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Luo ML, Chen H, Chen GY, Wang S, Wang Y, Yang FQ. Preparation of Alcohol Dehydrogenase-Zinc Phosphate Hybrid Nanoflowers through Biomimetic Mineralization and Its Application in the Inhibitor Screening. Molecules 2023; 28:5429. [PMID: 37513303 PMCID: PMC10386709 DOI: 10.3390/molecules28145429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
A biomimetic mineralization method was used in the facile and rapid preparation of nanoflowers for immobilizing alcohol dehydrogenase (ADH). The method mainly uses ADH as an organic component and zinc phosphate as an inorganic component to prepare flower-like ADH/Zn3(PO4)2 organic-inorganic hybrid nanoflowers (HNFs) with the high specific surface area through a self-assembly process. The synthesis conditions of the ADH HNFs were optimized and its morphology was characterized. Under the optimum enzymatic reaction conditions, the Michaelis-Menten constant (Km) of ADH HNFs (β-NAD+ as substrate) was measured to be 3.54 mM, and the half-maximal inhibitory concentration (IC50) of the positive control ranitidine (0.2-0.8 mM) was determined to be 0.49 mM. Subsequently, the inhibitory activity of natural medicine Penthorum chinense Pursh and nine small-molecule compounds on ADH was evaluated using ADH HNFs. The inhibition percentage of the aqueous extract of P. chinense is 57.9%. The vanillic acid, protocatechuic acid, gallic acid, and naringenin have obvious inhibitory effects on ADH, and their percentages of inhibition are 55.1%, 68.3%, 61.9%, and 75.5%, respectively. Moreover, molecular docking analysis was applied to explore the binding modes and sites of the four most active small-molecule compounds to ADH. The results of this study can broaden the application of immobilized enzymes through biomimetic mineralization, and provide a reference for the discovery of ADH inhibitors from natural products.
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Affiliation(s)
- Mao-Ling Luo
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Hua Chen
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Guo-Ying Chen
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Shengpeng Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Feng-Qing Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
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2
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Tomczyk MD, Kuźnik N, Walczak K. Cyclen-based artificial nucleases: Three decades of development (1989–2022). Part a – Hydrolysis of phosphate esters. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Scheithauer L, Thiem S, Schmelz S, Dellmann A, Büssow K, Brouwer RMHJ, Ünal CM, Blankenfeldt W, Steinert M. Zinc metalloprotease ProA of Legionella pneumophila increases alveolar septal thickness in human lung tissue explants by collagen IV degradation. Cell Microbiol 2021; 23:e13313. [PMID: 33491325 DOI: 10.1111/cmi.13313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/25/2023]
Abstract
ProA is a secreted zinc metalloprotease of Legionella pneumophila causing lung damage in animal models of Legionnaires' disease. Here we demonstrate that ProA promotes infection of human lung tissue explants (HLTEs) and dissect the contribution to cell type specific replication and extracellular virulence mechanisms. For the first time, we reveal that co-incubation of HLTEs with purified ProA causes a significant increase of the alveolar septal thickness. This destruction of connective tissue fibres was further substantiated by collagen IV degradation assays. The moderate attenuation of a proA-negative mutant in A549 epithelial cells and THP-1 macrophages suggests that effects of ProA in tissue mainly result from extracellular activity. Correspondingly, ProA contributes to dissemination and serum resistance of the pathogen, which further expands the versatile substrate spectrum of this thermolysin-like protease. The crystal structure of ProA at 1.48 Å resolution showed high congruence to pseudolysin of Pseudomonas aeruginosa, but revealed deviations in flexible loops, the substrate binding pocket S1 ' and the repertoire of cofactors, by which ProA can be distinguished from respective homologues. In sum, this work specified virulence features of ProA at different organisational levels by zooming in from histopathological effects in human lung tissue to atomic details of the protease substrate determination.
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Affiliation(s)
- Lina Scheithauer
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefanie Thiem
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Schmelz
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Ansgar Dellmann
- Institut für Pathologie, Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany
| | - Konrad Büssow
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - René M H J Brouwer
- Herz-, Thorax-, Gefäßchirurgie, Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany.,Institut für Psychologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Can M Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Fen Fakültesi, Turkish-German University, Istanbul, Turkey
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
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Hasan R, Rony MNH, Ahmed R. In silico characterization and structural modeling of bacterial metalloprotease of family M4. J Genet Eng Biotechnol 2021; 19:25. [PMID: 33528696 PMCID: PMC7851659 DOI: 10.1186/s43141-020-00105-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 12/15/2020] [Indexed: 01/20/2023]
Abstract
BACKGROUND The M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases. A large number of these enzymes are important virulence factors of pathogenic bacteria and therefore potential drug targets. Whereas some enzymes have potential for biotechnological applications, the M4 family of metalloproteases is known almost exclusively from bacteria. The aim of the study was to identify the structure and properties of M4 metalloprotease proteins. RESULTS A total of 31 protein sequences of M4 metalloprotease retrieved from UniProt representing different species of bacteria have been characterized for various physiochemical properties. They were thermostable, hydrophillic protein of a molecular mass ranging from 38 to 66 KDa. Correlation on the basis of both enzymes and respective genes has also been studied by phylogenetic tree. B. cereus M4 metalloprotease (PDB ID: 1NPC) was selected as a representative species for secondary and tertiary structures among the M4 metalloprotease proteins. The secondary structure displaying 11 helices (H1-H11) is involved in 15 helix-helix interactions, while 4 β-sheet motifs composed of 15 β-strands in PDBsum. Possible disulfide bridges were absent in most of the cases. The tertiary structure of B. cereus M4 metalloprotease was validated by QMEAN4 and SAVES server (Ramachandran plot, verify 3D, and ERRAT) which proved the stability, reliability, and consistency of the tertiary structure of the protein. Functional analysis was done in terms of membrane protein topology, disease-causing region prediction, proteolytic cleavage sites prediction, and network generation. Transmembrane helix prediction showed absence of transmembrane helix in protein. Protein-protein interaction networks demonstrated that bacillolysin of B. cereus interacted with ten other proteins in a high confidence score. Five disorder regions were identified. Active sites analysis showed the zinc-binding residues-His-143, His-147, and Glu-167, with Glu-144 acting as the catalytic residues. CONCLUSION Moreover, this theoretical overview will help researchers to get a details idea about the protein structure and it may also help to design enzymes with desirable characteristics for exploiting them at industrial level or potential drug targets.
