the natural source (kiwifruit). While Act d 11 is immunologically correlated with the birch pollen allergen Bet v 1 and other members of the pathogenesis-related protein family 10 (PR-10), it has low sequence similarity to PR-10 proteins. By sequence Act d 11 appears instead to belong to the major latex/ripening-related (MLP/RRP) family, but analysis of the crystal structures shows that Act d 11 has a fold very similar to that of Bet v 1 and other PR-10 related allergens regardless of the low sequence identity. The structures of both the natural and recombinant protein include an unidentified ligand, which is relatively small (about 250 Da by mass spectrometry experiments) and most likely contains an aromatic ring. The ligand-binding cavity in Act d 11 is also significantly smaller than those in PR-10 proteins. The binding of the ligand, which we were not able to unambiguously identify, results in conformational changes in the protein that may have physiological and immunological implications. Interestingly, the residue corresponding to Glu45 in Bet v 1 (Glu46), which is important for IgE binding to the birch pollen allergen, is conserved in Act d 11, even though it is not in other allergens with significantly higher sequence identity to Bet v 1. We suggest that the so-called Gly-rich loop (or P-loop), which is conserved in all PR-10 allergens, may be responsible for IgE cross-reactivity between Bet v 1 and Act d 11.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA,Corresponding authors: Maksymilian Chruszcz (), Wladek Minor (), MC: Phone: +1-803-777-7399; Fax +1-803-777-9521, WM: Phone: +1-434-243-6865; Fax: +1-434-982-1616
| | | | - Tomasz Osinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Ivana Giangrieco
- Institute of Protein Biochemistry, C.N.R., Via Pietro Castellino 111, I-80131 Napoli, Italy
| | - Jose Font
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Heimo Breiteneder
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology & Immunology, Medical University of Vienna, Waehringer Guertel 18-20, AKH-EBO-3Q, Vienna, 1090 Austria
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA,Corresponding authors: Maksymilian Chruszcz (), Wladek Minor (), MC: Phone: +1-803-777-7399; Fax +1-803-777-9521, WM: Phone: +1-434-243-6865; Fax: +1-434-982-1616
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Hurlburt BK, Offermann LR, McBride JK, Majorek KA, Maleki SJ, Chruszcz M. Structure and function of the peanut panallergen Ara h 8. J Biol Chem 2013; 288:36890-901. [PMID: 24253038 PMCID: PMC3873548 DOI: 10.1074/jbc.m113.517797] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/13/2013] [Indexed: 11/06/2022] Open
Abstract
The incidence of peanut allergy continues to rise in the United States and Europe. Whereas exposure to the major allergens Ara h 1, 2, 3, and 6 can cause fatal anaphylaxis, exposure to the minor allergens usually does not. Ara h 8 is a minor allergen. Importantly, it is the minor food allergens that are thought to be responsible for oral allergy syndrome (OAS), in which sensitization to airborne allergens causes a Type 2 allergic reaction to ingested foods. Furthermore, it is believed that similar protein structure rather than a similar linear sequence is the cause of OAS. Bet v 1 from birch pollen is a common sensitizing agent, and OAS results when patients consume certain fruits, vegetables, tree nuts, and peanuts. Here, we report the three-dimensional structure of Ara h 8, a Bet v 1 homolog. The overall fold is very similar to that of Bet v 1, Api g 1 (celery), Gly m 4 (soy), and Pru av 1 (cherry). Ara h 8 binds the isoflavones quercetin and apigenin as well as resveratrol avidly.
