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März C, Nölting S, Wollenschläger L, Pühler A, Kalinowski J. Role of MalQ Enzyme in a Reconstructed Maltose/Maltodextrin Pathway in Actinoplanes sp. SE50/110. Microorganisms 2024; 12:1221. [PMID: 38930603 PMCID: PMC11205506 DOI: 10.3390/microorganisms12061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The pseudotetrasaccharide acarbose, produced by Actinoplanes sp. SE50/110, is a relevant secondary metabolite used in diabetes type II medication. Although maltose plays a crucial role in acarbose biosynthesis, the understanding of the maltose/maltodextrin metabolism and its involvement in acarbose production is at an early stage. Here, we reconstructed the predicted maltose-maltodextrin pathway that involves four enzymes AmlE, MalZ, MalP, and MalQ. An investigation of enzyme activities was conducted through in vitro assays, leading to an expansion of previously postulated substrate spectra. The maltose-induced α-glucosidase AmlE is noteworthy for its high hydrolysis rate of linear α-1,4-glucans, and its capability to hydrolyze various glycosidic bonds. The predicted maltodextrin glucosidase MalZ showed slow hydrolysis activity on linear α-glucans, but it was resistant to acarbose and capable of releasing glucose from acarbose. AmlE compensates for the low activity of MalZ to ensure glucose supply. We determined the enzyme activity of MalP and its dual function as maltodextrin and glycogen phosphorylase. The 4-α-glucanotransferase MalQ plays a central role in the maltose/maltodextrin metabolism, alongside MalP. This study confirmed the simultaneous degradation and synthesis of long-chain α-glucans. The product distribution showed that with an increasing number of glycosidic bonds, less glucose is formed. We found that MalQ, like its sequence homolog AcbQ from the acarbose biosynthetic gene cluster, is involved in the formation of elongated acarviosyl metabolites. However, MalQ does not participate in the elongation of acarbose 7-phosphate, which is likely the more readily available acceptor molecule in vivo. Accordingly, MalQ is not involved in the formation of acarviosyl impurities in Actinoplanes sp. SE50/110.
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Affiliation(s)
- Camilla März
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
| | - Sophia Nölting
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
| | - Lars Wollenschläger
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
| | - Alfred Pühler
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; (C.M.); (S.N.); (L.W.)
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2
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Ofman TP, Heming JJA, Nin-Hill A, Küllmer F, Moran E, Bennett M, Steneker R, Klein AM, Ruijgrok G, Kok K, Armstrong ZWB, Aerts JMFG, van der Marel GA, Rovira C, Davies GJ, Artola M, Codée JDC, Overkleeft HS. Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining α-Glucosidase Inhibition. Chemistry 2024; 30:e202400723. [PMID: 38623783 DOI: 10.1002/chem.202400723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Glycoside hydrolases (glycosidases) take part in myriad biological processes and are important therapeutic targets. Competitive and mechanism-based inhibitors are useful tools to dissect their biological role and comprise a good starting point for drug discovery. The natural product, cyclophellitol, a mechanism-based, covalent and irreversible retaining β-glucosidase inhibitor has inspired the design of diverse α- and β-glycosidase inhibitor and activity-based probe scaffolds. Here, we sought to deepen our understanding of the structural and functional requirements of cyclophellitol-type compounds for effective human α-glucosidase inhibition. We synthesized a comprehensive set of α-configured 1,2- and 1,5a-cyclophellitol analogues bearing a variety of electrophilic traps. The inhibitory potency of these compounds was assessed towards both lysosomal and ER retaining α-glucosidases. These studies revealed the 1,5a-cyclophellitols to be the most potent retaining α-glucosidase inhibitors, with the nature of the electrophile determining inhibitory mode of action (covalent or non-covalent). DFT calculations support the ability of the 1,5a-cyclophellitols, but not the 1,2-congeners, to adopt conformations that mimic either the Michaelis complex or transition state of α-glucosidases.