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Affiliation(s)
- Rajnee Hasan
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207 Bangladesh
| | - Md. Nazmul Haq Rony
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207 Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207 Bangladesh
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Bian F, Yue S, Peng Z, Zhang X, Chen G, Yu J, Xuan N, Bi Y. A comprehensive alanine-scanning mutagenesis study reveals roles for salt bridges in the structure and activity of Pseudomonas aeruginosa elastase. PLoS One 2015; 10:e0121108. [PMID: 25815820 PMCID: PMC4376888 DOI: 10.1371/journal.pone.0121108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/12/2015] [Indexed: 11/18/2022] Open
Abstract
The relationship between salt bridges and stability/enzymatic activity is unclear. We studied this relationship by systematic alanine-scanning mutation analysis using the typical M4 family metalloprotease Pseudomonas aeruginosa elastase (PAE, also known as pseudolysin) as a model. Structural analysis revealed seven salt bridges in the PAE structure. We constructed ten mutants for six salt bridges. Among these mutants, six (Asp189Ala, Arg179Ala, Asp201Ala, Arg205Ala, Arg245Ala and Glu249Ala) were active and four (Asp168Ala, Arg198Ala, Arg253Ala, and Arg279Ala) were inactive. Five mutants were purified, and their catalytic efficiencies (kcat/Km), half-lives (t1/2) and thermal unfolding curves were compared with those of PAE. Mutants Asp189Ala and Arg179Ala both showed decreased thermal stabilities and increased activities, suggesting that the salt bridge Asp189-Arg179 stabilizes the protein at the expense of catalytic efficiency. In contrast, mutants Asp201Ala and Arg205Ala both showed slightly increased thermal stability and slightly decreased activity, suggesting that the salt bridge Asp201-Arg205 destabilizes the protein. Mutant Glu249Ala is related to a C-terminal salt bridge network and showed both decreased thermal stability and decreased activity. Furthermore, Glu249Ala showed a thermal unfolding curve with three discernable states [the native state (N), the partially unfolded state (I) and the unfolded state (U)]. In comparison, there were only two discernable states (N and U) in the thermal unfolding curve of PAE. These results suggest that Glu249 is important for catalytic efficiency, stability and unfolding cooperativity. This study represents a systematic mutational analyses of salt bridges in the model metalloprotease PAE and provides important insights into the structure-function relationship of enzymes.
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Affiliation(s)
- Fei Bian
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- * E-mail: (FB); (YB)
| | - Shousong Yue
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Zhenying Peng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xiaowei Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Gao Chen
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Jinhui Yu
- Shandong Crop Germplasm Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ning Xuan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Graduate Education Center, Shandong Academy of Agricultural Sciences, Jinan, China
- * E-mail: (FB); (YB)
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Cooper DR, Grelewska K, Kim CY, Joachimiak A, Derewenda ZS. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:219-24. [PMID: 20208147 PMCID: PMC2833023 DOI: 10.1107/s1744309109053913] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 12/14/2009] [Indexed: 03/23/2024]
Abstract
The crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 A resolution. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several Pfam families, yet their structures are quite similar and most (but not all) seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The structural similarities of these diverse proteins suggest that a new Pfam clan encompassing the families that share this fold should be created. The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms.
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Affiliation(s)
- David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- The Integrated Center for Structure and Function Innovation (ISFI), USA
| | - Katarzyna Grelewska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- The Integrated Center for Structure and Function Innovation (ISFI), USA
| | - Chang-Yub Kim
- The Integrated Center for Structure and Function Innovation (ISFI), USA
- Bioscience Division, Los Alamos National Laboratory, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- The Integrated Center for Structure and Function Innovation (ISFI), USA
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7
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Zheng M, Cooper DR, Grossoehme NE, Yu M, Hung LW, Cieslik M, Derewenda U, Lesley SA, Wilson IA, Giedroc DP, Derewenda ZS. Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:356-65. [PMID: 19307717 PMCID: PMC2659884 DOI: 10.1107/s0907444909004727] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/09/2009] [Indexed: 11/10/2022]
Abstract
The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-alpha-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni(2+) ions but that it is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(2+) is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.
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Affiliation(s)
- Meiying Zheng
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - David R. Cooper
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | | | - Minmin Yu
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
| | - Li-Wei Hung
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
- Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Marcin Cieslik
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - Urszula Derewenda
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - Scott A. Lesley
- The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ian A. Wilson
- The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | - Zygmunt S. Derewenda
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
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8
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The ins and outs of biological zinc sites. Biometals 2009; 22:141-8. [DOI: 10.1007/s10534-008-9184-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 12/07/2008] [Indexed: 10/21/2022]
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9
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Frison G, Ohanessian G. Metal-histidine-glutamate as a regulator of enzymatic cycles: a case study of carbonic anhydrase. Phys Chem Chem Phys 2009; 11:374-83. [DOI: 10.1039/b812916a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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11
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Demidyuk IV, Kalashnikov AE, Gromova TY, Gasanov EV, Safina DR, Zabolotskaya MV, Rudenskaya GN, Kostrov SV. Cloning, sequencing, expression, and characterization of protealysin, a novel neutral proteinase from Serratia proteamaculans representing a new group of thermolysin-like proteases with short N-terminal region of precursor. Protein Expr Purif 2006; 47:551-61. [PMID: 16442309 DOI: 10.1016/j.pep.2005.12.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 12/06/2005] [Accepted: 12/12/2005] [Indexed: 11/26/2022]
Abstract
The gene of Serratia proteamaculans proteinase, protealysin, was cloned, sequenced, and expressed in Escherichia coli. The gene encoded a precursor of 341 amino acids (AAs) with a significant homology to thermolysin-like proteinases (TLPs). The molecular weight of the purified mature active recombinant protein was 32 kDa, the N-terminal amino acid sequence was AKTSTGGEVI. The optimum pH for azocasein hydrolysis by protealysin was seven and it was completely inhibited by o-phenanthroline. The enzyme hydrolyzed 3-(2-furyl)acryloyl-glycyl-L-leucine amide, the standard substrate for TLPs, with k(cat)/K(m) ratio of (2.52 +/- 0.02) x 10(2) M(-1) s(-1). Protealysin maturation removes 50 AA from the N-terminus of the precursor. The removed region had no similarity with the preprosequence of thermolysin (232 AA) but was homologous to some other TLPs. These proteins shared a conserved 7-AA motif near the initial methionine. Such motif was also found in some nonproteolytic putative proteins; two of them were eukaryotic.
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Affiliation(s)
- Ilya V Demidyuk
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
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12
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Lin YL, Lim C. Factors Governing the Protonation State of Zn-Bound Histidine in Proteins: A DFT/CDM Study. J Am Chem Soc 2004; 126:2602-12. [PMID: 14982470 DOI: 10.1021/ja038827r] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.
