1
|
Anderson AC, Stangherlin S, Pimentel KN, Weadge JT, Clarke AJ. The SGNH hydrolase family: a template for carbohydrate diversity. Glycobiology 2022; 32:826-848. [PMID: 35871440 PMCID: PMC9487903 DOI: 10.1093/glycob/cwac045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/18/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
The substitution and de-substitution of carbohydrate materials are important steps in the biosynthesis and/or breakdown of a wide variety of biologically important polymers. The SGNH hydrolase superfamily is a group of related and well-studied proteins with a highly conserved catalytic fold and mechanism composed of 16 member families. SGNH hydrolases can be found in vertebrates, plants, fungi, bacteria, and archaea, and play a variety of important biological roles related to biomass conversion, pathogenesis, and cell signaling. The SGNH hydrolase superfamily is chiefly composed of a diverse range of carbohydrate-modifying enzymes, including but not limited to the carbohydrate esterase families 2, 3, 6, 12 and 17 under the carbohydrate-active enzyme classification system and database (CAZy.org). In this review, we summarize the structural and functional features that delineate these subfamilies of SGNH hydrolases, and which generate the wide variety of substrate preferences and enzymatic activities observed of these proteins to date.
Collapse
Affiliation(s)
- Alexander C Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Stefen Stangherlin
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo N2L3C5, Canada
| | - Kyle N Pimentel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Joel T Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo N2L3C5, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G2W1, Canada
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo N2L3C5, Canada
| |
Collapse
|
2
|
Liu C, Hashimoto J, Kudo K, Shin-Ya K, Kakeya H. An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides. Chem Asian J 2021; 16:1382-1387. [PMID: 33886165 DOI: 10.1002/asia.202100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/21/2021] [Revised: 04/02/2021] [Indexed: 11/07/2022]
Abstract
The incorporation of non-proteinogenic amino acids (NPAAs) enriches the structural diversity of nonribosomal peptides. Recently, four NPAA-containing cyclic hexapeptides, longicatenamides A-D, were isolated using a combined-culture strategy. Based on in silico analysis, we discovered their putative biosynthetic gene cluster (lon) and proposed a possible biosynthetic mechanism. Surprisingly, the lon22 gene encodes an atypical arginine dihydrolase, which can also catalyze the hydrolysis of citrulline to ornithine. Phylogenetic analysis showed that Lon22-like proteins form a novel clade that is separated from other guanidine-modifying enzymes. After rational design, the catalytic efficiencies of a Lon22 Y80F mutant for arginine and citrulline substrates were 2.31- and 4.70-fold that of the wild-type (WT), respectively. In addition, characterization of the Lon20-A4 adenylation domain suggested that it can incorporate both ornithine and lysine into the final products.
Collapse
Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| |
Collapse
|
3
|
Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
Collapse
Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| |
Collapse
|
4
|
Aučynaitė A, Rutkienė R, Tauraitė D, Meškys R, Urbonavičius J. Identification of a 2'- O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries. Molecules 2018; 23:molecules23112904. [PMID: 30405065 PMCID: PMC6278475 DOI: 10.3390/molecules23112904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 11/16/2022] Open
Abstract
Ribose methylation is among the most ubiquitous modifications found in RNA. 2'-O-methyluridine is found in rRNA, snRNA, snoRNA and tRNA of Archaea, Bacteria, and Eukaryota. Moreover, 2'-O-methylribonucleosides are promising starting materials for the production of nucleic acid-based drugs. Despite the countless possibilities of practical use for the metabolic enzymes associated with methylated nucleosides, there are very few reports regarding the metabolic fate and enzymes involved in the metabolism of 2'-O-alkyl nucleosides. The presented work focuses on the cellular degradation of 2'-O-methyluridine. A novel enzyme was found using a screening strategy that employs Escherichia coli uracil auxotroph and the metagenomic libraries. A 2'-O-methyluridine hydrolase (RK9NH) has been identified together with an aldolase (RK9DPA)-forming a part of a probable gene cluster that is involved in the degradation of 2'-O-methylated nucleosides. The RK9NH is functional in E. coli uracil auxotroph and in vitro. The RK9NH nucleoside hydrolase could be engineered to enzymatically produce 2'-O-methylated nucleosides that are of great demand as raw materials for production of nucleic acid-based drugs. Moreover, RK9NH nucleoside hydrolase converts 5-fluorouridine, 5-fluoro-2'-deoxyuridine and 5-fluoro-2'-O-methyluridine into 5-fluorouracil, which suggests it could be employed in cancer therapy.
Collapse
Affiliation(s)
- Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| |
Collapse
|
5
|
Danso D, Schmeisser C, Chow J, Zimmermann W, Wei R, Leggewie C, Li X, Hazen T, Streit WR. New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. Appl Environ Microbiol 2018; 84:e02773-17. [PMID: 29427431 PMCID: PMC5881046 DOI: 10.1128/aem.02773-17] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [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: 12/14/2017] [Accepted: 01/29/2018] [Indexed: 11/26/2022] Open
Abstract
Polyethylene terephthalate (PET) is one of the most important synthetic polymers used today. Unfortunately, the polymers accumulate in nature and to date no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly α- and β-hydrolases, like cutinases and related enzymes (EC 3.1.1). Currently, only a small number of such enzymes are well characterized. In this work, a search algorithm was developed that identified 504 possible PET hydrolase candidate genes from various databases. A further global search that comprised more than 16 Gb of sequence information within 108 marine and 25 terrestrial metagenomes obtained from the Integrated Microbial Genome (IMG) database detected 349 putative PET hydrolases. Heterologous expression of four such candidate enzymes verified the function of these enzymes and confirmed the usefulness of the developed search algorithm. In this way, two novel and thermostable enzymes with high potential for downstream application were partially characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phyla of Actinobacteria, Proteobacteria, and Bacteroidetes Within the Proteobacteria, the Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylum Bacteroidetes appear to be the main hosts of PET hydrolase genes, rather than Actinobacteria or Proteobacteria, as observed for the terrestrial metagenomes. Our data further imply that PET hydrolases are truly rare enzymes. The highest occurrence of 1.5 hits/Mb was observed in sequences from a sample site containing crude oil.IMPORTANCE Polyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although a few PET hydrolases are already known, it is still unknown how frequently they appear and with which main bacterial phyla they are affiliated. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed occur at very low frequencies in the environment. Furthermore, it was possible to link them to phyla that were previously not known to harbor such enzymes. This work contributes novel knowledge on the phylogenetic relationships, the recent evolution, and the global distribution of PET hydrolases. Finally, we describe the biochemical traits of four novel PET hydrolases.
Collapse
Affiliation(s)
- Dominik Danso
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Wolfgang Zimmermann
- Institute of Biochemistry, Department of Microbiology and Bioprocess Technology, Leipzig University, Leipzig, Germany
| | - Ren Wei
- Institute of Biochemistry, Department of Microbiology and Bioprocess Technology, Leipzig University, Leipzig, Germany
| | | | | | - Terry Hazen
- The University of Tennessee, Knoxville, Tennessee, USA
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| |
Collapse
|
6
|
Munro JE, Liew EF, Coleman NV. Adaptation of a membrane bioreactor to 1,2-dichloroethane revealed by 16S rDNA pyrosequencing and dhlA qPCR. Environ Sci Technol 2013; 47:13668-13676. [PMID: 24175727 DOI: 10.1021/es403292s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A pilot-scale membrane bioreactor (MBR) was tested for bioremediation of 1,2-dichloroethane (DCA) in groundwater. Pyrosequencing of 16S rDNA was used to study changes in the microbiology of the MBR over 137 days, including a 67 day initial adaptation phase of increasing DCA concentration. The bacterial community in the MBR was distinct from those in soil and groundwater at the same site, and was dominated by alpha- and beta- proteobacteria, including Rhodobacter, Methylibium, Rhodopseudomonas, Methyloversatilis, Caldilinea, Thiobacillus, Azoarcus, Hyphomicrobium, and Leptothrix. Biodegradation of DCA in the MBR began after 26 days, and was sustained for the remainder of the experiment. A quantitative PCR (qPCR) assay for the dehalogenase gene dhlA was developed to monitor DCA-degrading bacteria in the MBR, and a positive correlation was seen between dhlA gene abundance and the cumulative amount of DCA that had entered the MBR. Genera previously associated with aerobic DCA biodegradation (Xanthobacter, Ancylobacter, Azoarcus) were present in the MBR, and the abundance of Azoarcus correlated well with dhlA gene abundance. This study shows that MBRs can be an effective method for removal of DCA from groundwater, and that the dhlA qPCR is a rapid and sensitive method for detection of DCA-degrading bacteria.