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Affiliation(s)
- Tim P Ofman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jurriaan J A Heming
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques 1-11, E-08028, Barcelona, Spain
| | - Florian Küllmer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Elisha Moran
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Megan Bennett
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Roy Steneker
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anne-Mei Klein
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Ruijgrok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Ken Kok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Zach W B Armstrong
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques 1-11, E-08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020, Barcelona, Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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3
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
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Structural basis of glycogen metabolism in bacteria. Biochem J 2019; 476:2059-2092. [PMID: 31366571 DOI: 10.1042/bcj20170558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The evolution of metabolic pathways is a major force behind natural selection. In the spotlight of such process lies the structural evolution of the enzymatic machinery responsible for the central energy metabolism. Specifically, glycogen metabolism has emerged to allow organisms to save available environmental surplus of carbon and energy, using dedicated glucose polymers as a storage compartment that can be mobilized at future demand. The origins of such adaptive advantage rely on the acquisition of an enzymatic system for the biosynthesis and degradation of glycogen, along with mechanisms to balance the assembly and disassembly rate of this polysaccharide, in order to store and recover glucose according to cell energy needs. The first step in the classical bacterial glycogen biosynthetic pathway is carried out by the adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase. This allosteric enzyme synthesizes ADP-glucose and acts as a point of regulation. The second step is carried out by the glycogen synthase, an enzyme that generates linear α-(1→4)-linked glucose chains, whereas the third step catalyzed by the branching enzyme produces α-(1→6)-linked glucan branches in the polymer. Two enzymes facilitate glycogen degradation: glycogen phosphorylase, which functions as an α-(1→4)-depolymerizing enzyme, and the debranching enzyme that catalyzes the removal of α-(1→6)-linked ramifications. In this work, we rationalize the structural basis of glycogen metabolism in bacteria to the light of the current knowledge. We describe and discuss the remarkable progress made in the understanding of the molecular mechanisms of substrate recognition and product release, allosteric regulation and catalysis of all those enzymes.
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6
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Seo DH, Jung JH, Park CS. Improved polymerization activity of Deinococcus geothermalis amylosucrase by semi-rational design: Effect of loop flexibility on the polymerization reaction. Int J Biol Macromol 2019; 130:177-185. [DOI: 10.1016/j.ijbiomac.2019.02.139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 12/17/2022]
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7
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Thermostable alpha-glucan phosphorylases: characteristics and industrial applications. Appl Microbiol Biotechnol 2018; 102:8187-8202. [PMID: 30043268 DOI: 10.1007/s00253-018-9233-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
Abstract
α-Glucan phosphorylases (α-GPs) catalyze the reversible phosphorolysis of α-1,4-linked polysaccharides such as glycogen, starch, and maltodextrins, therefore playing a central role in the usage of storage polysaccharides. The discovery of these enzymes and their role in the course of catalytic conversion of glycogen was rewarded with the Nobel Prize in Physiology or Medicine in 1947. Nowadays, however, thermostable representatives attract special attention due to their vast potential in the enzymatic production of diverse carbohydrates and derivatives such as (functional) oligo- and (non-natural) polysaccharides, artificial starch, glycosides, and nucleotide sugars. One of the most recently explored utilizations of α-GPs is their role in the multi-enzymatic process of energy production stored in carbohydrate biobatteries. Regardless of their use, thermostable α-GPs offer significant advantages and facilitated bioprocess design due to their high operational temperatures. Here, we present an overview and comparison of up-to-date characterized thermostable α-GPs with a special focus on their reported biotechnological applications.
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8
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Weiss SC, Skerra A, Schiefner A. Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli. J Biol Chem 2015; 290:21352-64. [PMID: 26139606 DOI: 10.1074/jbc.m115.667337] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 11/06/2022] Open
Abstract
Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. To elucidate the molecular basis of transglycosylation by MalQ, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine-glucose-acarbose, at resolutions down to 2.1 Å. MalQ represents the first example of a mesophilic bacterial amylomaltase with known structure and exhibits an N-terminal extension of about 140 residues, in contrast with previously described thermophilic enzymes. This moiety seems unique to amylomaltases from Enterobacteriaceae and folds into two distinct subdomains that associate with different parts of the catalytic core. Intriguingly, the three MalQ crystal structures appear to correspond to distinct states of this enzyme, revealing considerable conformational changes during the catalytic cycle. In particular, the inhibitor complex highlights the requirement of both a 3-OH group and a 4-OH group (or α1-4-glycosidic bond) at the acceptor subsite +1 for the catalytically competent orientation of the acid/base catalyst Glu-496. Using an HPLC-based MalQ enzyme assay, we could demonstrate that the equilibrium concentration of maltodextrin products depends on the length of the initial substrate; with increasing numbers of glycosidic bonds, less glucose is formed. Thus, both structural and enzymatic data are consistent with the extremely low hydrolysis rates observed for amylomaltases and underline the importance of MalQ for the metabolism of maltodextrins in E. coli.