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Affiliation(s)
- Yen-lin Lin
- Institute of Biomedical Science, Academic Sinica, Taipei 11529, Taiwan ROC
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13
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Hirose J, Wilkins RG. Interaction of cobalt(II) complexes with apoarsanilazotyrosine-248 carboxypeptidase A. Biochemistry 2002. [DOI: 10.1021/bi00309a007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Boulanger MJ, Murphy MEP. Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases. J Mol Biol 2002; 315:1111-27. [PMID: 11827480 DOI: 10.1006/jmbi.2001.5251] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria gonorrhoeae is essential for cell growth under oxygen limiting conditions in the presence of nitrite and is protective against killing by human sera. A phylogenic analysis indicates that AniA is a member of a new class of copper-containing nitrite reductases. Expression of the soluble domain of AniA yields a protein capable of reducing nitrite with specific activity of 160 units/mg, approximately 50 % of that measured for the nitrite reductase from the strong soil denitrifier Alcaligenes faecalis S-6. The crystal structure of the soluble domain of AniA was solved by molecular replacement and sixfold averaging to a resolution of 2.4 A. The nitrite soaked AniA crystal structure refined to 1.95 A reveals a bidentate mode of substrate binding to the type II copper. Despite low sequence identity (approximately 30 %), the core cupredoxin fold of AniA is similar to that found in copper-containing nitrite reductases from soil bacteria. The main structural differences are localized to two attenuated surface loops that map to deletions in the sequence alignment. In soil nitrite reductases, one of these surface loops is positioned near the type I copper site and contributes residues to the docking surface for proteaceous electron donors. In AniA, the attenuation of this loop results in a restructured hydrophobic binding surface that may be required to interact with a lipid anchored azurin. The second attenuated loop is positioned on the opposite side of AniA and may facilitate a more intimate interaction with the lipid membrane. A unique combination of structural effectors surrounding the type I copper site of sAnia contribute to a unusual visible absorption spectra with components observed previously in either green or blue type I copper sites.
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Affiliation(s)
- Martin J Boulanger
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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16
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Krauss M. Ab initio structure of the active site of phosphotriesterase. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2001; 41:8-17. [PMID: 11206385 DOI: 10.1021/ci000046b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This research exploits two recent developments to obtain a fundamental understanding of the metalloenzyme active site using the bimetallic enzyme phosphotriesterase as an example of this class. First is the theoretical prediction that the structure and spectroscopy of a native metalloenzyme active site is qualitatively determined by the supermolecule complex of the metal(s) and the first shell of ligands with proper charge states including waters directly bonded to ionic ligands. The second is the development of an effective potential for representing the molecular environment interacting with an all-electron active site in the quantum Hamiltonian. The GAMESS suite of electronic structure codes has implemented this new methodology, effective fragment potentials (EFP), to make theoretical calculations on structure, spectroscopy, and reactivity tractable for systems involving hundreds of atoms. Since there are transition metal cations at the active site of these enzymes, the all-electron part of the complex is calculated with relativistic compact effective potentials (CEP) and their concomitant basis sets. A realistic representation of the active site with its protein environment can be obtained using a combination of the CEP and EFP. This presentation will determine the inherent electronic and structural characteristics of phosphotriesterase using ab initio quantum mechanical methods. A single X-ray structure for the Zn-Zn enzyme is leveraged to obtain the structure of the Cd-Cd enzyme and to examine the consequences of protonating the active site.
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Affiliation(s)
- M Krauss
- Center Advanced Research Biotechnology/NIST, Rockville, Maryland 20850, USA.
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17
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Differential effects of transition metal cations on the conformation and biological activities of nerve growth factor. Neurotox Res 2000. [DOI: 10.1007/bf03033341] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Kurisu G, Kai Y, Harada S. Structure of the zinc-binding site in the crystal structure of a zinc endoprotease from Streptomyces caespitosus at 1 A resolution. J Inorg Biochem 2000; 82:225-8. [PMID: 11132632 DOI: 10.1016/s0162-0134(00)00136-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A zinc endoprotease produced by Streptomyces caespitosus (ScNP) contains a H83E84TGH87VLG90LPD93-Met103 sequence. Except for D93, this amino acid sequence is the same as a characteristic consensus HEXXHXXGXXH-M motif found in one class of zinc endoprotease called 'metzincins'. We analyzed the structural and functional role of the consensus sequence located around a catalytically essential zinc ion based on the crystal structure of ScNP. The structure was determined at the highest level on resolution (1 A resolution) and accuracy among crystal structures of zinc endoproteases ever determined. The zinc ion of ScNP is tetrahedrally coordinated by three amino acid side-chains (H83, H87 and D93) and a water molecule. The distances between the zinc ion and the coordinating atoms are 2.01, 2.01 and 1.95 A for H83N epsilon, H87N epsilon and D93O delta, respectively. These distances agree very well with those normally found in crystal structures of zinc-containing small molecules in the Cambridge Structural Database. On the other hand, the distance between the zinc ion and the coordinating water molecule (1.93 A) is slightly shorter than the typical value (2.01 A) found in the database. In addition, E84O epsilon makes a short hydrogen bond to this water molecule with the distance of 2.54 A. Two hydrogen bonds (H83N delta-L102O, H87N delta-L91O) and van der Waals interactions between the side-chain of M103 and the two imidazole rings of H83 and H87 are also observed. These interactions are probably important for the imidazole rings to construct the tetrahedral coordination arrangement toward the zinc ion.
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Affiliation(s)
- G Kurisu
- Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan
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19
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van Aalten DM, Chong CR, Joshua-Tor L. Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes. Biochemistry 2000; 39:10082-9. [PMID: 10955996 DOI: 10.1021/bi000952h] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
D-Cysteine differs from the antiarthritis drug D-penicillamine by only two methyl groups on the beta-carbon yet inhibits carboxypeptidase A (CPD) by a distinct mechanism: D-cysteine binds tightly to the active site zinc, while D-penicillamine catalyzes metal removal. To investigate the structural basis for this difference, we solved the crystal structure of carboxypeptidase A complexed with D-cysteine (D-Cys) at 1.75-A resolution. D-Cys binds the active site zinc with a sulfur ligand and forms additional interactions with surrounding side chains of the enzyme. The structure explains the difference in potency between D-Cys and L-Cys and provides insight into the mechanism of D-penicillamine inhibition. D-Cys binding induces a concerted motion of the side chains around the zinc ion, similar to that found in other carboxypeptidase-inhibitor crystal structures and along a limited path. Analysis of concerted motions of CPD and CPD-inhibitor crystal structures reveals a clustering of these structures into distinct groups. Using the restricted conformational flexibility of a drug target in this type of analysis could greatly enhance efficiency in drug design.
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Affiliation(s)
- D M van Aalten
- W. M. Keck Structural Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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20
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Abstract
Zinc is required for the activity of > 300 enzymes, covering all six classes of enzymes. Zinc binding sites in proteins are often distorted tetrahedral or trigonal bipyramidal geometry, made up of the sulfur of cysteine, the nitrogen of histidine or the oxygen of aspartate and glutamate, or a combination. Zinc in proteins can either participate directly in chemical catalysis or be important for maintaining protein structure and stability. In all catalytic sites, the zinc ion functions as a Lewis acid. Researchers in our laboratory are dissecting the determinants of molecular recognition and catalysis in the zinc-binding site of carbonic anhydrase. These studies demonstrate that the chemical nature of the direct ligands and the structure of the surrounding hydrogen bond network are crucial for both the activity of carbonic anhydrase and the metal ion affinity of the zinc-binding site. An understanding of naturally occurring zinc-binding sites will aid in creating de novo zinc-binding proteins and in designing new metal sites in existing proteins for novel purposes such as to serve as metal ion biosensors.