Collapse
Affiliation(s)
- Jacob E Munro
- School of Molecular Bioscience, Building G08, University of Sydney , Darlington, New South Wales, 2006, Australia
| | | | | |
Collapse
|
7
|
Tian Y, Liu W, Cai J, Zhang LY, Wong KB, Feddermann N, Boller T, Xie ZP, Staehelin C. The nodulation factor hydrolase of Medicago truncatula: characterization of an enzyme specifically cleaving rhizobial nodulation signals. Plant Physiol 2013; 163:1179-90. [PMID: 24082029 PMCID: PMC3813642 DOI: 10.1104/pp.113.223966] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/28/2013] [Indexed: 05/03/2023]
Abstract
Nodule formation induced by nitrogen-fixing rhizobia depends on bacterial nodulation factors (NFs), modified chitin oligosaccharides with a fatty acid moiety. Certain NFs can be cleaved and inactivated by plant chitinases. However, the most abundant NF of Sinorhizobium meliloti, an O-acetylated and sulfated tetramer, is resistant to hydrolysis by all plant chitinases tested so far. Nevertheless, this NF is rapidly degraded in the host rhizosphere. Here, we identify and characterize MtNFH1 (for Medicago truncatula Nod factor hydrolase 1), a legume enzyme structurally related to defense-related class V chitinases (glycoside hydrolase family 18). MtNFH1 lacks chitinase activity but efficiently hydrolyzes all tested NFs of S. meliloti. The enzyme shows a high cleavage preference, releasing exclusively lipodisaccharides from NFs. Substrate specificity and kinetic properties of MtNFH1 were compared with those of class V chitinases from Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum), which cannot hydrolyze tetrameric NFs of S. meliloti. The Michaelis-Menten constants of MtNFH1 for NFs are in the micromolar concentration range, whereas nonmodified chitin oligosaccharides represent neither substrates nor inhibitors for MtNFH1. The three-dimensional structure of MtNFH1 was modeled on the basis of the known structure of class V chitinases. Docking simulation of NFs to MtNFH1 predicted a distinct binding cleft for the fatty acid moiety, which is absent in the class V chitinases. Point mutation analysis confirmed the modeled NF-MtNFH1 interaction. Silencing of MtNFH1 by RNA interference resulted in reduced NF degradation in the rhizosphere of M. truncatula. In conclusion, we have found a novel legume hydrolase that specifically inactivates NFs.
Collapse
MESH Headings
- Amino Acid Sequence
- Carbohydrate Sequence
- Chitin/chemistry
- Chitin/metabolism
- Cloning, Molecular
- Host-Pathogen Interactions
- Hydrolases/classification
- Hydrolases/genetics
- Hydrolases/metabolism
- Immunoblotting
- Kinetics
- Medicago truncatula/enzymology
- Medicago truncatula/genetics
- Medicago truncatula/microbiology
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- Oligosaccharides/chemistry
- Oligosaccharides/metabolism
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Root Nodulation
- Protein Structure, Tertiary
- Root Nodules, Plant/enzymology
- Root Nodules, Plant/genetics
- Root Nodules, Plant/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Signal Transduction
- Sinorhizobium meliloti/metabolism
- Sinorhizobium meliloti/physiology
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Substrate Specificity
- Symbiosis
Collapse
Affiliation(s)
| | | | - Jie Cai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, 510006 Guangzhou, China (Y.T., W.L., J.C., L.-Y.Z., Z.-P.X., C.S.)
- School of Life Sciences and Center for Protein Science and Crystallography, Chinese University of Hong Kong, Shatin, Hong Kong, China (K.-B.W.); and
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, 4056 Basel, Switzerland (N.F., T.B.)
| | - Lan-Yue Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, 510006 Guangzhou, China (Y.T., W.L., J.C., L.-Y.Z., Z.-P.X., C.S.)
- School of Life Sciences and Center for Protein Science and Crystallography, Chinese University of Hong Kong, Shatin, Hong Kong, China (K.-B.W.); and
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, 4056 Basel, Switzerland (N.F., T.B.)
| | - Kam-Bo Wong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, 510006 Guangzhou, China (Y.T., W.L., J.C., L.-Y.Z., Z.-P.X., C.S.)
- School of Life Sciences and Center for Protein Science and Crystallography, Chinese University of Hong Kong, Shatin, Hong Kong, China (K.-B.W.); and
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, 4056 Basel, Switzerland (N.F., T.B.)
| | | | - Thomas Boller
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, 510006 Guangzhou, China (Y.T., W.L., J.C., L.-Y.Z., Z.-P.X., C.S.)
- School of Life Sciences and Center for Protein Science and Crystallography, Chinese University of Hong Kong, Shatin, Hong Kong, China (K.-B.W.); and
- Botanisches Institut der Universität Basel, Zurich Basel Plant Science Center, 4056 Basel, Switzerland (N.F., T.B.)
| | | | | |
Collapse
|
8
|
Naumov DG, Karreras M. [New program PSI protein classifier automatizes the PSI-BLAST results analysis]. Mol Biol (Mosk) 2009; 43:709-721. [PMID: 19807035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
PSI Protein Classifier is a new program that allows to summarize the consecutive and independent PSI-BLAST iteration results. The technical opportunities of the program are explained. Two examples of the PSI Protein Classifier application are given. Iterative screening of the protein database allowed to reveal feasible evolutionary relationship among GH5, GH13, GH27, GH31, GH36, GH66, GH101, and GH114 families of glycoside hydrolases. Family GH31 is divided into 38 subfamilies on the basis of statistically significant sequence similarity analysis (E-value analysis).
Collapse
|
9
|
Schelbert S, Aubry S, Burla B, Agne B, Kessler F, Krupinska K, Hörtensteiner S. Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis. Plant Cell 2009; 21:767-85. [PMID: 19304936 PMCID: PMC2671698 DOI: 10.1105/tpc.108.064089] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 02/12/2009] [Accepted: 03/08/2009] [Indexed: 05/08/2023]
Abstract
During leaf senescence, chlorophyll is removed from thylakoid membranes and converted in a multistep pathway to colorless breakdown products that are stored in vacuoles. Dephytylation, an early step of this pathway, increases water solubility of the breakdown products. It is widely accepted that chlorophyll is converted into pheophorbide via chlorophyllide. However, chlorophyllase, which converts chlorophyll to chlorophyllide, was found not to be essential for dephytylation in Arabidopsis thaliana. Here, we identify pheophytinase (PPH), a chloroplast-located and senescence-induced hydrolase widely distributed in algae and land plants. In vitro, Arabidopsis PPH specifically dephytylates the Mg-free chlorophyll pigment, pheophytin (phein), yielding pheophorbide. An Arabidopsis mutant deficient in PPH (pph-1) is unable to degrade chlorophyll during senescence and therefore exhibits a stay-green phenotype. Furthermore, pph-1 accumulates phein during senescence. Therefore, PPH is an important component of the chlorophyll breakdown machinery of senescent leaves, and we propose that the sequence of early chlorophyll catabolic reactions be revised. Removal of Mg most likely precedes dephytylation, resulting in the following order of early breakdown intermediates: chlorophyll --> pheophytin --> pheophorbide. Chlorophyllide, the last precursor of chlorophyll biosynthesis, is most likely not an intermediate of breakdown. Thus, chlorophyll anabolic and catabolic reactions are metabolically separated.
Collapse
Affiliation(s)
- Silvia Schelbert
- Institute of Plant Biology, University of Zürich, CH-8008 Zurich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
10
|
Beneito-Cambra M, Herrero-Martínez JM, Simó-Alfonso EF, Ramis-Ramos G. Rapid classification of enzymes in cleaning products by hydrolysis, mass spectrometry and linear discriminant analysis. Rapid Commun Mass Spectrom 2008; 22:3667-3672. [PMID: 18946864 DOI: 10.1002/rcm.3778] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A method for the rapid classification of proteases, lipases, amylases and cellulases used as enhancers in cleaning products, based on precipitation with acetone, hydrolysis with HCl, dilution of the hydrolysates with ethanol, and direct infusion into the electrospray ion source of an ion-trap mass spectrometer, has been developed. The abundances of the ([M+H]+ ions of the amino acids, from the hydrolysates of both the enzyme industrial concentrates and the detergent bases spiked with them, were used to construct linear discriminant analysis models, capable of distinguishing between the enzyme classes. For this purpose, the variables were normalized as follows: (A) the ion abundance of each amino acid was divided by the sum of the ion abundances of all the amino acids in the corresponding mass spectrum; (B) the ratios of pairs of ion abundances were obtained by dividing the ion abundance of each amino acid by each one of the ion abundances of the other 17 amino acids in the corresponding mass spectrum. Using normalization procedure B, excellent class-resolution between proteases, lipases, amylases and cellulases was achieved. In all cases, enzymes in industrial concentrates and manufactured cleaning products were correctly classified with >98% assignment probability.