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Affiliation(s)
- Simon C Weiss
- From the Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
| | - Arne Skerra
- From the Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
| | - André Schiefner
- From the Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85350 Freising-Weihenstephan, Germany
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9
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Puchart V. Glycoside phosphorylases: Structure, catalytic properties and biotechnological potential. Biotechnol Adv 2015; 33:261-76. [DOI: 10.1016/j.biotechadv.2015.02.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 12/20/2022]
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10
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The α-glucan phosphorylase MalP of Corynebacterium glutamicum is subject to transcriptional regulation and competitive inhibition by ADP-glucose. J Bacteriol 2015; 197:1394-407. [PMID: 25666133 DOI: 10.1128/jb.02395-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED α-Glucan phosphorylases contribute to degradation of glycogen and maltodextrins formed in the course of maltose metabolism in bacteria. Accordingly, bacterial α-glucan phosphorylases are classified as either glycogen or maltodextrin phosphorylase, GlgP or MalP, respectively. GlgP and MalP enzymes follow the same catalytic mechanism, and thus their substrate spectra overlap; however, they differ in their regulation: GlgP genes are constitutively expressed and the enzymes are controlled on the activity level, whereas expression of MalP genes are transcriptionally controlled in response to the carbon source used for cultivation. We characterize here the modes of control of the α-glucan phosphorylase MalP of the Gram-positive Corynebacterium glutamicum. In accordance to the proposed function of the malP gene product as MalP, we found transcription of malP to be regulated in response to the carbon source. Moreover, malP transcription is shown to depend on the growth phase and to occur independently of the cell glycogen content. Surprisingly, we also found MalP activity to be tightly regulated competitively by the presence of ADP-glucose, an intermediate of glycogen synthesis. Since the latter is considered a typical feature of GlgPs, we propose that C. glutamicum MalP acts as both maltodextrin and glycogen phosphorylase and, based on these findings, we question the current system for classification of bacterial α-glucan phosphorylases. IMPORTANCE Bacterial α-glucan phosphorylases have been classified conferring to their purpose as either glycogen or maltodextrin phosphorylases. We found transcription of malP in C. glutamicum to be regulated in response to the carbon source, which is recognized as typical for maltodextrin phosphorylases. Surprisingly, we also found MalP activity to be tightly regulated competitively by the presence of ADP-glucose, an intermediate of glycogen synthesis. The latter is considered a typical feature of GlgPs. These findings, taken together, suggest that C. glutamicum MalP is the first α-glucan phosphorylase that does not fit into the current system for classification of bacterial α-glucan phosphorylases and exemplifies the complex mechanisms underlying the control of glycogen content and maltose metabolism in this model organism.
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11
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Park KH. Roles of Enzymes in Glycogen Metabolism and Degradation in Escherichia coli. J Appl Glycosci (1999) 2015. [DOI: 10.5458/jag.jag.jag-2015_005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Kwan-Hwa Park
- Department of Foodservice Management and Nutrition, Sangmyung University
- Department of Food Science and Biotechnology, Seoul National University
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12
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Martín M, Wayllace NZ, Valdez HA, Gomez-Casati DF, Busi MV. Improving the glycosyltransferase activity of Agrobacterium tumefaciens glycogen synthase by fusion of N-terminal starch binding domains (SBDs). Biochimie 2013; 95:1865-70. [DOI: 10.1016/j.biochi.2013.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/13/2013] [Indexed: 11/17/2022]
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13
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Enzymatic characteristics of cellobiose phosphorylase from Ruminococcus albus NE1 and kinetic mechanism of unusual substrate inhibition in reverse phosphorolysis. Biosci Biotechnol Biochem 2012; 76:812-8. [PMID: 22484959 DOI: 10.1271/bbb.110954] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cellobiose phosphorylase (CBP) catalyzes the reversible phosphorolysis of cellobiose to produce α-D-glucopyranosyl phosphate (Glc1P) and D-glucose. It is an essential enzyme for the metabolism of cello-oligosaccharides in a ruminal bacterium, Ruminococcus albus. In this study, recombinant R. albus CBP (RaCBP) produced in Escherichia coli was characterized. It showed highest activity at pH 6.2 at 50 °C, and was stable in a pH range of 5.5-8.8 and at below 40 °C. It phosphorolyzed only cellobiose efficiently, and the reaction proceeded through a random-ordered bi bi mechanism, by which inorganic phosphate and cellobiose bind in random order and D-glucose is released before Glc1P. In the synthetic reaction, RaCBP showed highest activity to D-glucose, followed by 6-deoxy-D-glucose. D-Mannose, 2-deoxy-D-glucose, D-glucosamine, D-xylose, 1,5-anhydro-D-glucitol, and gentiobiose also served as acceptors, although the activities for them were much lower than for D-glucose. D-Glucose acted as a competitive-uncompetitive inhibitor of the reverse synthetic reaction, which bound not only the Glc1P site (competitive) but also the ternary enzyme-Glc1P-D-glucose complex (uncompetitive).