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Affiliation(s)
- Barry K. Hurlburt
- From the Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, Louisiana 70124
| | - Lesa R. Offermann
- the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and
| | - Jane K. McBride
- From the Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, Louisiana 70124
| | - Karolina A. Majorek
- the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Soheila J. Maleki
- From the Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, Louisiana 70124
| | - Maksymilian Chruszcz
- the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and
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Majorek KA, Kuhn ML, Chruszcz M, Anderson WF, Minor W. Structural, functional, and inhibition studies of a Gcn5-related N-acetyltransferase (GNAT) superfamily protein PA4794: a new C-terminal lysine protein acetyltransferase from pseudomonas aeruginosa. J Biol Chem 2013; 288:30223-30235. [PMID: 24003232 DOI: 10.1074/jbc.m113.501353] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Gcn5-related N-acetyltransferase (GNAT) superfamily is a large group of evolutionarily related acetyltransferases, with multiple paralogs in organisms from all kingdoms of life. The functionally characterized GNATs have been shown to catalyze the transfer of an acetyl group from acetyl-coenzyme A (Ac-CoA) to the amine of a wide range of substrates, including small molecules and proteins. GNATs are prevalent and implicated in a myriad of aspects of eukaryotic and prokaryotic physiology, but functions of many GNATs remain unknown. In this work, we used a multi-pronged approach of x-ray crystallography and biochemical characterization to elucidate the sequence-structure-function relationship of the GNAT superfamily member PA4794 from Pseudomonas aeruginosa. We determined that PA4794 acetylates the Nε amine of a C-terminal lysine residue of a peptide, suggesting it is a protein acetyltransferase specific for a C-terminal lysine of a substrate protein or proteins. Furthermore, we identified a number of molecules, including cephalosporin antibiotics, which are inhibitors of PA4794 and bind in its substrate-binding site. Often, these molecules mimic the conformation of the acetylated peptide product. We have determined structures of PA4794 in the apo-form, in complexes with Ac-CoA, CoA, several antibiotics and other small molecules, and a ternary complex with the products of the reaction: CoA and acetylated peptide. Also, we analyzed PA4794 mutants to identify residues important for substrate binding and catalysis.
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Affiliation(s)
- Karolina A Majorek
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,; the Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland,; the Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, and; the Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Misty L Kuhn
- the Center for Structural Genomics of Infectious Diseases (CSGID); the Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Maksymilian Chruszcz
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,; the Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, and; the Center for Structural Genomics of Infectious Diseases (CSGID); the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Wayne F Anderson
- the Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, and; the Center for Structural Genomics of Infectious Diseases (CSGID); the Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Wladek Minor
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,; the Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, and; the Center for Structural Genomics of Infectious Diseases (CSGID).
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20
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Chruszcz M, Mikolajczak K, Mank N, Majorek KA, Porebski PJ, Minor W. Serum albumins-unusual allergens. Biochim Biophys Acta Gen Subj 2013; 1830:5375-81. [PMID: 23811341 DOI: 10.1016/j.bbagen.2013.06.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 01/27/2023]
Abstract
BACKGROUND Albumins are multifunctional proteins present in the blood serum of animals. They can bind and transport a wide variety of ligands which they accommodate due to their conformational flexibility. Serum albumins are highly conserved both in amino acid sequence and three-dimensional structure. Several mammalian and avian serum albumins (SAs) are also allergens. Sensitization to one of the SAs coupled with the high degree of conservation between SAs may result in cross-reactive antibodies in allergic individuals. Sensitivity to SA generally begins with exposure to an aeroallergen, which can then lead to cross-sensitization to serum albumins present in food. SCOPE OF REVIEW This review focuses on the allergenicity of SAs presented in a structural context. MAJOR CONCLUSIONS SA allergenicity is unusual taking into account the high sequence identity and similarity between SA from different species and human serum albumin. Cross-reactivity of human antibodies towards different SAs is one of the most important characteristics of these allergens. GENERAL SIGNIFICANCE Establishing a relationship between sequence and structure of different SAs and their interactions with antibodies is crucial for understanding the mechanisms of cross-sensitization of atopic individuals. Structural information can also lead to better design and production of recombinant SAs to replace natural proteins in allergy testing and desensitization. Therefore, structural analyses are important for diagnostic and treatment purposes. This article is part of a Special Issue entitled Serum Albumin.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.