Collapse
Affiliation(s)
- Miriam Beneito-Cambra
- Department of Analytical Chemistry, Faculty of Chemistry, University of Valencia, 46100 Burjassot, Valencia, Spain
| | | | | | | |
Collapse
|
11
|
Affiliation(s)
- Bernard Testa
- Department of Pharmacy, University Hospital Centre (CHUV), Rue du Bugnon, CH-1011 Lausanne.
| | | |
Collapse
|
12
|
Affiliation(s)
- Séverine Vandevoorde
- Unité de chimie pharmaceutique et radiopharmacie, UCL/CMFA 7340, Avenue E. Mounier, B-1200 Brussels.
| | | |
Collapse
|
13
|
Abstract
Entomopathogenic and mycoparasitic fungi synthesize hydrolytic enzymes such as chitinases, proteinases and beta-glucanases. These enzymes can act synergistically, helping fungi to control insect pests and pathogens that attack productive crops, and offer potential economic benefit to agribusiness. A number of hydrolytic enzymes have also been utilized in industrial applications. This review focuses on biochemical and structural analyses of fungal enzymes, together with current research information on secretion mechanisms.
Collapse
Affiliation(s)
- J L Pereira
- Centro de Análises Proteômicas e Bioquímica, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal - Brazil
| | | | | | | |
Collapse
|
14
|
Bennett JP, Whittingham JL, Brzozowski AM, Leonard PM, Grogan G. Structural characterization of a beta-diketone hydrolase from the cyanobacterium Anabaena sp. PCC 7120 in native and product-bound forms, a coenzyme A-independent member of the crotonase suprafamily. Biochemistry 2007; 46:137-44. [PMID: 17198383 DOI: 10.1021/bi061900g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gene alr4455 from the well-studied cyanobacterium Anabaena sp. PCC 7120 encodes a crotonase orthologue that displays beta-diketone hydrolase activity. Anabaena beta-diketone hydrolase (ABDH), in common with 6-oxocamphor hydrolase (OCH) from Rhodococcus sp. NCIMB 9784, catalyzes the desymmetrization of bicyclo[2.2.2]octane-2,6-dione to yield [(S)-3-oxocyclohexyl]acetic acid, a reaction unusual among the crotonase superfamily as the substrate is not an acyl-CoA thioester. The structure of ABDH has been determined to a resolution of 1.5 A in both native and ligand-bound forms. ABDH forms a hexamer similar to OCH and features one active site per enzyme monomer. The arrangement of side chains in the active site indicates that while the catalytic chemistry may be conserved in OCH orthologues, the structural determinants of substrate specificity are different. In the active site of ligand-bound forms that had been cocrystallized with the bicyclic diketone substrate bicyclo[2.2.2]octane-2,6-dione was found the product of the asymmetric enzymatic retro-Claisen reaction [(S)-3-oxocyclohexyl]acetic acid. The structures of ABDH in both native and ligand-bound forms reveal further details about structural variation and modes of coenzyme A-independent activity within the crotonases and provide further evidence of a wider suprafamily of enzymes that have recruited the crotonase fold for the catalysis of reactions other than those regularly attributed to canonical superfamily members.
Collapse
Affiliation(s)
- Joseph P Bennett
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
| | | | | | | | | |
Collapse
|
15
|
Abstract
Haloalkane dehalogenases (HLDs) are enzymes that catalyze the cleavage of carbon-halogen bonds by a hydrolytic mechanism. Although comparative biochemical analyses have been published, no classification system has been proposed for HLDs, to date, that reconciles their phylogenetic and functional relationships. In the study presented here, we have analyzed all sequences and structures of genuine HLDs and their homologs detectable by database searches. Phylogenetic analyses revealed that the HLD family can be divided into three subfamilies denoted HLD-I, HLD-II, and HLD-III, of which HLD-I and HLD-III are predicted to be sister-groups. A mismatch between the HLD protein tree and the tree of species, as well as the presence of more than one HLD gene in a few genomes, suggest that horizontal gene transfers, and perhaps also multiple gene duplications and losses have been involved in the evolution of this family. Most of the biochemically characterized HLDs are found in the HLD-II subfamily. The dehalogenating activity of two members of the newly identified HLD-III subfamily has only recently been confirmed, in a study motivated by this phylogenetic analysis. A novel type of the catalytic pentad (Asp-His-Asp+Asn-Trp) was predicted for members of the HLD-III subfamily. Calculation of the evolutionary rates and lineage-specific innovations revealed a common conserved core as well as a set of residues that characterizes each HLD subfamily. The N-terminal part of the cap domain is one of the most variable regions within the whole family as well as within individual subfamilies, and serves as a preferential site for the location of relatively long insertions. The highest variability of discrete sites was observed among residues that are structural components of the access channels. Mutations at these sites modify the anatomy of the channels, which are important for the exchange of ligands between the buried active site and the bulk solvent, thus creating a structural basis for the molecular evolution of new substrate specificities. Our analysis sheds light on the evolutionary history of HLDs and provides a structural framework for designing enzymes with new specificities.
Collapse
Affiliation(s)
- Eva Chovancová
- Loschmidt Laboratories, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | | | | |
Collapse
|
16
|
Ramsay AG, Scott KP, Martin JC, Rincon MT, Flint HJ. Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon. Microbiology (Reading) 2007; 152:3281-3290. [PMID: 17074899 DOI: 10.1099/mic.0.29233-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Selected butyrate-producing bacteria from the human colon that are related to Roseburia spp. and Butyrivibrio fibrisolvens showed a good ability to utilize a variety of starches for growth when compared with the Gram-negative amylolytic anaerobe Bacteroides thetaiotaomicron. A major cell-associated amylase of high molecular mass (140-210 kDa) was detected in each strain by SDS-PAGE zymogram analysis, and genes corresponding to these enzymes were analysed for two representative strains. Amy13B from But. fibrisolvens 16/4 is a multi-domain enzyme of 144.6 kDa that includes a family 13 glycoside hydrolase domain, and duplicated family 26 carbohydrate-binding modules. Amy13A (182.4 kDa), from Roseburia inulinivorans A2-194, also includes a family 13 domain, which is preceded by two repeat units of approximately 116 aa rich in aromatic residues, an isoamylase N-terminal domain, a pullulanase-associated domain, and an additional unidentified domain. Both Amy13A and Amy13B have N-terminal signal peptides and C-terminal cell-wall sorting signals, including a modified LPXTG motif similar to that involved in interactions with the cell surface in other Gram-positive bacteria, a hydrophobic transmembrane segment, and a basic C terminus. The overexpressed family 13 domains showed an absolute requirement for Mg2+ or Ca2+ for activity, and functioned as 1,4-alpha-glucanohydrolases (alpha-amylases; EC 3.2.1.1). These major starch-degrading enzymes thus appear to be anchored to the cell wall in this important group of human gut bacteria.
Collapse
Affiliation(s)
- Alan G Ramsay
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Karen P Scott
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jenny C Martin
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Marco T Rincon
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| |
Collapse
|
17
|
Simon GM, Cravatt BF. Endocannabinoid Biosynthesis Proceeding through Glycerophospho-N-acyl Ethanolamine and a Role for α/β-Hydrolase 4 in This Pathway. J Biol Chem 2006; 281:26465-72. [PMID: 16818490 DOI: 10.1074/jbc.m604660200] [Citation(s) in RCA: 263] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-Acyl ethanolamines (NAEs) are a large class of signaling lipids implicated in diverse physiological processes, including nociception, cognition, anxiety, appetite, and inflammation. It has been proposed that NAEs are biosynthesized from their corresponding N-acyl phosphatidylethanolamines (NAPEs) in a single enzymatic step catalyzed by a phospholipase D (NAPE-PLD). The recent generation of NAPE-PLD(-/-) mice has revealed that these animals possess lower brain levels of saturated NAEs but essentially unchanged concentrations of polyunsaturated NAEs, including the endogenous cannabinoid anandamide. These findings suggest the existence of additional enzymatic routes for the production of NAEs in vivo. Here, we report evidence for an alternative pathway for NAE biosynthesis that proceeds through the serine hydrolase-catalyzed double-deacylation of NAPE to generate glycerophospho-NAE, followed by the phosphodiesterase-mediated cleavage of this intermediate to liberate NAE. Furthermore, we describe the functional proteomic isolation and identification of a heretofore uncharacterized enzyme alpha/beta-hydrolase 4 (Abh4) as a lysophospholipase/phospholipase B that selectively hydrolyzes NAPEs and lysoNAPEs. Abh4 accepts lysoNAPEs bearing both saturated and polyunsaturated N-acyl chains as substrates and displays a distribution that closely mirrors lysoNAPE-lipase activity in mouse tissues. These results support the existence of an NAPE-PLD-independent route for NAE biosynthesis and suggest that Abh4 plays a role in this metabolic pathway by acting as a (lyso)NAPE-selective lipase.