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14
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RAMANATHAN K, SETHUMADHAVAN RAO. EXPLORING THE ROLE OF C–H … π INTERACTIONS ON THE STRUCTURAL STABILITY OF ANTIMICROBIAL PEPTIDES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609005155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A computational analysis on the C – H … π interactions in a group of 53 antimicrobial peptides was investigated. A total of 162 C – H … π interactions were observed. Side-chain to side-chain C – H … π interactions are the predominant type of interactions in antimicrobial peptides data set. There was an average of one significant C – H … π interaction for every 7 residues in the antimicrobial peptides investigated. Long-range C – H … π interactions are the predominant type of interactions. The secondary structure preference, solvent accessibility and stabilization centers of these of C – H … π interacting residues were estimated. It is likely that the C – H … π interactions contribute significantly to the overall stability of antimicrobial peptides. These interactions were observed after a molecular dynamics study on these set of antimicrobial peptides using CHARMM force field.
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Affiliation(s)
- K. RAMANATHAN
- School of Biotechnology, Chemical and Biomedical Engineering, Bioinformatics Division, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - RAO SETHUMADHAVAN
- School of Biotechnology, Chemical and Biomedical Engineering, Bioinformatics Division, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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15
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Ramanathan K, Shanthi V, Sethumadhavan R. A compact review on the comparison of conventional and non-conventional interactions on the structural stability of therapeutic proteins. Interdiscip Sci 2011; 3:144-60. [PMID: 21541844 DOI: 10.1007/s12539-011-0082-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 06/21/2010] [Accepted: 06/24/2010] [Indexed: 11/28/2022]
Abstract
Therapeutic proteins carry out the most difficult tasks in living cells. They do so by interacting specifically with other molecules. This requires that they fold to a unique and more stable conformation. A prerequisite for comprehending the folding processes in their immense complexity entails a thorough understanding of many weak interactions. The purpose of this review is to systematically study the role of weak interactions such as cation-π, C-H......π, N-H......π and O-H......π, in the set of 49 therapeutic proteins. The importance of many of these interactions (for example, cationic residues interacting with π system) is revealed by the higher degree of conservation observed for them in protein structures. These interactions are mainly formed by long-range contacts and significant percentage of cation-π, C-H......π, N-H......π and O-H......π interacting residues had one or more stabilization centers. Further, a comparison of conventional and nonconventional interactions in the present data set unambiguously highlights the significance of these weak interactions in the structural stability of therapeutic proteins. We propose that the incorporation of the entirety of these interactions leads to a more complete description of the problem, and that this could provide new perspectives and new possible answers.
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Affiliation(s)
- K Ramanathan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
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16
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Ye X, Rollin J, Zhang YHP. Thermophilic α-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.01.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Guerin ME, Schaeffer F, Chaffotte A, Gest P, Giganti D, Korduláková J, van der Woerd M, Jackson M, Alzari PM. Substrate-induced conformational changes in the essential peripheral membrane-associated mannosyltransferase PimA from mycobacteria: implications for catalysis. J Biol Chem 2009; 284:21613-25. [PMID: 19520856 PMCID: PMC2755885 DOI: 10.1074/jbc.m109.003947] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/03/2009] [Indexed: 11/06/2022] Open
Abstract
Phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential glycosyltransferase (GT) involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs), which are key components of the mycobacterial cell envelope. PimA is the paradigm of a large family of peripheral membrane-binding GTs for which the molecular mechanism of substrate/membrane recognition and catalysis is still unknown. Strong evidence is provided showing that PimA undergoes significant conformational changes upon substrate binding. Specifically, the binding of the donor GDP-Man triggered an important interdomain rearrangement that stabilized the enzyme and generated the binding site for the acceptor substrate, phosphatidyl-myo-inositol (PI). The interaction of PimA with the beta-phosphate of GDP-Man was essential for this conformational change to occur. In contrast, binding of PI had the opposite effect, inducing the formation of a more relaxed complex with PimA. Interestingly, GDP-Man stabilized and PI destabilized PimA by a similar enthalpic amount, suggesting that they formed or disrupted an equivalent number of interactions within the PimA complexes. Furthermore, molecular docking and site-directed mutagenesis experiments provided novel insights into the architecture of the myo-inositol 1-phosphate binding site and the involvement of an essential amphiphatic alpha-helix in membrane binding. Altogether, our experimental data support a model wherein the flexibility and conformational transitions confer the adaptability of PimA to the donor and acceptor substrates, which seems to be of importance during catalysis. The proposed mechanism has implications for the comprehension of the peripheral membrane-binding GTs at the molecular level.