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Chruszcz M, Pomes A, Osinski T, Majorek KA, Glesner J, Minor W, Vailes LD, Chapman MD. Structural Analysis Reveals Molecular Basis for Interactions of Group 1 Allergens with Species Specific and Cross-Reactive Antibodies. J Allergy Clin Immunol 2013. [DOI: 10.1016/j.jaci.2012.12.732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Hurlburt BK, Celeste L, Majorek KA, McBride J, Maleki SJ, Minor W, Chruszcz M. Structure and Function of the Peanut Panallergen Ara h 8. J Allergy Clin Immunol 2013. [DOI: 10.1016/j.jaci.2012.12.748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Kuhn ML, Majorek KA, Minor W, Anderson WF. Broad-substrate screen as a tool to identify substrates for bacterial Gcn5-related N-acetyltransferases with unknown substrate specificity. Protein Sci 2013; 22:222-30. [PMID: 23184347 PMCID: PMC3588918 DOI: 10.1002/pro.2199] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 11/15/2012] [Accepted: 11/15/2012] [Indexed: 12/21/2022]
Abstract
Due to a combination of efforts from individual laboratories and structural genomics centers, there has been a surge in the number of members of the Gcn5-related acetyltransferasesuperfamily that have been structurally determined within the past decade. Although the number of three-dimensional structures is increasing steadily, we know little about the individual functions of these enzymes. Part of the difficulty in assigning functions for members of this superfamily is the lack of information regarding how substrates bind to the active site of the protein. The majority of the structures do not show ligand bound in the active site, and since the substrate-binding domain is not strictly conserved, it is difficult to predict the function based on structure alone. Additionally, the enzymes are capable of acetylating a wide variety of metabolites and many may exhibit promiscuity regarding their ability to acetylate multiple classes of substrates, possibly having multiple functions for the same enzyme. Herein, we present an approach to identify potential substrates for previously uncharacterized members of the Gcn5-related acetyltransferase superfamily using a variety of metabolites including polyamines, amino acids, antibiotics, peptides, vitamins, catecholamines, and other metabolites. We have identified potential substrates for eight bacterial enzymes of this superfamily. This information will be used to further structurally and functionally characterize them.
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Affiliation(s)
- Misty L Kuhn
- Department of Pharmacology and Cellular Biology, Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of MedicineChicago, Illinois 60611
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Wayne F Anderson
- Department of Pharmacology and Cellular Biology, Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of MedicineChicago, Illinois 60611
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Majorek KA, Porebski PJ, Dayal A, Zimmerman MD, Jablonska K, Stewart AJ, Chruszcz M, Minor W. Structural and immunologic characterization of bovine, horse, and rabbit serum albumins. Mol Immunol 2012; 52:174-82. [PMID: 22677715 PMCID: PMC3401331 DOI: 10.1016/j.molimm.2012.05.011] [Citation(s) in RCA: 611] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 01/07/2023]
Abstract
Serum albumin (SA) is the most abundant plasma protein in mammals. SA is a multifunctional protein with extraordinary ligand binding capacity, making it a transporter molecule for a diverse range of metabolites, drugs, nutrients, metals and other molecules. Due to its ligand binding properties, albumins have wide clinical, pharmaceutical, and biochemical applications. Albumins are also allergenic, and exhibit a high degree of cross-reactivity due to significant sequence and structure similarity of SAs from different organisms. Here we present crystal structures of albumins from cattle (BSA), horse (ESA) and rabbit (RSA) sera. The structural data are correlated with the results of immunological studies of SAs. We also analyze the conservation or divergence of structures and sequences of SAs in the context of their potential allergenicity and cross-reactivity. In addition, we identified a previously uncharacterized ligand binding site in the structure of RSA, and calcium binding sites in the structure of BSA, which is the first serum albumin structure to contain metal ions.
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Affiliation(s)
- Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA,Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 98, 61-614 Poznan, Poland,New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Arjun Dayal
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA,New York Structural Genomics Research Consortium (NYSGRC), USA
| | - Kamila Jablonska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Alan J. Stewart
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA,New York Structural Genomics Research Consortium (NYSGRC), USA,To whom correspondence may be addressed: Dept. of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. Tel.: 434-243-0033; Fax: 434-982-1616;
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA,New York Structural Genomics Research Consortium (NYSGRC), USA,To whom correspondence may be addressed: Dept. of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave., Charlottesville, VA 22908. Tel.: 434-243-6865; Fax: 434-982-1616;
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Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W. A multi-faceted analysis of RutD reveals a novel family of α/β hydrolases. Proteins 2012; 80:2359-68. [PMID: 22641504 DOI: 10.1002/prot.24122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/09/2012] [Accepted: 05/14/2012] [Indexed: 11/05/2022]
Abstract
The rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the α/β hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the α/β hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys, or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the α/β hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3-oxoadipate-enol-lactonase with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism.