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Affiliation(s)
- K A McCall
- Duke University Medical Center, Durham, NC 27710, USA
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21
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Shamovsky IL, Ross GM, Riopelle RJ, Weaver DF. Theoretical and Biochemical Studies on the Selectivity of Nerve Growth Factor for Transition Metal Cations. J Am Chem Soc 1999. [DOI: 10.1021/ja983303q] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor L. Shamovsky
- Contribution from the Department of Medicine, Department of Chemistry, and Department of Pharmacology & Toxicology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Gregory M. Ross
- Contribution from the Department of Medicine, Department of Chemistry, and Department of Pharmacology & Toxicology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Richard J. Riopelle
- Contribution from the Department of Medicine, Department of Chemistry, and Department of Pharmacology & Toxicology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Donald F. Weaver
- Contribution from the Department of Medicine, Department of Chemistry, and Department of Pharmacology & Toxicology, Queen's University, Kingston, Ontario, Canada K7L 3N6
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22
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Abstract
The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.
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Affiliation(s)
- I L Alberts
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England
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23
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Christianson DW. Structural chemistry and biology of manganese metalloenzymes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 67:217-52. [PMID: 9446936 DOI: 10.1016/s0079-6107(97)88477-5] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- D W Christianson
- Department of Chemistry, University of Pennsylvania 19104-6323, USA
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24
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Cha J, Auld DS. Site-directed mutagenesis of the active site glutamate in human matrilysin: investigation of its role in catalysis. Biochemistry 1997; 36:16019-24. [PMID: 9398337 DOI: 10.1021/bi972223g] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Glu-198 of human matrilysin is a conserved residue in the matrix metalloproteinases and is considered to play an important role in catalysis by acting as a general base catalyst toward the zinc-bound water molecule, on the basis of mechanistic proposals for other zinc proteases. In the present study, Glu-198 is mutated into Asp, Cys, Gln, and Ala, and the zinc binding properties, kinetic parameters, and pH dependence of each mutant are determined in order to examine the role of Glu-198 in catalysis. The mutations chosen either modify (C and D) or eliminate (A and Q) the general base properties of residue-198. All the mutants bind 2 mol of zinc per mol of enzyme, indicating that Glu-198 is not crucial to the binding of the catalytic zinc to the enzyme. The value of kcat/Km for the E198D mutant is only 4-fold lower than that of wild-type enzyme at the pH optimum of 7.5, while that for the E198C mutant is decreased by 160-fold. The E198Q and E198A enzymes containing the mutations that have eliminated the nucleophilic and acid/base properties of the residue are still active, having lower kcat/Km values of 590- and 1900-fold, respectively. The decrease in activity of all the mutants is essentially due to a decrease in kcat. The kcat/Km values of the mutants as a function of pH display broad bell-shaped curves that are similar to the wild-type enzyme. The acidic pKa value is not greatly affected by the change in the chemical properties of residue-198. The similarity in the pH profiles for the mutant and wild-type enzymes indicates that the ionization of Glu-198 is not responsible for the acidic pKa. Ionization of the zinc-bound water may be responsible for this pKa since the three His ligands and the scaffolding of the matrilysin catalytic zinc site are different from that observed in carboxypeptidase A and would predict a lower pKa for the metal-bound water. If the zinc-bound water is the nucleophile in the reaction, the role of Glu-198 in catalysis may be to stabilize the transition state or act as a general acid catalyst after the rate-determining step.
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Affiliation(s)
- J Cha
- Center for Biochemical and Biophysical Sciences and Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Murphy ME, Turley S, Adman ET. Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications. J Biol Chem 1997; 272:28455-60. [PMID: 9353305 DOI: 10.1074/jbc.272.45.28455] [Citation(s) in RCA: 181] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
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Affiliation(s)
- M E Murphy
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, Washington 98195-7420, USA
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26
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Ross GM, Shamovsky IL, Lawrance G, Solc M, Dostaler SM, Jimmo SL, Weaver DF, Riopelle RJ. Zinc alters conformation and inhibits biological activities of nerve growth factor and related neurotrophins. Nat Med 1997; 3:872-8. [PMID: 9256278 DOI: 10.1038/nm0897-872] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A role for Zn2+ in a variety of neurological conditions such as stroke, epilepsy and Alzheimer's disease has been postulated. In many instances, susceptible neurons are located in regions rich in Zn2+ where nerve growth factor (NGF) levels rise as a result of insult. Although the interaction of Zn2+ with this neurotrophin has previously been suggested, the direct actions of the ion on NGF function have not been explored. Molecular modeling studies predict that Zn2+ binding to NGF will induce structural changes within domains of this neurotrophin that participate in the recognition of TrkA and p75NTR. We demonstrate here that Zn2+ alters the conformation of NGF, rendering it unable to bind to p75NTR or TrkA receptors or to activate signal transduction pathways and biological outcomes normally induced by this protein. Similar actions of Zn2+ are also observed with other members of the NGF family, suggesting a modulatory role for this metal ion in neurotrophin function.
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Affiliation(s)
- G M Ross
- Department of Medicine, KGH, Queen's University, Kingston, Ontario, Canada
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27
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28
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Kajiwara H, Hemmings AM, Hirano H. Evidence of metal binding activities of pentadecapeptide from Panax ginseng. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL APPLICATIONS 1996; 687:443-8. [PMID: 9017469 DOI: 10.1016/s0378-4347(96)00240-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A tetradecapeptide from ginseng (Panax ginseng) root showing anti-lipolytic activity in an isolated rat fat cell assay was chemically synthesized for analysis of metal binding activities in vitro. Binding activities against several metal ions were analysed by measuring mobility shifts during capillary zone electrophoresis experiments. The ginseng polypeptide (GPP) showed the greatest increase in effective molecular electrophoretic mobility in the presence of Mg2+. Mobility was also affected in the presence of La3+, Mn2+, Ca2+ and Zn2+ ions. Analysis with the dye Stains-all revealed GPP to possess a cation binding site similar to those in Ca(2+)-binding proteins. GPP thus appears to be a metal binding peptide. The results of this analysis suggested that GPP may perform its anti-lipolytic activities through an ability to modulate the level of free cellular Mg2+ and Mn2+ ions.