Collapse
Affiliation(s)
- Gabriel M Simon
- Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | | |
Collapse
|
18
|
Abstract
UNLABELLED Universal ontology of catalytic sites is required to systematize enzyme catalytic sites, their evolution as well as relations between catalytic sites and protein families, organisms and chemical reactions. Here we present a classification of hydrolases catalytic sites based on hierarchical organization. The web-accessible database provides information on the catalytic sites, protein folds, EC numbers and source organisms of the enzymes and includes software allowing for analysis and visualization of the relations between them. AVAILABILITY http://www.enzyme.chem.msu.ru/hcs/
Collapse
Affiliation(s)
- Igor A Gariev
- School of Enzymology, Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
| | | |
Collapse
|
19
|
Tribble GD, Mao S, James CE, Lamont RJ. A Porphyromonas gingivalis haloacid dehalogenase family phosphatase interacts with human phosphoproteins and is important for invasion. Proc Natl Acad Sci U S A 2006; 103:11027-32. [PMID: 16832066 PMCID: PMC1544168 DOI: 10.1073/pnas.0509813103] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [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: 11/10/2005] [Indexed: 12/23/2022] Open
Abstract
Haloacid dehalogenase (HAD) family phosphatases are widespread in prokaryotes and are generally involved in metabolic processes. Porphyromonas gingivalis, an invasive periodontal pathogen, secretes the HAD family phosphoserine phosphatase SerB653 when in contact with gingival epithelial cells. Here we characterize the structure and enzymatic activity of SerB653 and show that a SerB653 allelic replacement mutant of P. gingivalis is deficient in internalization and persistence in gingival epithelial cells. In contrast, mutation of a second HAD family serine phosphatase of P. gingivalis (SerB1170), or of a serine transporter, did not affect invasion. A pull-down assay identified GAPDH and heat-shock protein 90 as potential substrates for SerB653. Furthermore, exogenous phosphatase regulated microtubule dynamics in host cells. These data indicate that P. gingivalis has adapted a formerly metabolic enzyme to facilitate entry into host cells by modulating host cytoskeletal architecture. Our findings define a virulence-related role of a HAD family phosphatase and reveal an invasin of an important periodontal pathogen.
Collapse
Affiliation(s)
- Gena D. Tribble
- Department of Oral Biology, University of Florida School of Dentistry, Gainesville, FL 32610-0424
| | - Song Mao
- Department of Oral Biology, University of Florida School of Dentistry, Gainesville, FL 32610-0424
| | - Chloe E. James
- Department of Oral Biology, University of Florida School of Dentistry, Gainesville, FL 32610-0424
| | - Richard J. Lamont
- Department of Oral Biology, University of Florida School of Dentistry, Gainesville, FL 32610-0424
| |
Collapse
|
20
|
Tyagi S, Pleiss J. Biochemical profiling in silico—Predicting substrate specificities of large enzyme families. J Biotechnol 2006; 124:108-16. [PMID: 16519956 DOI: 10.1016/j.jbiotec.2006.01.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 12/13/2005] [Accepted: 01/13/2006] [Indexed: 10/24/2022]
Abstract
A general high-throughput method for in silico biochemical profiling of enzyme families has been developed based on covalent docking of potential substrates into the binding sites of target enzymes. The method has been tested by systematically docking transition state--analogous intermediates of 12 substrates into the binding sites of 20 alpha/beta hydrolases from 15 homologous families. To evaluate the effect of side chain orientations to the docking results, 137 crystal structures were included in the analysis. A good substrate must fulfil two criteria: it must bind in a productive geometry with four hydrogen bonds between the substrate and the catalytic histidine and the oxyanion hole, and a high affinity of the enzyme-substrate complex as predicted by a high docking score. The modelling results in general reproduce experimental data on substrate specificity and stereoselectivity: the differences in substrate specificity of cholinesterases toward acetyl- and butyrylcholine, the changes of activity of lipases and esterases upon the size of the acid moieties, activity of lipases and esterases toward tertiary alcohols, and the stereopreference of lipases and esterases toward chiral secondary alcohols. Rigidity of the docking procedure was the major reason for false positive and false negative predictions, as the geometry of the complex and docking score may sensitively depend on the orientation of individual side chains. Therefore, appropriate structures have to be identified. In silico biochemical profiling provides a time efficient and cost saving protocol for virtual screening to identify the potential substrates of the members of large enzyme family from a library of molecules.
Collapse
Affiliation(s)
- Sadhna Tyagi
- Institute of Technical Biochemistry, University of Stuttgart, Germany
| | | |
Collapse
|
21
|
De Jaco A, Kovarik Z, Comoletti D, Jennings LL, Gaietta G, Ellisman MH, Taylor P. A single mutation near the C-terminus in alpha/beta hydrolase fold protein family causes a defect in protein processing. Chem Biol Interact 2006; 157-158:371-2. [PMID: 16429495 DOI: 10.1016/j.cbi.2005.10.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An Arg to Cys mutation in the extracellular domain of neuroligin-3 (NL3) was recently found in a twin set with autism [S. Jamain, H. Quach, C. Betancur, M. Rastam, C. Colineaux, I.C. Gillberg, H. Soderstrom, B. Giros, M. Leboyer, C. Gillberg, T. Bourgeron, Paris Autism Research International Sibpair Study, mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism, Nat. Genet. 34 (2003) 27-29]. The Cys substitution in NL3 causes altered intracellular protein trafficking, intracellular retention and diminished association with its cognate partner, beta-neurexin [D. Comoletti, A. De Jaco, L.L. Jennings, R.E. Flynn, G. Gaietta, I. Tsigelny, M.H. Ellisman, P. Taylor, The R451C-neuroligin-3 mutation associated with autism reveals a defect in protein processing, J. Neurosci. 24 (2004) 4889-4893]. NL3, butyrylcholinesterase (BuChE), and acetylcholinesterase (AChE), as members of the (/(-hydrolase fold family of proteins, share over 30% of amino acid identity in their extracellular domains. In particular, Arg451 in NL3 is conserved in the alpha/beta-hydrolase fold family being homologous to Arg386 in BuChE and Arg395 in AChE. A Cys substitution at the homologous Arg in the BuChE was found studying post-succinylcholine apnea in an Australian population [T. Yen, B.N. Nightingale, J.C. Burns, D.R. Sullivan, P.M. Stewart, Butyrylcholinesterase (BCHE) genotyping for post-succinylcholine apnea in an Australian population, Clin. Chem. 49 (2003) 1297-308]. We have made the homologous mutation in the mouse AChE and BuChE genes and showed that the Arg to Cys mutations resulted in identical alterations in the cellular phenotype for the various members of the alpha/beta-hydrolase fold family proteins.
Collapse
Affiliation(s)
- Antonella De Jaco
- Department of Pharmacology and National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA 92093-0636, USA.
| | | | | | | | | | | | | |
Collapse
|
22
|
Nijman SMB, Luna-Vargas MPA, Velds A, Brummelkamp TR, Dirac AMG, Sixma TK, Bernards R. A genomic and functional inventory of deubiquitinating enzymes. Cell 2006; 123:773-86. [PMID: 16325574 DOI: 10.1016/j.cell.2005.11.007] [Citation(s) in RCA: 1400] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Posttranslational modification of proteins by the small molecule ubiquitin is a key regulatory event, and the enzymes catalyzing these modifications have been the focus of many studies. Deubiquitinating enzymes, which mediate the removal and processing of ubiquitin, may be functionally as important but are less well understood. Here, we present an inventory of the deubiquitinating enzymes encoded in the human genome. In addition, we review the literature concerning these enzymes, with particular emphasis on their function, specificity, and the regulation of their activity.
Collapse
Affiliation(s)
- Sebastian M B Nijman
- Division of Molecular Carcinogenesis and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
23
|
Costa RAC, da Cruz-Landim C. Hydrolases in the hypopharyngeal glands of workers of Scaptotrigona postica and Apis mellifera (Hymenoptera, Apinae). Genet Mol Res 2005; 4:616-23. [PMID: 16475106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Hydrolytic enzymes from hypopharyngeal gland extracts of newly emerged, nurse and foraging workers of two eusocial bees, Scaptotrigona postica, a native Brazilian stingless bee, and the Africanized honey bee (Apis mellifera) in Brazil, were compared. The hypopharyngeal gland is rich in enzymes in both species. Fifteen different enzymes were found in the extracts, with only a few quantitative differences between the species. Some of the enzymes present in the extracts may have intracellular functions, while others seem to be digestive enzymes. Scaptotrigona postica, had lower beta-glucosidase and higher lipase esterase activities than A. mellifera. The differences may be due to different feeding habits and behavioral peculiarities of the two species.
Collapse
Affiliation(s)
- Rosiléia A C Costa
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Avenida 24A, 1515, Bela Vista 13506-900 Rio Claro, SP, Brasil
| | | |
Collapse
|
24
|
Renault L, Nègre V, Hotelier T, Cousin X, Marchot P, Chatonnet A. New friendly tools for users of ESTHER, the database of the α/β-hydrolase fold superfamily of proteins. Chem Biol Interact 2005; 157-158:339-43. [PMID: 16297901 DOI: 10.1016/j.cbi.2005.10.100] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The structural alpha/beta-hydrolase fold is characterized by a beta-sheet core of five to eight strands connected by alpha-helices to form a alpha/beta/alpha sandwich. The superfamily members, exemplified by the cholinesterases, diverged from a common ancestor into a number of hydrolytic enzymes displaying a wide range of substrate specificities, along with proteins with no recognized hydrolytic activity. In the enzymes, the catalytic triad residues are presented on loops of which one, the nucleophile elbow, is the most conserved feature of the fold. Of the other proteins, which all lack from one to all of the catalytic residues, some may simply be 'inactive' enzymes while others have been shown to be involved in heterologous surface recognition functions. The ESTHER (for esterases, alpha/beta-hydrolase enzymes and relatives) database (http://bioweb.ensam.inra.fr.esther) gathers and annotates all the published pieces of information (gene and protein sequences; biochemical, pharmacological, and structural data) related to the superfamily, and connects them together to provide the bases for studying structure-function relationships within the superfamily. The most recent developments of the database are presented.