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Affiliation(s)
- Marcelo E Guerin
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, USA.
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Seibel J, Jördening HJ, Buchholz K. Glycosylation with activated sugars using glycosyltransferases and transglycosidases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420600986811] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Grieβler R, Pickl M, D'auria S, Tanfani F, Nidetzky B. Oxyanion-Mediated Protein Stabilization: Differential Roles of Phosphate for Preventing Inactivation of Bacterial α-Glucan Phosphorylases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420108992025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Leterrier M, Holappa LD, Broglie KE, Beckles DM. Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications. BMC PLANT BIOLOGY 2008; 8:98. [PMID: 18826586 PMCID: PMC2576272 DOI: 10.1186/1471-2229-8-98] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 09/30/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Starch is of great importance to humans as a food and biomaterial, and the amount and structure of starch made in plants is determined in part by starch synthase (SS) activity. Five SS isoforms, SSI, II, III, IV and Granule Bound SSI, have been identified, each with a unique catalytic role in starch synthesis. The basic mode of action of SSs is known; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete. To gain a better understanding of the differences in SS sequences that underscore their specificity, the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done. RESULTS The wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement. The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock. Phylogenetic analysis showed that in plants, SSIV is closely related to SSIII, while SSI, SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation. Further, identified differences at the amino acid level in their glycosyltransferase domains, predicted secondary structures, global conformations and conserved residues might be indicative of intragroup functional associations. CONCLUSION Based on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases (GSs), it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI, SSI and SSII. In GBSSI, the Ile485 residue may partially explain that enzyme's unique catalytic features. The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly.
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MESH Headings
- Amino Acid Sequence
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Cloning, Molecular
- DNA, Complementary/genetics
- Evolution, Molecular
- Expressed Sequence Tags
- Gene Expression
- Gene Library
- Genes, Plant
- Genome, Plant
- Molecular Sequence Data
- Phylogeny
- Plant Leaves/enzymology
- Plant Leaves/genetics
- Plant Proteins/genetics
- Protein Structure, Secondary
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Starch Synthase/genetics
- Triticum/enzymology
- Triticum/genetics
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Affiliation(s)
- Marina Leterrier
- Department of Plant Sciences, One Peter Shield Avenue, University of California, Davis, CA 95616-8617, USA
| | - Lynn D Holappa
- Department of Plant Sciences, One Peter Shield Avenue, University of California, Davis, CA 95616-8617, USA
- Department of Organismic & Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge MA 02138, USA
| | - Karen E Broglie
- DuPont-Pioneer, Crop Genetics Research, Experimental Station, Wilmington, DE 19808, USA
| | - Diane M Beckles
- Department of Plant Sciences, One Peter Shield Avenue, University of California, Davis, CA 95616-8617, USA
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21
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Lairson LL, Henrissat B, Davies GJ, Withers SG. Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem 2008; 77:521-55. [PMID: 18518825 DOI: 10.1146/annurev.biochem.76.061005.092322] [Citation(s) in RCA: 1374] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycosyltransferases catalyze glycosidic bond formation using sugar donors containing a nucleoside phosphate or a lipid phosphate leaving group. Only two structural folds, GT-A and GT-B, have been identified for the nucleotide sugar-dependent enzymes, but other folds are now appearing for the soluble domains of lipid phosphosugar-dependent glycosyl transferases. Structural and kinetic studies have provided new insights. Inverting glycosyltransferases utilize a direct displacement S(N)2-like mechanism involving an enzymatic base catalyst. Leaving group departure in GT-A fold enzymes is typically facilitated via a coordinated divalent cation, whereas GT-B fold enzymes instead use positively charged side chains and/or hydroxyls and helix dipoles. The mechanism of retaining glycosyltransferases is less clear. The expected two-step double-displacement mechanism is rendered less likely by the lack of conserved architecture in the region where a catalytic nucleophile would be expected. A mechanism involving a short-lived oxocarbenium ion intermediate now seems the most likely, with the leaving phosphate serving as the base.