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Affiliation(s)
- H Kajiwara
- Department of Molecular Biology, National Institute of Agrobiological Resources, Tsukuba, Japan
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29
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Murphy ME, Turley S, Kukimoto M, Nishiyama M, Horinouchi S, Sasaki H, Tanokura M, Adman ET. Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc. Biochemistry 1995; 34:12107-17. [PMID: 7547950 DOI: 10.1021/bi00038a003] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The structures at 2.0 and 2.25 A resolution of native and recombinant nitrite reductase from Alcaligenes faecalis show that they are identical to each other and very similar to nitrite reductase from Achromobacter cycloclastes. The crystallographic structure of a mutant, M150E, which unlike the wild-type protein cannot be reduced by pseudoazurin, shows that the glutamate replacement for methionine binds to a metal at the type I Cu site via only one oxygen. Anomalous scattering data collected at wavelengths of 1.040 and 1.377 A reveal that the metal at the type I site is a Zn. No significant differences from the native structure other than local perturbations at the type I site are seen. A local pseudo 2-fold axis relates the two domains of different monomers which form the active site. The two residues, Asp98 and His255, believed to be involved in catalysis are related by this 2-fold. An unusual (+)-(+) charge interaction between Lys269, Glu279, and His100 helps to orient the active site Cu ligand, His100. A number of negatively charged surface residues create an electrostatic field whose shape suggests that it may serve to direct incoming negatively charged nitrite as well as to dock the electron donor partner, pseudoazurin.
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Affiliation(s)
- M E Murphy
- Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195-7420, USA
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30
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Nakai T, Yasuhara T, Fujiki Y, Ohashi A. Multiple genes, including a member of the AAA family, are essential for degradation of unassembled subunit 2 of cytochrome c oxidase in yeast mitochondria. Mol Cell Biol 1995; 15:4441-52. [PMID: 7623837 PMCID: PMC230684 DOI: 10.1128/mcb.15.8.4441] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cytochrome c oxidase consists of three mitochondrion- and several nucleus-encoded subunits. We previously found that in a mutant of Saccharomyces cerevisiae lacking nucleus-encoded subunit 4 of this enzyme (CoxIV), subunits 2 and 3 (CoxII and CoxIII), both encoded by the mitochondrial DNA, were unstable and rapidly degraded in mitochondria, presumably because the subunits cannot assemble normally. To analyze the molecular machinery involved in this proteolytic pathway, we obtained four mutants defective in the degradation of unassembled CoxII (osd mutants) by screening CoxIV-deficient cells for the accumulation of CoxII. All of the mutants were recessive and were classified into three different complementation groups. Tetrad analyses revealed that the phenotype of each mutant was caused by a single nuclear mutation. These results suggest strongly that at least three nuclear genes (the OSD genes) are required for this degradation system. Interestingly, degradation of CoxIII was not affected in the mutants, implying that the two subunits are degraded by distinct pathways. We also cloned the OSD1 gene by complementation of the temperature sensitivity of osd1-1 mutants with a COXIV+ genetic background on a nonfermentable glycerol medium. We found it to encode a member of a family (the AAA family) of putative ATPases, which proved to be identical to recently described YME1 and YTA11. Immunological analyses revealed that Osd1 protein is localized to the mitochondrial inner membrane. Disruption of the predicted ATP-binding cassette by site-directed mutagenesis eliminated biological activities, thereby underscoring the importance of ATP for function.
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Affiliation(s)
- T Nakai
- Meiji Institute of Health Science, Kanagawa, Japan
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31
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Le Moual H, Dion N, Roques BP, Crine P, Boileau G. Asp650 is crucial for catalytic activity of neutral endopeptidase 24-11. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 221:475-80. [PMID: 8168535 DOI: 10.1111/j.1432-1033.1994.tb18760.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neutral endopeptidase (NEP) is a membrane-bound mammalian ectopeptidase that contains a catalytic zinc ion in its active site. Previous studies showed that the active site, and especially the zinc-binding site of NEP, have features in common with the prototypical bacterial zinc protease, thermolysin. Sequence comparison reveals that both enzymes have a conserved Asp residue (Asp650 in NEP and Asp170 in thermolysin) located four positions on the C-side of the third zinc ligand. In thermolysin, this residue is involved in a carboxylate-histidine-zinc interaction whose functional role has never been established [Christianson, D. W. & Alexander, R. S. (1990) Nature 346, 225]. To test the hypothesis that, in NEP, this residue is important for catalysis, we have changed Asp650 of NEP by site-directed mutagenesis and expressed the mutant enzymes in COS-1 cells. Substitution of Glu, Asn or Ala for Asp650 resulted in mutant enzymes exhibiting drastic decreases in specific activity. Binding experiments using the zinc-chelating inhibitor [3H]-N-[(2RS)-4-(hydroxyamino)-1,4-dioxo-2-(phenylmethyl)butyl]glycine suggested that the zinc ion is present in the active site of these mutant enzymes. These results strongly support the conclusion that Asp650 in NEP is crucial for hydrolytic activity.
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Affiliation(s)
- H Le Moual
- Département de Biochimie, Université de Montréal, Canada
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32
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Hourdou ML, Guinand M, Vacheron MJ, Michel G, Denoroy L, Duez C, Englebert S, Joris B, Weber G, Ghuysen JM. Characterization of the sporulation-related gamma-D-glutamyl-(L)meso-diaminopimelic-acid-hydrolysing peptidase I of Bacillus sphaericus NCTC 9602 as a member of the metallo(zinc) carboxypeptidase A family. Modular design of the protein. Biochem J 1993; 292 ( Pt 2):563-70. [PMID: 8503890 PMCID: PMC1134247 DOI: 10.1042/bj2920563] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The sporulation-related gamma-D-glutamyl-(L)meso-diaminopimelic-acid-hydrolysing peptidase I of Bacillus sphaericus NCTC 9602 has been analysed by proton-induced X-ray emission. It contains 1 equivalent Zn2+ per mol of protein. As derived from gene cloning and sequencing, the B. sphaericus Zn peptidase I is a two-module protein. A 100-amino-acid-residue N-terminal domain consisting of two tandem segments of similar sequences, is fused to a 296-amino-acid-residue C-terminal catalytic domain. The catalytic domain belongs to the Zn carboxypeptidase A family, the closest match being observed with the Streptomyces griseus carboxypeptidase [Narahashi (1990) J. Biochem. 107, 879-886] and with the family prototype, bovine carboxypeptidase A. The catalytic domain of the B. sphaericus peptidase I possesses, distributed along the amino-acid sequence, peptide segments, a triad His162-Glu165-His307 and a dyad Tyr347-Glu366 that are equivalent to secondary structures, the zinc-binding triad His69-Glu72-His196 and the catalytic dyad Tyr248-Glu270 of bovine carboxypeptidase A respectively. The N-terminal repeats of the B. sphaericus peptidase I have similarity with the C-terminal repeats of the Enterococcus hirae muramidase 2, the Streptococcus (now Enterococcus) faecalis autolysin and the Bacillus phi PZA and phi 29 lysozymes, to which a role in the recognition of a particular moiety of the bacterial cell envelope has been tentatively assigned. Detergents enhance considerably the specific activity of the B. sphaericus peptidase I.