Collapse
Affiliation(s)
- Ludovic Renault
- Ingénierie des Protéines CNRS, IFR Jean Roche, Université de la Méditerranée, Marseille, France
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
The amidohydrolase superfamily comprises hundreds of hydrolytic enzymes of the (beta/alpha)8 barrel fold with mono- or binuclear active-site metal centers, and a diverse spectrum of substrates and reactions. Promiscuous activities, or cross-reactivities, between different members of the same superfamily may provide important hints regarding evolutionary and mechanistic relationships. We examined three members: dihydroorotase (DHO), phosphotriesterase (PTE), and PTE-homology protein (PHP). Of particular interest are PTE, which is thought to have evolved within the last several decades, and PHP, an amidohydrolase superfamily member of unknown function, and the closest known homologue of PTE. We found a diverse and partially overlapping pattern of promiscuous activities in these enzymes, including a significant lactonase activity in PTE, esterase activities in both PTE and PHP, and a weak PTE activity in DHO. Directed evolution was applied to improve the promiscuous esterase activities of PTE and PHP. Remarkably, the most recurrent mutation increasing esterase activity in PTE, or PHP, maps to the same location in their superposed 3D structures. The evolved variants also exhibit newly acquired promiscuous activities that were not selected for, including very weak, yet measurable, paraoxonase activity in PHP. Our results illustrate the mechanistic, structural, and evolutionary links between these enzymes, and highlight the importance of studying laboratory evolution intermediates that might resemble node intermediates along the evolutionary pathways leading to the divergence of enzyme superfamilies.
Collapse
Affiliation(s)
- Cintia Roodveldt
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | | |
Collapse
|
26
|
Caruthers J, Zucker F, Worthey E, Myler PJ, Buckner F, Van Voorhuis W, Mehlin C, Boni E, Feist T, Luft J, Gulde S, Lauricella A, Kaluzhniy O, Anderson L, Le Trong I, Holmes MA, Earnest T, Soltis M, Hodgson KO, Hol WGJ, Merritt EA. Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily. Protein Sci 2005; 14:2887-94. [PMID: 16199669 PMCID: PMC2253213 DOI: 10.1110/ps.051783005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We have determined the crystal structures of three homologous proteins from the pathogenic protozoans Leishmania donovani, Leishmania major, and Trypanosoma cruzi. We propose that these proteins represent a new subfamily within the isochorismatase superfamily (CDD classification cd004310). Their overall fold and key active site residues are structurally homologous both to the biochemically well-characterized N-carbamoylsarcosine-amidohydrolase, a cysteine hydrolase, and to the phenazine biosynthesis protein PHZD (isochorismase), an aspartyl hydrolase. All three proteins are annotated as mitochondrial-associated ribonuclease Mar1, based on a previous characterization of the homologous protein from L. tarentolae. This would constitute a new enzymatic activity for this structural superfamily, but this is not strongly supported by the observed structures. In these protozoan proteins, the extended active site is formed by inter-subunit association within a tetramer, which implies a distinct evolutionary history and substrate specificity from the previously characterized members of the isochorismatase superfamily. The characterization of the active site is supported crystallographically by the presence of an unidentified ligand bound at the active site cysteine of the T. cruzi structure.
Collapse
Affiliation(s)
- Jonathan Caruthers
- Biomolecular Structure Center M/S 357742, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Siew N, Saini HK, Fischer D. A putative novel alpha/beta hydrolase ORFan family in Bacillus. FEBS Lett 2005; 579:3175-82. [PMID: 15922334 DOI: 10.1016/j.febslet.2005.04.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 03/25/2005] [Accepted: 04/11/2005] [Indexed: 10/25/2022]
Abstract
A large number of sequences in each newly sequenced genome correspond to lineage and species-specific proteins, also known as ORFans. Amongst these ORFans, a large number are sequences with unknown structures and functions. We have identified a family of sequences, annotated as hypothetical proteins, which are specific to Bacillus and have carried out a computational study aimed at characterizing this family. Fold-recognition methods predict that these sequences belong to the alpha/beta hydrolase fold. We suggest possible catalytic triads for the ORFans and propose a hypothesis regarding the possible families within the alpha/beta hydrolase superfamily to which they may belong.
Collapse
Affiliation(s)
- Naomi Siew
- Department of Chemistry, Ben Gurion University, Beer-Sheva 84105, Israel
| | | | | |
Collapse
|
28
|
Bretonnet AS, Jordheim LP, Dumontet C, Lancelin JM. Regulation and activity of cytosolic 5′-nucleotidase II. FEBS Lett 2005; 579:3363-8. [PMID: 15946667 DOI: 10.1016/j.febslet.2005.05.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 05/17/2005] [Accepted: 05/18/2005] [Indexed: 11/20/2022]
Abstract
In many vertebrate tissues, cytosolic 5'-nucleotidase II (cN-II) either hydrolyses or phosphorylates a number of purine (monophosphorylated) nucleosides through a scheme common to the Haloacid Dehalogenase superfamily members. It possesses a pivotal role in purine cellular metabolism and it acts on anti-tumoural and antiviral nucleoside analogues, thus being of potential therapeutic importance. cN-II is Mg2+-dependent, regulated and stabilised by several factors such as allosteric effectors ATP and 2,3-DPG, although these are not directly involved in the reaction stoichiometry. We review herein the experimental knowledge currently available about this remarkable enzymatic activity.
Collapse
Affiliation(s)
- A S Bretonnet
- Laboratoire de RMN Biomoléculaire, Université Claude Bernard--Lyon I, UMR CNRS 5180 Sciences Analytiques, ESCPE Lyon, 69622 Villeurbanne, France
| | | | | | | |
Collapse
|
29
|
Kleeberg I, Welzel K, Vandenheuvel J, Müller RJ, Deckwer WD. Characterization of a New Extracellular Hydrolase fromThermobifida fuscaDegrading Aliphatic−Aromatic Copolyesters. Biomacromolecules 2005; 6:262-70. [PMID: 15638529 DOI: 10.1021/bm049582t] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paper describes the purification, biochemical characterization, sequence determination, and classification of a novel thermophilic hydrolase from Thermobifida fusca (TfH) which is highly active in hydrolyzing aliphatic-aromatic copolyesters. The secretion of the extracellular enzyme is induced by the presence of aliphatic-aromatic copolyesters but also by adding several other esters to the medium. The hydrophobic enzyme could be purified applying a combination of (NH(4))SO(4)-precipitation, cation-exchange chromatography, and hydrophobic interaction chromatography. The 28 kDa enzyme exhibits a temperature maximum of activity between 65 and 70 degrees C and a pH maximum between pH 6 and 7 depending on the ion strength of the solution. According to the amino sequence determination, the enzyme consists of 261 amino acids and was classified as a serine hydrolase showing high sequence similarity to a triacylglycerol lipase from Streptomyces albus G and triacylglycerol-aclyhydrolase from Streptomyces sp. M11. The comparison with other lipases and esterases revealed the TfH exhibits a catalytic behavior between a lipase and an esterase. Such enzymes often are named as cutinases. However, the results obtained here show, that classifying enzymes as cutinases seems to be generally questionable.
Collapse
Affiliation(s)
- I Kleeberg
- Gesellschaft für biotechnologische Forschung mbH, D-38124 Braunschweig, Germany
| | | | | | | | | |
Collapse
|
30
|
Abstract
Enzyme function is much less conserved than anticipated, i.e., the requirement for sequence similarity that implies similarity in enzymatic function is much higher than the requirement that implies similarity in protein structure. This is because the function of an enzyme is an extremely complicated problem that may involve very subtle structural details as well as many other physical chemistry factors. Accordingly, if simply based on the sequence similarity approach, it would hardly get a decent success rate in predicting enzyme sub-class even for a dataset consisting of samples with 50% sequence identity. To cope with such a situation, the GO-PseAA predictor was adopted to identify the sub-class for each of the six main enzyme families. It has been observed that, even for the much more stringent datasets in which none of the enzymes has 25% sequence identity to any others, the overall success rates are 73-95%, suggesting that the GO-PseAA predictor can catch the core features of the statistical samples concerned and may become a useful high throughput tool in proteomics and bioinformatics.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, CA 92130, USA.
| | | |
Collapse
|
31
|
Sambandam T, Belousova M, Accaviti-Loper MA, Blanquicett C, Guercello V, Raijmakers R, Nicholas AP. Increased peptidylarginine deiminase type II in hypoxic astrocytes. Biochem Biophys Res Commun 2004; 325:1324-9. [PMID: 15555572 DOI: 10.1016/j.bbrc.2004.10.173] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Indexed: 10/26/2022]
Abstract
Peptidylarginine deiminase type II (PAD 2) is the primary enzyme responsible for conversion of protein bound arginine to citrulline in the central nervous system. Evidence suggests that glial fibrillary acidic protein (GFAP), the main intermediate filament in astrocytes, is deiminated, but not much is known regarding factors that control this enzymatic reaction. The present study demonstrated that PAD 2 activity (as determined by Western blot analysis of citrullinated GFAP isoforms) was increased in human cultured astrocytes by hypoxic conditions. PAD 2 mRNA increased markedly during the first 2h of hypoxia, but using a single chain antibody against human PAD 2 produced from the ETH-2 phage library, it took approximately 8h of hypoxia to see marked increases in PAD 2 protein. Thus, this is the first report to demonstrate a measurable response in the amounts of PAD 2 mRNA, protein and activity in human astrocytes by prolonged hypoxic exposure.