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Affiliation(s)
- L L Lairson
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
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22
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Hong Y, Wu L, Liu B, Peng C, Sheng D, Ni J, Shen Y. Characterization of a glucan phosphorylase from the thermophilic archaeon Sulfolobus tokodaii strain 7. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Busi MV, Palopoli N, Valdez HA, Fornasari MS, Wayllace NZ, Gomez-Casati DF, Parisi G, Ugalde RA. Functional and structural characterization of the catalytic domain of the starch synthase III from Arabidopsis thaliana. Proteins 2008; 70:31-40. [PMID: 17623838 DOI: 10.1002/prot.21469] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Glycogen and starch are the major energy storage compounds in most living organisms. The metabolic pathways leading to their synthesis involve the action of several enzymes, among which glycogen synthase (GS) or starch synthase (SS) catalyze the elongation of the alpha-1,4-glucan backbone. At least five SS isoforms were described in Arabidopsis thaliana; it has been reported that the isoform III (SSIII) has a regulatory function on the synthesis of transient plant starch. The catalytic C-terminal domain of A. thaliana SSIII (SSIII-CD) was cloned and expressed. SSIII-CD fully complements the production of glycogen by an Agrobacterium tumefaciens glycogen synthase null mutant, suggesting that this truncated isoform restores in vivo the novo synthesis of bacterial glycogen. In vitro studies revealed that recombinant SSIII-CD uses with more efficiency rabbit muscle glycogen than amylopectin as primer and display a high apparent affinity for ADP-Glc. Fold class assignment methods followed by homology modeling predict a high global similarity to A. tumefaciens GS showing a fully conservation of the ADP-binding residues. On the other hand, this comparison revealed important divergences of the polysaccharide binding domain between AtGS and SSIII-CD.
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Affiliation(s)
- Maria V Busi
- IIB-INTECH, CONICET-UNSAM, Camino Circunvalación km 6, 7130, Chascomús, Buenos Aires, Argentina
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24
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Sonnet PE, Mascavage LM, Dalton DR. The first steps. The attack on the carbonyl carbon of pyridoxal cofactor in pyridoxal-dependent enzymes. Bioorg Med Chem Lett 2008; 18:744-8. [DOI: 10.1016/j.bmcl.2007.11.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Accepted: 11/12/2007] [Indexed: 10/22/2022]
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25
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Campagnolo M, Campa C, Zorzi RD, Wuerges J, Geremia S. X-ray studies on ternary complexes of maltodextrin phosphorylase. Arch Biochem Biophys 2007; 471:11-9. [PMID: 18164678 DOI: 10.1016/j.abb.2007.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 11/14/2007] [Accepted: 11/18/2007] [Indexed: 10/22/2022]
Abstract
We report crystal structures of ternary complexes of maltodextrin phosphorylase with natural oligosaccharide and phosphate mimicking anions: nitrate, sulphate and vanadate. Electron density maps obtained from crystals grown in presence of Al(NO3)3 show a nitrate ion instead of the expected AlF4- in the catalytic site. The trigonal NO3- is coplanar with the Arg569 guanidinium group and mimics three of the four oxygen atoms of phosphate. The ternary complex with sulphate shows a partial occupancy of the anionic site. The low affinity of the sulphate ion, observed when the alpha-glucosyl substrate is present in the catalytic channel, is ascribed to restricted space for the anion. Even lower occupancy is observed for the larger vanadate anion. The Malp/G5/VO43- structure shows the partial occupancy of the oligosaccharide and the dislocation of the 380's loop. This has been attributed to the formation of oligosaccharide vanadate derivatives (confirmed by capillary electrophoresis) that reduces their effective concentration. The difficulty to trap a ternary complex mimicking the ground state has been correlated to the apparent lower affinity that natural substrates show regarding the intermediates of the enzymatic reaction.