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Affiliation(s)
- M L Hourdou
- Centre d'Ingénierie des Protéines, Université de Liège, Belgium
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33
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Transition structures for carbon dioxide and formaldehyde hydroxylation reactions in the coordinate sphere of zinc. ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf01374590] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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35
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Bouayad A, Bitit N, Deydier E, Menu MJ, Dartiguenave M, Dartiguenave Y, Duran H, Gorrichon L, Simard M, Beauchamp AL. Interaction of Zn2+ with N-(2-pyridyl)-3-phenyl-2-propene amide, a model in lignin biosynthesis inhibition by cinnamides. Crystal and molecular structure of [Zn(ON)2(CH3OH)2](CF3SO3)2. Inorganica Chim Acta 1991. [DOI: 10.1016/s0020-1693(00)80234-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Abstract
The biological function of zinc is governed by the composition of its tetrahedral coordination polyhedron in the metalloprotein, and each ligand group that coordinates to the metal ion does so with a well-defined stereochemical preference. Consequently, protein-zinc recognition and discrimination requires proper chemical composition and proper stereochemistry of the metal-ligand environment. However, it should be noted that the entire protein behaves as the "zinc ligand," since residues that are quite distant from the metal affect recognition and function by through-space (either solvent or the protein milieu) or through-hydrogen bond coulombic interactions. Additionally, long-range interactions across hydrogen bonds serve to orient ligands and therefore minimize the entropy loss incurred on metal binding. Since zinc is not subject to ligand field stabilization effects, it is easy for the tetrahedral protein-binding site to discriminate zinc from other first-row transition metal ions: It is only for Zn2+ that the change from an octahedral to a tetrahedral ligand field is not energetically disfavored. Structural considerations such as these must illuminate the engineering of de novo zinc-binding sites in proteins. Zinc serves chemical, structural, and regulatory roles in biological systems. In biological chemistry zinc serves as an electrophilic catalyst; that is, it stabilizes negative charges encountered during an enzyme-catalyzed reaction. The coordination polyhedron of catalytic zinc is usually dominated by histidine side chains. In biological structure zinc is typically sequestered from solvent, and its coordination polyhedron is almost exclusively dominated by cysteine thiolates. Structural or regulatory zinc is found as either a single metal ion or as part of a cluster of two or more metals. In multinuclear clusters cysteine thiolates either bridge two metal ions or serve as terminal ligands to a single metal ion. Even in complex multinuclear clusters, Zn2+ displays tetrahedral coordination. The structural biology of zinc continues to receive attention in catalytic and regulatory systems such as leucine aminopeptidase, alkaline phosphatase, transcription factors, and steroid receptors. For example, zinc-mediated hormone-receptor association has recently been demonstrated in the binding of human growth hormone to the extracellular binding domain of the human prolactin receptor (Cunningham et al., 1990). To be sure, structural studies of zinc in biology will continue to be a fruitful source of bioinorganic advances, as well as surprises, in the future.
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Affiliation(s)
- D W Christianson
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104
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37
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Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket. Proc Natl Acad Sci U S A 1990; 87:6654-8. [PMID: 2395868 PMCID: PMC54595 DOI: 10.1073/pnas.87.17.6654] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To develop a general approach to designing cofactor-binding sites for catalytic antibodies, we characterized structural patterns in the binding sites of antibodies and zinc enzymes. Superposition of eight sets of antibody light- and heavy-chain variable domains identified structurally conserved sites within the sequence-variable complementarity determining regions. The pattern for catalytic zinc sites included two ligands close in sequence, a sequence-distant ligand, and a main-chain hydrogen bond joining two ligands. In both the light- and heavy-chain variable domains, the stereochemistry of five structurally conserved sites general to all known antibody structures matched that of the zinc ligands of carbonic anhydrase: three residues on two hydrogen-bonded antiparallel beta-strands. For one such general site, an antibody model replacing residue 34 on the first complementarity determining region of the light chain (L1) and residues 89 and 91 on the third complementarity determining region of the light chain (L3) with histidine ligands formed a zinc-binding site with an open coordination position at the bottom of the antibody binding pocket. For the anti-fluorescein antibody 4-4-20, this L1-L3 site placed the zinc ion about 4 A from the bound fluorescein, an indicator for metal binding. This predicted zinc-binding mutant was created in the single-chain variable domain construct, expressed, and found by fluorescence quenching to bind metal ion with an affinity constant of 10(6) M-1. Thus, our template-based multisite design proved successful for remodeling an antibody to contain a cofactor-binding site, without requiring further mutagenesis and screening. Combination of a specific light or heavy chain containing a catalytic metal site with a library of complementary chains raised to potential substrates or transition state analogs should greatly improve the production of catalytic antibodies with desired activities and specificities.
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38
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Baltas M, Cazaux L, de BA, Gorrichon L, Tisnes P. Synthesis of thiooxamates from t-butyl sulfinamoyl acetates. Occurrence of a new rearrangement involving a thione S-imide intermediate. Tetrahedron Lett 1990. [DOI: 10.1016/s0040-4039(00)97646-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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39
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Affiliation(s)
- J F Bazan
- Department of Biophysics, University of California, Berkeley 94720
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Kronman MJ. Metal-ion binding and the molecular conformational properties of alpha lactalbumin. Crit Rev Biochem Mol Biol 1989; 24:565-667. [PMID: 2691213 DOI: 10.3109/10409238909080054] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mammary galactosyltransferase and alpha lactalbumin are the two protein components of lactose synthase which catalyze the transfer of galactose from UDP-gal to glucose in the presence of divalent cations. Recent studies suggest that alpha lactalbumin may have a broader function in modifying cell surface carbohydrates in cell-cell interactions and cell differentiation. Since the discovery that alpha lactalbumin, like galactosyltransferase, is a metalloprotein, there has been a great deal of interest in the metal-binding properties of this protein and how these relate to the metal-ion requirements of the lactose synthase reaction. The recent availability of an X-ray crystal structure of alpha lactalbumin has provided further impetus for establishing the molecular determinants of its biological activity. This review is directed toward critically examining and integrating our present knowledge of the properties of this protein, particularly the relationship between metal-ion binding and conformational state, and how these might relate to its biological function.