Collapse
Affiliation(s)
- Thiagarajan Sambandam
- Department of Neurology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL 35294, USA
| | | | | | | | | | | | | |
Collapse
|
32
|
Peisach E, Selengut JD, Dunaway-Mariano D, Allen KN. X-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase MDP-1 of the Haloacid Dehalogenase Superfamily,. Biochemistry 2004; 43:12770-9. [PMID: 15461449 DOI: 10.1021/bi0490688] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The haloacid dehalogenase (HAD) superfamily is comprised of structurally homologous enzymes that share several conserved sequence motifs (loops I-IV) in their active site. The majority of HAD members are phosphohydrolases and may be divided into three subclasses depending on domain organization. In classes I and II, a mobile "cap" domain reorients upon substrate binding, closing the active site to bulk solvent. Members of the third class lack this additional domain. Herein, we report the 1.9 A X-ray crystal structures of a member of the third subclass, magnesium-dependent phosphatase-1 (MDP-1) both in its unliganded form and with the product analogue, tungstate, bound to the active site. The secondary structure of MDP-1 is similar to that of the "core" domain of other type I and type II HAD members with the addition of a small, 28-amino acid insert that does not close down to exclude bulk solvent in the presence of ligand. In addition, the monomeric oligomeric state of MDP-1 does not allow the participation of a second subunit in the formation and solvent protection of the active site. The binding sites for the phosphate portion of the substrate and Mg(II) cofactor are also similar to those of other HAD members, with all previously observed contacts conserved. Unlike other subclass III HAD members, MDP-1 appears to be equally able to dephosphorylate phosphotyrosine and closed-ring phosphosugars. Modeling of possible substrates in the active site of MDP-1 reveals very few potential interactions with the substrate leaving group. The mapping of conserved residues in sequences of MDP-1 from different eukaryotic organisms reveals that they colocalize to a large region on the surface of the protein outside the active site. This observation combined with the modeling studies suggests that the target of MDP-1 is most likely a phosphotyrosine in an unknown protein rather than a small sugar-based substrate.
Collapse
Affiliation(s)
- Ezra Peisach
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2394, USA
| | | | | | | |
Collapse
|
33
|
Bjerkan TM, Bender CL, Ertesvåg H, Drabløs F, Fakhr MK, Preston LA, Skjak-Braek G, Valla S. The Pseudomonas syringae Genome Encodes a Combined Mannuronan C-5-epimerase and O-Acetylhydrolase, Which Strongly Enhances the Predicted Gel-forming Properties of Alginates. J Biol Chem 2004; 279:28920-9. [PMID: 15123694 DOI: 10.1074/jbc.m313293200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alginates are industrially important, linear copolymers of beta-d-mannuronic acid (M) and its C-5-epimer alpha-l-guluronic acid (G). The G residues originate from a postpolymerization reaction catalyzed by mannuronan C-5-epimerases (MEs), leading to extensive variability in M/G ratios and distribution patterns. Alginates containing long continuous stretches of G residues (G blocks) can form strong gels, a polymer type not found in alginate-producing bacteria belonging to the genus Pseudomonas. Here we show that the Pseudomonas syringae genome encodes a Ca(2+)-dependent ME (PsmE) that efficiently forms such G blocks in vitro. The deduced PsmE protein consists of 1610 amino acids and is a modular enzyme related to the previously characterized family of Azotobacter vinelandii ME (AlgE1-7). A- and R-like modules with sequence similarity to those in the AlgE enzymes are found in PsmE, and the A module of PsmE (PsmEA) was found to be sufficient for epimerization. Interestingly, an R module from AlgE4 stimulated Ps-mEA activity. PsmE contains two regions designated M and RTX, both presumably involved in the binding of Ca(2+). Bacterial alginates are partly acetylated, and such modified residues cannot be epimerized. Based on a detailed computer-assisted analysis and experimental studies another PsmE region, designated N, was found to encode an acetylhydrolase. By the combined action of N and A PsmE was capable of redesigning an extensively acetylated alginate low in G from a non gel-forming to a gel-forming state. Such a property has to our knowledge not been previously reported for an enzyme acting on a polysaccharide.
Collapse
Affiliation(s)
- Tonje M Bjerkan
- Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Ahn YO, Mizutani M, Saino H, Sakata K. Furcatin Hydrolase from Viburnum furcatum Blume Is a Novel Disaccharide-specific Acuminosidase in Glycosyl Hydrolase Family 1. J Biol Chem 2004; 279:23405-14. [PMID: 14976214 DOI: 10.1074/jbc.m311379200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Furcatin hydrolase (FH) is a unique disaccharide-specific acuminosidase, which hydrolyzes furcatin (p-allylphenyl 6-O-beta-D-apiofuranosyl-beta-D-glucopyranoside (acuminoside)) into p-allylphenol and the disaccharide acuminose. We have isolated a cDNA coding for FH from Viburnum furcatum leaves. The open reading frame in the cDNA encoded a 538-amino acid polypeptide including a putative chloroplast transit peptide. The deduced protein showed 64% identity with tea leaf beta-primeverosidase, which is another disaccharide glycosidase specific to beta-primeverosides (6-O-beta-D-xylopyranosyl-beta-D-glucopyranosides). The deduced FH also shared greater than 50% identity with various plant beta-glucosidases in glycosyl hydrolase family 1. The recombinant FH expressed in Escherichia coli exhibited the highest level of activity toward furcatin with a Km value of 2.2 mm and specifically hydrolyzed the beta-glycosidic bond between p-allylphenol and acuminose, confirming FH as a disaccharide glycosidase. The FH also hydrolyzed beta-primeverosides and beta-vicianoside (6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside) but poorly hydrolyzed beta-gentiobiosides (6-O-beta-D-glucopyranosyl-beta-d-glucopyranosides), indicating high substrate specificity for the disaccharide glycone moiety. The FH exhibited activity toward p-allylphenyl beta-D-glucopyranoside containing the same aglycone as furcatin but little activity toward the other beta-D-glucopyranosides. Stereochemical analysis using 1H NMR spectroscopy revealed that FH is a retaining glycosidase. The subcellular localization of FH was analyzed using green fluorescent protein fused with the putative N-terminal signal peptide, indicating that FH is localized to the chloroplast. Phylogenetic analysis of plant beta-glucosidases revealed that FH clusters with beta-primeverosidase, and this suggests that the disaccharide glycosidases will form a new subfamily in glycosyl hydrolase family 1.
Collapse
Affiliation(s)
- Young Ock Ahn
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | | | | |
Collapse
|
35
|
Abstract
UNLABELLED The epoxide hydrolases and haloalkane dehalogenases database (EH/HD) integrates sequence and structure of a highly diverse protein family, including mainly the Asp-hydrolases of EHs and HDs but also proteins, such as Ser-hydrolases non-heme peroxidases, prolyl iminopetidases and 2-hydroxymuconic semialdehyde hydrolases. These proteins have a highly conserved structure, but display a remarkable diversity in sequence and function. A total of 305 protein entries were assigned to 14 homologous families, forming two superfamilies. Annotated multisequence alignments and phylogenetic trees are provided for each homologous family and superfamily. Experimentally derived structures of 19 proteins are superposed and consistently annotated. Sequence and structure of all 305 proteins were systematically analysed. Thus, deeper insight is gained into the role of a highly conserved sequence motifs and structural elements. AVAILABILITY The EH/HD database is available at http://www.led.uni-stuttgart.de
Collapse
Affiliation(s)
- Sandra Barth
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | | | | | | |
Collapse
|
36
|
Abstract
We show that three-dimensional signatures consisting of only a few functionally important residues can be diagnostic of membership in superfamilies of enzymes. Using the enolase superfamily as a model system, we demonstrate that such a signature, or template, can identify superfamily members in structural databases with high sensitivity and specificity. This is remarkable because superfamilies can be highly diverse, with members catalyzing many different overall reactions; the unifying principle can be a conserved partial reaction or chemical capability. Our definition of a superfamily thus hinges on the disposition of residues involved in a conserved function, rather than on fold similarity alone. A clear advantage of basing structure searches on such active site templates rather than on fold similarity is the specificity with which superfamilies with distinct functional characteristics can be identified within a large set of proteins with the same fold, such as the (beta/alpha)8 barrels. Preliminary results are presented for an additional group of enzymes with a different fold, the haloacid dehalogenase superfamily, suggesting that this approach may be generally useful for assigning reading frames of unknown function to specific superfamilies and thereby allowing inference of some of their functional properties.