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Affiliation(s)
- Mara Campagnolo
- CEB-Centre of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
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26
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Schwarz A, Brecker L, Nidetzky B. Probing the active site of Corynebacterium callunae starch phosphorylase through the characterization of wild-type and His334-->Gly mutant enzymes. FEBS J 2007; 274:5105-15. [PMID: 17803683 DOI: 10.1111/j.1742-4658.2007.06030.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
His334 facilitates catalysis by Corynebacterium callunae starch phosphorylase through selective stabilization of the transition state of the reaction, partly derived from a hydrogen bond between its side chain and the C-6 hydroxy group of the glucosyl residue undergoing transfer to and from phosphate. We have substituted His334 by a Gly and measured the disruptive effects of the site-directed replacement on active site function using steady-state kinetics and NMR spectroscopic characterization of the cofactor pyridoxal 5'-phosphate and binding of carbohydrate ligands. Purified H334G showed 0.05% and 1.3% of wild-type catalytic center activity for phosphorolysis of maltopentaose (kcatP = 0.033 s(-1)) and substrate binding affinity in the ternary complex with enzyme bound to phosphate (Km = 280 mm), respectively. The 31P chemical shift of pyridoxal 5'-phosphate in the wild-type was pH-dependent and not perturbed by binding of arsenate. At pH 7.25, it was not sensitive to the replacement His334-->Gly. Analysis of interactions of alpha-d-glucose 1-phosphate and alpha-d-xylose 1-phosphate upon binding to wild-type and H334G phosphorylase, derived from saturation transfer difference NMR experiments, suggested that disruption of enzyme-substrate interactions in H334G was strictly local, affecting the protein environment of sugar carbon 6. pH profiles of the phosphorolysis rate for wild-type and H334G were both bell-shaped, with the broad pH range of optimum activity in the wild-type (pH 6.5-7.5) being narrowed and markedly shifted to lower pH values in the mutant (pH 6.5-7.0). External imidazole partly restored the activity lost in the mutant, without, however, participating as an alternative nucleophile in the reaction. It caused displacement of the entire pH profile of H334G by + 0.5 pH units. A possible role for His334 in the formation of the oxocarbenium ion-like transition state is suggested, where the hydrogen bond between its side chain and the 6-hydroxyl polarizes and positions O-6 such that electron density in the reactive center is enhanced.
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Affiliation(s)
- Alexandra Schwarz
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Austria
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27
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Anbarasu A, Anand S, Babu MM, Sethumadhavan R. Investigations on C–H⋯π interactions in RNA binding proteins. Int J Biol Macromol 2007; 41:251-9. [PMID: 17420044 DOI: 10.1016/j.ijbiomac.2007.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Revised: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
We have investigated the roles played by C-Hcdots, three dots, centeredpi interactions in RNA binding proteins. There was an average of 55 C-Hcdots, three dots, centeredpi interactions per protein and also there was an average of one significant C-Hcdots, three dots, centeredpi interaction for every nine residues in the 59 RNA binding proteins studied. Main-chain to side-chain C-Hcdots, three dots, centeredpi interactions is the predominant type of interactions in RNA binding proteins. The donor atom contribution to C-Hcdots, three dots, centeredpi interactions was mainly from Phe, Tyr, Trp, Pro, Gly, Lys, His and Ala residues. The acceptor atom contribution to main-chain to side-chain C-Hcdots, three dots, centeredpi and side-chain to side-chain C-Hcdots, three dots, centeredpi interactions was mainly from Phe and Tyr residues. On the contrary, the acceptor atoms of Trp residues contributed to all the four types of C-Hcdots, three dots, centeredpi interactions. Also, Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain five-member aromatic ring and side-chain to side-chain C-Hcdots, three dots, centeredpi interactions. The secondary structure preference analysis of C-Hcdots, three dots, centeredpi interacting residues showed that, Arg, Gln, Glu, His, Ile, Leu, Lys, Met, Phe and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Trp and Val preferred to be in strand conformation. Long-range C-Hcdots, three dots, centeredpi interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C-Hcdots, three dots, centeredpi interacting residues had a higher conservation score. Significant percentage of C-Hcdots, three dots, centeredpi interacting residues had one or more stabilization centers. Seven percent of the theoretically predicted stabilizing residues were also involved in C-Hcdots, three dots, centeredpi interactions and hence these residues may also contribute additional stability to RNA binding proteins.
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Affiliation(s)
- Anand Anbarasu
- School of Bio-Technology, Chemical and Bio-Medical Engineering, VIT University, Vellore 632014, India
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28
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Martinez-Fleites C, Proctor M, Roberts S, Bolam DN, Gilbert HJ, Davies GJ. Insights into the Synthesis of Lipopolysaccharide and Antibiotics through the Structures of Two Retaining Glycosyltransferases from Family GT4. ACTA ACUST UNITED AC 2006; 13:1143-52. [PMID: 17113996 DOI: 10.1016/j.chembiol.2006.09.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Revised: 08/21/2006] [Accepted: 09/11/2006] [Indexed: 11/22/2022]
Abstract
Glycosyltransferases (GTs) catalyze the synthesis of the myriad glycoconjugates that are central to life. One of the largest families is GT4, which contains several enzymes of therapeutic significance, exemplified by WaaG and AviGT4. WaaG catalyses a key step in lipopolysaccharide synthesis, while AviGT4, produced by Streptomyces viridochromogenes, contributes to the synthesis of the antibiotic avilamycin A. Here we present the crystal structure of both WaaG and AviGT4. The two enzymes contain two "Rossmann-like" (beta/alpha/beta) domains characteristic of the GT-B fold. Both recognition of the donor substrate and the catalytic machinery is similar to other retaining GTs that display the GT-B fold. Structural information is discussed with respect to the evolution of GTs and the therapeutic significance of the two enzymes.