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Affiliation(s)
- Aleksandra A Knapik
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, USA
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Chruszcz M, Chapman MD, Osinski T, Solberg R, Demas M, Porebski PJ, Majorek KA, Pomés A, Minor W. Alternaria alternata allergen Alt a 1: a unique β-barrel protein dimer found exclusively in fungi. J Allergy Clin Immunol 2012; 130:241-7.e9. [PMID: 22664167 DOI: 10.1016/j.jaci.2012.03.047] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/21/2012] [Accepted: 03/27/2012] [Indexed: 12/16/2022]
Abstract
BACKGROUND Alternaria species is one of the most common molds associated with allergic diseases, and 80% of Alternaria species-sensitive patients produce IgE antibodies to a major protein allergen, Alt a 1. The structure and function of Alt a 1 is unknown. OBJECTIVE We sought to obtain a high-resolution structure of Alt a 1 using x-ray crystallography and to investigate structural relationships between Alt a 1 and other allergens and proteins reported in the Protein Data Bank. METHODS X-ray crystallography was used to determine the structure of Alt a 1 by using a custom-designed set of crystallization conditions. An initial Alt a 1 model was determined by the application of a Ta(6)Br(12)(2+) cluster and single-wavelength anomalous diffraction. Bioinformatic analyses were used to compare the Alt a 1 sequence and structure with that of other proteins. RESULTS Alt a 1 is a unique β-barrel comprising 11 β-strands and forms a "butterfly-like" dimer linked by a single disulfide bond with a large (1345 Å(2)) dimer interface. Intramolecular disulfide bonds are conserved among Alt a 1 homologs. Currently, the Alt a 1 structure has no equivalent in the Protein Data Bank. Bioinformatics analyses suggest that the structure is found exclusively in fungi. Four previously reported putative IgE-binding peptides have been located on the Alt a 1 structure. CONCLUSIONS Alt a 1 has a unique, dimeric β-barrel structure that appears to define a new protein family with unknown function found exclusively in fungi. The location of IgE antibody-binding epitopes is in agreement with the structural analysis of Alt a 1. The Alt a 1 structure will allow mechanistic structure/function studies and immunologic studies directed toward new forms of immunotherapy for Alternaria species-sensitive allergic patients.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
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27
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Chruszcz M, Pomés A, Glesner J, Vailes LD, Osinski T, Porebski PJ, Majorek KA, Heymann PW, Platts-Mills TAE, Minor W, Chapman MD. Molecular determinants for antibody binding on group 1 house dust mite allergens. J Biol Chem 2011; 287:7388-98. [PMID: 22210776 DOI: 10.1074/jbc.m111.311159] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
House dust mites produce potent allergens, Der p 1 and Der f 1, that cause allergic sensitization and asthma. Der p 1 and Der f 1 are cysteine proteases that elicit IgE responses in 80% of mite-allergic subjects and have proinflammatory properties. Their antigenic structure is unknown. Here, we present crystal structures of natural Der p 1 and Der f 1 in complex with a monoclonal antibody, 4C1, which binds to a unique cross-reactive epitope on both allergens associated with IgE recognition. The 4C1 epitope is formed by almost identical amino acid sequences and contact residues. Mutations of the contact residues abrogate mAb 4C1 binding and reduce IgE antibody binding. These surface-exposed residues are molecular targets that can be exploited for development of recombinant allergen vaccines.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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Chruszcz M, Maleki SJ, Majorek KA, Demas M, Bublin M, Solberg R, Hurlburt BK, Ruan S, Mattison CP, Breiteneder H, Minor W. Structural and immunologic characterization of Ara h 1, a major peanut allergen. J Biol Chem 2011. [DOI: 10.1074/jbc.a111.270132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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Chruszcz M, Maleki SJ, Majorek KA, Demas M, Bublin M, Solberg R, Hurlburt BK, Ruan S, Mattisohn CP, Breiteneder H, Minor W. Structural and immunologic characterization of Ara h 1, a major peanut allergen. J Biol Chem 2011; 286:39318-27. [PMID: 21917921 PMCID: PMC3234756 DOI: 10.1074/jbc.m111.270132] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/10/2011] [Indexed: 11/06/2022] Open