Collapse
Affiliation(s)
- Elaine C Meng
- Department of Pharmaceutical Chemistry, University of California, Genentech Hall, 600 Sixteenth Street, San Francisco, CA 94143-2240, USA
| | | | | |
Collapse
|
37
|
Vossenaar ER, Zendman AJW, van Venrooij WJ, Pruijn GJM. PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. Bioessays 2004; 25:1106-18. [PMID: 14579251 DOI: 10.1002/bies.10357] [Citation(s) in RCA: 691] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Peptidylarginine deiminase (PAD, EC 3.5.3.15) enzymes catalyze the conversion of protein-bound arginine to citrulline. This post-translational modification may have a big impact on the structure and function of the target protein. In this review, we will discuss the effects of citrullination and its involvement in several human diseases, including rheumatoid arthritis and multiple sclerosis. So far, four isotypes of PAD have been described in mammals. We describe the existence of PAD in non-mammalian vertebrates and the existence of a fifth mammalian PAD. In addition, tissue-specific expression, genomic organization and evolutionary conservation of the different PAD isotypes will be discussed in detail. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/2003/25/v25.1106.html.
Collapse
Affiliation(s)
- Erik R Vossenaar
- Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands.
| | | | | | | |
Collapse
|
38
|
Watanabe M, Sumida N, Yanai K, Murakami T. A novel saponin hydrolase from Neocosmospora vasinfecta var. vasinfecta. Appl Environ Microbiol 2004; 70:865-72. [PMID: 14766566 PMCID: PMC348887 DOI: 10.1128/aem.70.2.865-872.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2003] [Accepted: 10/22/2003] [Indexed: 11/20/2022] Open
Abstract
We isolated a soybean saponin hydrolase from Neocosmospora vasinfecta var. vasinfecta PF1225, a filamentous fungus that can degrade soybean saponin and generate soyasapogenol B. This enzyme was found to be a monomer with a molecular mass of about 77 kDa and a glycoprotein. Nucleotide sequence analysis of the corresponding gene (sdn1) indicated that this enzyme consisted of 612 amino acids and had a molecular mass of 65,724 Da, in close agreement with that of the apoenzyme after the removal of carbohydrates. The sdn1 gene was successfully expressed in Trichoderma viride under the control of the cellobiohydrolase I gene promoter. The molecular mass of the recombinant enzyme, about 69 kDa, was smaller than that of the native enzyme due to fewer carbohydrate modifications. Examination of the degradation products obtained by treatment of soyasaponin I with the recombinant enzyme showed that the enzyme hydrolyzed soyasaponin I to soyasapogenol B and triose [alpha-L-rhamnopyranosyl (1-->2)-beta-D-galactopyranosyl (1-->2)-D-glucuronopyranoside]. Also, when soyasaponin II and soyasaponin V, which are different from soyasaponin I only in constituent saccharides, were treated with the enzyme, the ratio of the reaction velocities for soyasaponin I, soyasaponin II, and soyasaponin V was 2,680:886:1. These results indicate that this enzyme recognizes the fine structure of the carbohydrate moiety of soyasaponin in its catalytic reaction. The amino acid sequence of this enzyme predicted from the DNA sequence shows no clear homology with those of any of the enzymes involved in the hydrolysis of carbohydrates.
Collapse
Affiliation(s)
- Manabu Watanabe
- Microbiological Resources and Technology Laboratories, Meiji Seika Kaisha, Ltd., Odawara-shi, Kanagawa 250-0852, Japan.
| | | | | | | |
Collapse
|
39
|
Mamos AR, Kurnatowska A. [Multifocal mycoses in women: prevalence, species characteristics, and some intraspecific features]. Wiad Parazytol 2004; 50:373-9. [PMID: 16865940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The aim of this study was to detect fungi in three ontocenoses of 947 women (aged 20-45). The prevalence of multifocal fungal infections in women varied from 62.2 +/- 2.99% to 81.0 +/- 3.92% in different ontocenoses. They assumed the following mean values: 38.4 +/- 1.77% for the vagina, 42.2 +/- 1.80% for the oral cavity, and 25.0 +/- 1.58% for the anus. The clinical manifestations of sexual organs inflammations were statistically significantly (p < 0.01) more frequent in women infected with fungi than in those without fungi in the vaginal ontocenosis. The highest convergence of the fungi presence with subjective and objective symptoms (assessed using the Yule Q index value) concerned: pruritus of the vulva or/and vaginal walls, burning sensation or painful urethra, as well as oedema of the external opening of the urethra, vulva or/and the vagina (Q from +0.808 to +0.970). However, there was no statistically significant convergence between occurrence of the fungi and vaginal discharge and painful hypogastrium. Based on more than 40 phenotypical features (morphological, biochemical) of the axenic strains originating from vaginal, oral, and anal ontocenoses, a total of 12 species of fungi were identified: Candida albicans, C. guilliermondii, C. krusei, C. tropicalis, C. kefyr, C. utilis, C. humicola, C. viswanathii, C. glabrata, C. parapsilosis, Rhodotorula mucilaginosa, and Geotrichum candidum. For intraspecific features, depending on the profile of the compounds used for auxanogram, 9 codes were read for Candida albicans and only one code for each of other species was detected. In API ZYM test based on assessment of 19 hydrolase activities the enzymograms of species included from 6 to 11 enzymes.
Collapse
Affiliation(s)
- Aneta Renata Mamos
- Katedra Biologii i Genetyki Medycznej, Zakład Biologii i Parazytologii Lekarskiej, Uniwersytet Medyczny, Lódź
| | | |
Collapse
|
40
|
Abstract
A range of cross-linked enzyme aggregates (CLEAs) was prepared from commercially available aminoacylase I. Results from three test reactions showed that aminoacylase does not possess aminolysis or alcoholysis activity, both previously ascribed to this enzyme. This result was confirmed using aminoacylase purified by chromatographic techniques, which leads us to conclude that the previously observed acylations of esters and amines is due to other enzymes present as impurities in the crude aminoacylase I.
Collapse
Affiliation(s)
- Moira L Bode
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands.
| | | | | |
Collapse
|
41
|
Eley BM, Cox SW. Proteolytic and hydrolytic enzymes from putative periodontal pathogens: characterization, molecular genetics, effects on host defenses and tissues and detection in gingival crevice fluid. Periodontol 2000 2003; 31:105-24. [PMID: 12656998 DOI: 10.1034/j.1600-0757.2003.03107.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
42
|
Nagy I, Banerjee T, Tamura T, Schoofs G, Gils A, Proost P, Tamura N, Baumeister W, De Mot R. Characterization of a novel intracellular endopeptidase of the alpha/beta hydrolase family from Streptomyces coelicolor A3(2). J Bacteriol 2003; 185:496-503. [PMID: 12511496 PMCID: PMC145308 DOI: 10.1128/jb.185.2.496-503.2003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a proteasome-lacking mutant of Streptomyces coelicolor A3(2), an intracellular enzyme with chymotrypsin-like activity, absent from the wild type, was detected. Complementation that restored proteasome function did not suppress expression of the endopeptidase. Since the enzyme was not found in two other S. coelicolor proteasome mutants, its expression probably resulted from a secondary mutation arisen in the proteasome mutant. Purification of the endopeptidase revealed its identity to SCO7095, a putative hydrolase encoded by the S. coelicolor A3(2) genome with no known homologue. Based on the prediction of a Ser-Asp-His catalytic triad and an alpha/beta hydrolase fold, SCO7095 was assigned to peptidase clan SC. N-terminally His-tagged SCO7095 was efficiently expressed in Escherichia coli cells and purified for further characterization. Although SCO7095 is distantly related to several proline iminopeptidases, including Thermoplasma acidophilum tricorn-interacting F1, no aminopeptidase activity was detected. On synthetic substrates, the monomeric enzyme exhibited not only chymotrypsin-like activity but also thrombin-like activity.
Collapse
Affiliation(s)
- István Nagy
- Centre of Microbial and Plant Genetics, Catholic University of Leuven, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Brzeziński K, Janowski R, Podkowiński J, Jaskólski M. Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus). Acta Biochim Pol 2002; 48:477-83. [PMID: 11732617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The coding sequences of two S-adenosyl-L-homocysteine hydrolases (SAHases) were identified in yellow lupine by screenig of a cDNA library. One of them, corresponding to the complete protein, was sequenced and compared with 52 other SAHase sequences. Phylogenetic analysis of these proteins identified three groups of the enzymes. Group A comprises only bacterial sequences. Group B is subdivided into two subgroups, one of which (B1) is formed by animal sequences. Subgroup B2 consist of two distinct clusters, B2a and B2b. Cluster B2b comprises all known plant sequences, including the yellow lupine enzyme, which are distinguished by a 50-residue insert. Group C is heterogeneous and contains SAHases from Archaea as well as a new class of animal enzymes, distinctly different from those in group B1.