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Affiliation(s)
- M J Kronman
- Department of Biochemistry and Molecular Biology, SUNY Health Center, Syracuse
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41
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Bazan JF, Fletterick RJ. Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc Natl Acad Sci U S A 1988; 85:7872-6. [PMID: 3186696 PMCID: PMC282299 DOI: 10.1073/pnas.85.21.7872] [Citation(s) in RCA: 284] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Proteases that are encoded by animal picornaviruses and plant como- and potyviruses form a related group of cysteine-active-center enzymes that are essential for virus maturation. We show that these proteins are homologous to the family of trypsin-like serine proteases. In our model, the active-site nucleophile of the trypsin catalytic triad, Ser-195, is changed to a Cys residue in these viral proteases. The other two residues of the triad, His-57 and Asp-102, are otherwise absolutely conserved in all the viral protease sequences. Secondary structure analysis of aligned sequences suggests the location of the component strands of the twin beta-barrel trypsin fold in the viral proteases. Unexpectedly, the 2a and 3c subclasses of viral cysteine proteases are, respectively, homologous to the small and large structural subclasses of trypsin-like serine proteases. This classification allows the molecular mapping of residues from viral sequences onto related tertiary structures; we precisely identify amino acids that are strong determinants of specificity for both small and large viral cysteine proteases.
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Affiliation(s)
- J F Bazan
- Department of Biophysics, University of California, Berkeley 94720
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42
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Tsonis PA, Sowadski JM, Goetinck PF. A consensus sequence in the N-terminus of exported proteins: resemblance with metal binding domains and implications in protein translocation across membranes. Biochem Biophys Res Commun 1988; 156:99-107. [PMID: 3178854 DOI: 10.1016/s0006-291x(88)80810-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
By analyzing and comparing the N-terminus of several exported proteins we identified two consensus sequences that resemble metal binding domains. The consensus sequences are part of the signal peptide and part of the adjacent sequences of the mature protein. Three-dimensional modelling of one such domain suggests a conformation with implication in signal peptide insertion.
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Affiliation(s)
- P A Tsonis
- La Jolla Cancer Research Foundation, Cancer Research Center, CA 92037
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43
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Andrews PR, Iskander MN, Issa J, Reiss JA. Molecular Modelling of the Active Site of Enkephalin-Degrading Neutral Endopeptidase-24.11 (Enkephalinase) An Active Site Model for Neutral Endopeptidase-24.11. ACTA ACUST UNITED AC 1988. [DOI: 10.1002/qsar.19880070102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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44
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Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg AC, Parks GD, Nicklin MJ, Wimmer E. Implications of the picornavirus capsid structure for polyprotein processing. Proc Natl Acad Sci U S A 1987; 84:21-5. [PMID: 3467351 PMCID: PMC304133 DOI: 10.1073/pnas.84.1.21] [Citation(s) in RCA: 139] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mature picornaviral proteins are derived by progressive, posttranslational cleavage of a precursor polyprotein. These cleavages play a role in the control of virus functions. Although the processed termini are separated by as much as 75 A in the native virus capsid, the fold and arrangement of polypeptide chains in a protomer before proteolysis are likely to be similar to that found in the mature virus. The three-dimensional structures of rhinovirus and Mengo virus suggest that the cleavage sites within the protomeric precursor are in structurally flexible regions. The final proteolytic processing event, maturation of the virion peptide VP0 (also called peptide 1AB) appears to occur by an unusual autocatalytic serine protease-type mechanism possibly involving viral RNA basic groups that would serve as proton-abstractors during the cleavage reaction.
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45
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Lee MH, Cowling RA, Sander EG, Pettigrew DW. Bovine liver dihydropyrimidine amidohydrolase: pH dependencies of inactivation by chelators and steady-state kinetic properties. Arch Biochem Biophys 1986; 248:368-78. [PMID: 3089167 DOI: 10.1016/0003-9861(86)90433-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dihydropyrimidine amidohydrolase (EC 3.5.2.2) catalyzes the reversible hydrolysis of 5,6-dihydropyrimidines to the corresponding beta-ureido acids. Previous work has shown that incubation of this Zn2+ metalloenzyme with 2,6-dipicolinic acid, 8-hydroxyquinoline-5-sulfonic acid, or o-phenanthroline results in inactivation by Zn2+ removal by a reaction pathway involving formation of a ternary enzyme-Zn2+-chelator complex which subsequently dissociates to yield apoenzyme and the Zn2+-chelate (K. P. Brooks, E. A. Jones, B. D. Kim, and E. G. Sander, (1983) Arch. Biochem. Biophys. 226, 469-483). In the present work, the pH dependence of chelator inactivation is studied. The equilibrium constant for formation of the ternary complex is strongly pH dependent and increases with decreasing pH for all three chelators. There is a positive correlation between the value of the equilibrium constant observed for each chelator and the value of its stability constant for formation of Zn2+-chelate. The affinity of the chelators for the enzyme increases in the order 8-hydroxyquinoline-5-sulfonic acid greater than o-phenanthroline greater than 2,6-dipicolinic acid. The first-order rate constant for breakdown of the ternary complex to yield apoenzyme and Zn2+-chelate is invariant with pH for a given chelator but is different for each chelator, increasing in the reverse order. The pH dependence of the inactivation shows that two ionizable groups on the enzyme are involved in the inactivation. On the other hand, the steady-state kinetic behavior of the enzyme is well-described by ionization of a single group with a pK of 6.0 in the free enzyme. The basic form of the group is required for catalysis; protonation of the group decreases both Vmax and the apparent affinity for substrate. Conversely, binding of substrate decreases the pK of this group to about 5. L-Dihydroorotic acid is shown to be a competitive inhibitor of dihydropyrimidine amidohydrolase. Binding of L-dihydroorotic acid increases the pK of the ionizable group to 6.5. The agreement between the pK in the enzyme-L-dihydroorotic acid complex and the higher pK observed in the pH dependence of inactivation by chelators suggests that the same group is involved in the binding of acid, and chelators. The different effects of substrate and L-dihydroorotic acid on the pK suggest that the binding modes of these two ligands may be different and suggest a structural basis for the mutally exclusive substrate specificities of dihydropyrimidine amidohydrolase and dihydroorotase.