Abstract
Allergic reactions to peanuts and tree nuts are major causes of anaphylaxis in the United States. We compare different properties of natural and recombinant versions of Ara h 1, a major peanut allergen, through structural, immunologic, and bioinformatics analyses. Small angle x-ray scattering studies show that natural Ara h 1 forms higher molecular weight aggregates in solution. In contrast, the full-length recombinant protein is partially unfolded and exists as a monomer. The crystal structure of the Ara h 1 core (residues 170-586) shows that the central part of the allergen has a bicupin fold, which is in agreement with our bioinformatics analysis. In its crystalline state, the core region of Ara h 1 forms trimeric assemblies, while in solution the protein exists as higher molecular weight assemblies. This finding reveals that the residues forming the core region of the protein are sufficient for formation of Ara h 1 trimers and higher order oligomers. Natural and recombinant variants of proteins tested in in vitro gastric and duodenal digestion assays show that the natural protein is the most stable form, followed by the recombinant Ara h 1 core fragment and the full-length recombinant protein. Additionally, IgE binding studies reveal that the natural and recombinant allergens have different patterns of interaction with IgE antibodies. The molecular basis of cross-reactivity between vicilin allergens is also elucidated.
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Affiliation(s)
- Maksymilian Chruszcz
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Soheila J. Maleki
- the Agriculture Research Service, Southern Regional Research Center, United States Department of Agriculture, New Orleans, Louisiana 70124, and
| | - Karolina A. Majorek
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Matthew Demas
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Merima Bublin
- the Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology & Immunology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna, 1090 Austria
| | - Robert Solberg
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Barry K. Hurlburt
- the Agriculture Research Service, Southern Regional Research Center, United States Department of Agriculture, New Orleans, Louisiana 70124, and
| | - Sanbao Ruan
- the Agriculture Research Service, Southern Regional Research Center, United States Department of Agriculture, New Orleans, Louisiana 70124, and
| | - Christopher P. Mattisohn
- the Agriculture Research Service, Southern Regional Research Center, United States Department of Agriculture, New Orleans, Louisiana 70124, and
| | - Heimo Breiteneder
- the Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology & Immunology, Medical University of Vienna, Waehringer Guertel 18-20, Vienna, 1090 Austria
| | - Wladek Minor
- From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
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Majorek KA, Bujnicki JM. Modeling of Escherichia coli Endonuclease V structure in complex with DNA. J Mol Model 2008; 15:173-82. [PMID: 19043748 DOI: 10.1007/s00894-008-0414-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 10/02/2008] [Indexed: 01/24/2023]
Abstract
Endonuclease V (EndoV) is a metal-dependent DNA repair enzyme involved in removal of deaminated bases (e.g., deoxyuridine, deoxyinosine, and deoxyxanthosine), with pairing specificities different from the original bases. Homologs of EndoV are present in all major phyla from bacteria to humans and their function is quite well analyzed. EndoV has been combined with DNA ligase to develop an enzymatic method for mutation scanning and has been engineered to obtain variants with different substrate specificities that serve as improved tools in mutation recognition and cancer mutation scanning. However, little is known about the structure and mechanism of substrate DNA binding by EndoV. Here, we present the results of a bioinformatic analysis and a structural model of EndoV from Escherichia coli in complex with DNA. The structure was obtained by a combination of fold-recognition, comparative modeling, de novo modeling and docking methods. The modeled structure provides a convenient tool to study protein sequence-structure-function relationships in EndoV and to engineer its further variants.
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Affiliation(s)
- Karolina A Majorek
- Institute for Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
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