Collapse
Affiliation(s)
- K Brzeziński
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | | | | | | |
Collapse
|
44
|
Abstract
We have cloned 3 novel murine cDNAs encoding proteins containing an alpha/beta hydrolase fold; a catalytic domain found in a very wide range of enzymes. These proteins belong to the prosite UPF0017 uncharacterized protein family and we have named them lung alpha/beta hydrolase 1, 2, and 3 (LABH) since they were cloned from lung cDNA. All have 9 coding exons, encoding 412, 425, and 411 residue proteins respectively (46-48 kDa); LABH1 being closely related to LABH3 having 45% identity. All 3 proteins have a single predicted amino-terminus transmembrane domain. An alignment of family members from different phyla enabled the identification of the LABH1 catalytic triad as Ser211, Asp337, and His366. mRNA expression levels of LABH1 and 3 were highest in liver and LABH2 highest in testis. These findings suggest that the LABH proteins consist of a novel family of membrane bound enzymes whose function has yet to be determined.
Collapse
Affiliation(s)
- Alasdair J Edgar
- Tissue Engineering Centre, Division of Investigative Science, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, United Kingdom.
| | | |
Collapse
|
45
|
Morona JK, Morona R, Miller DC, Paton JC. Streptococcus pneumoniae capsule biosynthesis protein CpsB is a novel manganese-dependent phosphotyrosine-protein phosphatase. J Bacteriol 2002; 184:577-83. [PMID: 11751838 PMCID: PMC139577 DOI: 10.1128/jb.184.2.577-583.2002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first four genes of the capsule locus (cps) of Streptococcus pneumoniae (cpsA to cpsD) are common to most serotypes. We have previously determined that CpsD is an autophosphorylating protein-tyrosine kinase, demonstrated that CpsC is required for CpsD tyrosine-phosphorylation, and shown that CpsB is required for dephosphorylation of CpsD. In the present study we show that CpsB is a novel manganese-dependent phosphotyrosine-protein phosphatase that belongs to the PHP (polymerase and histidinol phosphatase) family of phosphoesterases. We also show that an S. pneumoniae strain with point mutations in cpsB, affecting one of the conserved motifs of CpsB, is unencapsulated and appears to be morphologically identical to a strain in which the cpsB gene had been deleted.
Collapse
Affiliation(s)
- Judy K Morona
- Department of Molecular Biosciences, Adelaide University, Adelaide, South Australia 5005, Australia
| | | | | | | |
Collapse
|
46
|
Kurnatowska A, Kurnatowska I, Kacprzyk F, Chrzanowski W. [Characteristics of phenotypic specific and intraspecific features of fungal strains isolated from the organ ontocenoses in patients after renal transplantation]. Wiad Parazytol 2002; 48:425-33. [PMID: 16894727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Characteristics of phenotypic specific and intraspecific features of fungal strains isolated from the organ ontocenoses in patients after renal transplantation. The aim of present study was to describe 60 specific and intraspecific features of fungal strains isolated from the organ ontocenoses: oral cavity, rectum and genital organs in 32 patients undergoing permanent immunosupression after renal transplantation. Fungal strains identified using API 20 C and API 20 C AUX (bioMérieux). The activity of 19 hydrolases was investigated using API ZYM. Among 41 strains of fungi the following were found: Candida albicans (31 strains), C. glabrata (5), C. guilliermondii (2), C. krusei (2) and Saccharomyces cerevisiae (1). The number of fungal strains isolated from the oral cavity was the highest (21), less numerous from rectum (12) and the least from the genital organs (8). The enzymograms were described for all strains and the highest activity was noted in case of: e6 - leucine arylamidase, e11 - phosphatase acid, e3 - esterase (C4), e12 - naphtol-AS-BI-phosphohydrolase. The activity of these enzymes is connected with higher pathogenicity of C. albicans strains.
Collapse
Affiliation(s)
- Alicja Kurnatowska
- Katedra Biologii i Parazytologii Lekarskiej, Uniwersytet Medyczny, al. Kokciuszki 85, 90-436 Lódź.
| | | | | | | |
Collapse
|
47
|
Abstract
The evolutionary history of serine proteases can be accounted for by highly conserved amino acids that form crucial structural and chemical elements of the catalytic apparatus. These residues display non- random dichotomies in either amino acid choice or serine codon usage and serve as discrete markers for tracking changes in the active site environment and supporting structures. These markers categorize serine proteases of the chymotrypsin-like, subtilisin-like and alpha/beta-hydrolase fold clans according to phylogenetic lineages, and indicate the relative ages and order of appearance of those lineages. A common theme among these three unrelated clans of serine proteases is the development or maintenance of a catalytic tetrad, the fourth member of which is a Ser or Cys whose side chain helps stabilize other residues of the standard catalytic triad. A genetic mechanism for mutation of conserved markers, domain duplication followed by gene splitting, is suggested by analysis of evolutionary markers from newly sequenced genes with multiple protease domains.
Collapse
Affiliation(s)
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St Louis, MO 63110-1093, USA
Corresponding author e-mail:
| |
Collapse
|
48
|
Głowacka A, Ochecka-Szymańska A. [The enzymatic activity of fungi strains isolated from the skin and skin appendages of humans returning from the tropics]. Wiad Parazytol 2001; 47:729-33. [PMID: 16886418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The aim of the work was to assess the enzymatic activity of 11 fungi strains isolated from the skin of 10 Lódź residents who had visited the tropics over 1998-1999. The strains were cultured by Jeske and Lupa of The Voivodeship Outpatient Clinic of Infectious, Parasitic and Tropical Diseases and Fungal Infections in Lódź. They were as follows: Trichophyton rubrum and Acremonium kiliense from Zambia, Myriodontium keratinophilum, Beauveria bassiana, Cladosporium herbarum, Candida famata and Trichophyton yaoundei from Sudan, Trichophyton tonsurans from Ethiopia, Trichophyton phaseliforme from Egypt, Acremonium strictum from Zimbabwe and Microsporum racemosus from Tanzania. The enzymatic activity was determined with the use of API ZYM of bioMérieux enabling 19 hydrolases to be revealed. In general, all tropical strains were characterised by a weak hydrolytic activity.
Collapse
Affiliation(s)
- A Głowacka
- Katedra Biologii i Parazytologii Lekarskiej, Akademia Medyczna, 90-436 Lódź, al. Kościuszki 85
| | | |
Collapse
|
49
|
Wójcik A, Kurnatowski P, Materla M, Rózga A. [Hydrolytic activity yeast-like fungi strains isolated from Sulejów reservoir water]. Wiad Parazytol 2001; 47:903-9. [PMID: 16886445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have investigated the hydrolytic activity of 21 species of yeast-like fungi from Candida genus and 1 species of yeast S. cerevisiae isolated from Sulej6w Reservoir water. The activity of hydrolytic enzymes of the studied fungi was different than that of standard strains and also of fungi isolated from patients. This difference demonstrates the capability of the studied fungi to adapt to various environmental conditions.
Collapse
Affiliation(s)
- A Wójcik
- Katedra Biologii i Parazytologii Lekarskiej, Akademia Medyczna, 90-436 Lódź, al.Kościuszki 85
| | | | | | | |
Collapse
|
50
|
Abstract
BACKGROUND Many proteins undergo posttranslational modifications involving covalent attachment of lipid groups. Among them is palmitoylation, a dynamic, reversible process that affects trimeric G proteins and Ras and constitutes a regulatory mechanism for signal transduction pathways. Recently, an acylhydrolase previously identified as lysophospholipase has been shown to function as an acyl protein thioesterase, which catalyzes depalmitoylation of Galpha proteins as well as Ras. Its amino acid sequence suggested that the protein is evolutionarily related to neutral lipases and other thioesterases, but direct structural information was not available. RESULTS We have solved the crystal structure of the human putative Galpha-regulatory protein acyl thioesterase (hAPT1) with a single data set collected from a crystal containing the wild-type protein. The phases were calculated to 1.8 A resolution based on anomalous scattering from Br(-) ions introduced in the cryoprotectant solution in which the crystal was soaked for 20 s. The model was refined against data extending to a resolution of 1.5 A to an R factor of 18.6%. The enzyme is a member of the ubiquitous alpha/beta hydrolase family, which includes other acylhydrolases such as the palmitoyl protein thioesterase (PPT1). CONCLUSIONS The human APT1 is closely related to a previously described carboxylesterase from Pseudomonas fluorescens. The active site contains a catalytic triad of Ser-114, His-203, and Asp-169. Like carboxylesterase, hAPT1 appears to be dimeric, although the mutual disposition of molecules in the two dimers differs. Unlike carboxylesterase, the substrate binding pocket and the active site of hAPT1 are occluded by the dimer interface, suggesting that the enzyme must dissociate upon interaction with substrate.
Collapse
Affiliation(s)
- Y Devedjiev
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences System Charlottesville, VA 22908, USA
| | | | | | | | | |
Collapse
|