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46
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Tronrud DE, Monzingo AF, Matthews BW. Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 157:261-8. [PMID: 3709536 DOI: 10.1111/j.1432-1033.1986.tb09664.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The mode of binding to thermolysin of the unsubstituted phosphoramidate inhibitor N-phosphoryl-L-leucinamide (P-Leu-NH2) has been determined crystallographically and refined at high resolution (R = 17.9% to 0.16-nm resolution). The mode of binding of the naturally occurring thermolysin inhibitor phosphoramidon reported previously [Weaver, L. H., Kester, W. R. and Matthews, B. W. (1977) J. Mol. Biol. 114, 119-132] has also been confirmed by crystallographic refinement (R = 17.4% to 0.23-nm resolution). Phosphoramidon binds to the enzyme with a single oxygen of the phosphoramidate moiety as a zinc ligand. Together with three ligands to the metal from the protein the resultant complex has approximately tetrahedral geometry. However, in the case of P-Leu-NH2, two of the phosphoramidate oxygens interact with the zinc to form a complex that tends towards pentacoordinate. In this respect, P-Leu-NH2 appears to be a better transition-state analog than is phosphoramidon. In addition, the phosphorus-nitrogen bond length in P-Leu-NH2 is 0.18 nm, suggesting that the nitrogen is protonated whereas the same bond in phosphoramidon is much shorter (0.15 nm) suggesting that the nitrogen does not carry a charge. In phosphoramidon the distance from the phosphoramide nitrogen to Glu-143 is 0.39 nm whereas in P-Leu-NH2 this distance decreases to 0.34 nm. Taken together, these observations provide additional evidence in support of the participation of pentacoordinate intermediates in the mechanism of action of thermolysin [Holmes, M. A. and Matthews, B. W. (1981) Biochemistry 20, 6912-6920] and the role of Glu-143 in first promoting the attack of a water molecule on the carbonyl carbon of the scissile bond and subsequently acting as a 'proton shuttle' to transfer the proton to the leaving nitrogen [Monzingo, A. F. and Matthews, B. W. (1984) Biochemistry 23, 5724-5729; Hangauer, D. G., Monzingo, A. F. and Matthews, B. W. (1984) Biochemistry 23, 5730-5741].
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Sowadski JM, Handschumacher MD, Murthy HM, Foster BA, Wyckoff HW. Refined structure of alkaline phosphatase from Escherichia coli at 2.8 A resolution. J Mol Biol 1985; 186:417-33. [PMID: 3910843 DOI: 10.1016/0022-2836(85)90115-9] [Citation(s) in RCA: 176] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The structure of alkaline phosphatase from Escherichia coli has been determined to 2.8 A resolution. The multiple isomorphous replacement electron density map of the dimer at 3.4 A was substantially improved by molecular symmetry averaging and solvent flattening. From these maps, polypeptide chains of the dimer were built using the published amino acid sequence. Stereochemically restrained least-squares refinement of this model against native data, starting with 3.4 A data and extending in steps to 2.8 A resolution, proceeded to a final overall crystallographic R factor of 0.256. Alkaline phosphatase-phosphomonoester hydrolase (EC 3.1.3.1) is a metalloenzyme that forms an isologous dimer with two reactive centers 32 A apart. The topology of the polypeptide fold of the subunit is of the alpha/beta class of proteins. Despite the similarities in the overall alpha/beta fold with other proteins, alkaline phosphatase does not have a characteristic binding cleft formed at the carboxyl end of the parallel sheet, but rather an active pocket that contains a cluster of three functional metal sites located off the plane of the central ten-stranded sheet. This active pocket is located near the carboxyl ends of four strands and the amino end of the antiparallel strand, between the plane of the sheet and two helices on the same side. Alkaline phosphatase is a non-specific phosphomonoesterase that hydrolyzes small phosphomonoesters as well as the phosphate termini of DNA. The accessibility calculations based on the refined co-ordinates of the enzyme show that the active pocket barely accommodates inorganic phosphate. Thus, the alcoholic or phenolic portion of the substrate would have to be exposed on the surface of the enzyme. Two metal sites, M1 and M2, 3.9 A apart, are occupied by zinc. The third site, M3, 5 A from site M2 and 7 A from site M1, is occupied by magnesium or, in the absence of magnesium, by zinc. As with other zinc-containing enzymes, histidine residues are ligands to zinc site M1 (three) and to zinc site M2 (one). Ligand assignment and metal preference indicate that the crystallographically found metal sites M1, M2 and M3 correspond to the spectroscopically deduced metal sites A, B and C, respectively. Arsenate, a product analog and enzyme inhibitor, binds between Ser102 and zinc sites M1 and M2. The position of the guanidinium group of Arg 166 is within hydrogen-bonding distance from the arsenate site.(ABSTRACT TRUNCATED AT 400 WORDS)
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Hasnain SS, Wardell EM, Garner CD, Schlösser M, Beyersmann D. Extended-X-ray-absorption-fine-structure investigations of zinc in 5-aminolaevulinate dehydratase. Biochem J 1985; 230:625-33. [PMID: 4062868 PMCID: PMC1152664 DOI: 10.1042/bj2300625] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The zinc co-ordination in 5-aminolaevulinate dehydratase (5-aminolaevulinate hydro-lyase, EC 4.2.1.24) was investigated by recording and interpreting the extended X-ray-absorption fine structure (e.x.a.f.s.) associated with the zinc K-edge. The enzyme has a molecular mass of 280 000 Da and consists of eight subunits of 35 000 Da each; the samples studied contained approx. 1 g-atom of zinc/mol of subunit. Four forms of the enzyme were investigated and details of the zinc environment were elucidated, as follows. In the native enzyme, zinc is considered to be co-ordinated to three sulphur atoms at 0.228(2)nm [2.28(2)A] and a lower-Z atom at 0.192(5)nm [1.92(5)A] (if nitrogen) or 0.189(5)nm [1.89(5)A] (if oxygen). Reaction of the enzyme with the inhibitor 2-bromo-3-(imidazol-5-yl)propionic acid produced significant changes in the e.x.a.f.s., the nature of which are consistent with co-ordination by about three sulphur atoms at 0.222(2)nm [2.22(2)A], a nitrogen atom at 0.193(5)nm [1.93(5)A] and a nitrogen atom from the inhibitor at 0.214(5)nm [2.14(5)A]. Inactivation of the enzyme by air-oxidation of essential thiol groups and binding of the substrate produce slight changes in the e.x.a.f.s. consistent with slight re-arrangement of ligands with additional lighter ligands (nitrogen or oxygen). These results, when combined with previous findings, are taken to indicate that zinc has a structural rather than a direct catalytic role in 5-aminolaevulinate dehydratase.
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49
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Brown RS, Sander C, Argos P. The primary structure of transcription factor TFIIIA has 12 consecutive repeats. FEBS Lett 1985; 186:271-4. [PMID: 4007166 DOI: 10.1016/0014-5793(85)80723-7] [Citation(s) in RCA: 358] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Analysis of the amino acid sequence of transcription factor TFIIIA from Xenopus laevis reveals the presence of 12 repeating structures, each about 30 residues in length. These segments have been aligned and their secondary structure predicted. The repeats each contain two invariant cysteines and two invariant histidines, perhaps to coordinate a zinc cation. Possible nucleic acid interaction modes are discussed.
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50
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Bauer R. Perturbed angular correlation spectroscopy and its application to metal sites in proteins: possibilities and limitations. Q Rev Biophys 1985; 18:1-64. [PMID: 2933759 DOI: 10.1017/s0033583500004972] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The present review describes the methodology of perturbed angular correlation of gamma rays (PAC) applied to biological problems. A large part of the present review focuses on the application of PAC spectroscopy to the study of coordination geometry for the metal site in zinc enzymes. Applications to conformation and dynamics of biomolecules and the use of the method to identify the intracellular sites of either metals or labelled proteins are also discussed.
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