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Affiliation(s)
- Carlos Martinez-Fleites
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom
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29
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Hidaka M, Kitaoka M, Hayashi K, Wakagi T, Shoun H, Fushinobu S. Structural dissection of the reaction mechanism of cellobiose phosphorylase. Biochem J 2006; 398:37-43. [PMID: 16646954 PMCID: PMC1525018 DOI: 10.1042/bj20060274] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cellobiose phosphorylase, a member of the glycoside hydrolase family 94, catalyses the reversible phosphorolysis of cellobiose into alpha-D-glucose 1-phosphate and D-glucose with inversion of the anomeric configuration. The substrate specificity and reaction mechanism of cellobiose phosphorylase from Cellvibrio gilvus have been investigated in detail. We have determined the crystal structure of the glucose-sulphate and glucose-phosphate complexes of this enzyme at a maximal resolution of 2.0 A (1 A=0.1 nm). The phosphate ion is strongly held through several hydrogen bonds, and the configuration appears to be suitable for direct nucleophilic attack to an anomeric centre. Structural features around the sugar-donor and sugar-acceptor sites were consistent with the results of extensive kinetic studies. When we compared this structure with that of homologous chitobiose phosphorylase, we identified key residues for substrate discrimination between glucose and N-acetylglucosamine in both the sugar-donor and sugar-acceptor sites. We found that the active site pocket of cellobiose phosphorylase was covered by an additional loop, indicating that some conformational change is required upon substrate binding. Information on the three-dimensional structure of cellobiose phosphorylase will facilitate engineering of this enzyme, the application of which to practical oligosaccharide synthesis has already been established.
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Affiliation(s)
- Masafumi Hidaka
- *Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- †National Food Research Institute, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Motomitsu Kitaoka
- †National Food Research Institute, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Kiyoshi Hayashi
- †National Food Research Institute, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Takayoshi Wakagi
- *Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirofumi Shoun
- *Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shinya Fushinobu
- *Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- To whom correspondence should be addressed (email )
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Dippel R, Bergmiller T, Böhm A, Boos W. The maltodextrin system of Escherichia coli: glycogen-derived endogenous induction and osmoregulation. J Bacteriol 2006; 187:8332-9. [PMID: 16321937 PMCID: PMC1316995 DOI: 10.1128/jb.187.24.8332-8339.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strains of Escherichia coli lacking MalQ (maltodextrin glucanotransferase or amylomaltase) are endogenously induced for the maltose regulon by maltotriose that is derived from the degradation of glycogen (glycogen-dependent endogenous induction). A high level of induction was dependent on the presence of MalP, maltodextrin phosphorylase, while expression was counteracted by MalZ, maltodextrin glucosidase. Glycogen-derived endogenous induction was sensitive to high osmolarity. This osmodependence was caused by MalZ. malZ, the gene encoding this enzyme, was found to be induced by high osmolarity even in the absence of MalT, the central regulator of all mal genes. The osmodependent expression of malZ was neither RpoS nor OmpR dependent. In contrast, the malPQ operon, whose expression was also increased at a high osmolarity, was partially dependent on RpoS. In the absence of glycogen, residual endogenous induction of the mal genes that is sensitive to increasing osmolarity can still be observed. This glycogen-independent endogenous induction is not understood, and it is not affected by altering the expression of MalP, MalQ, and MalZ. In particular, its independence from MalZ suggests that the responsible inducer is not maltotriose.
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Affiliation(s)
- Renate Dippel
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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31
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Yanase M, Takata H, Fujii K, Takaha T, Kuriki T. Cumulative effect of amino acid replacements results in enhanced thermostability of potato type L alpha-glucan phosphorylase. Appl Environ Microbiol 2005; 71:5433-9. [PMID: 16151135 PMCID: PMC1214682 DOI: 10.1128/aem.71.9.5433-5439.2005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The thermostability of potato type L alpha-glucan phosphorylase (EC 2.4.1.1) was enhanced by random and site-directed mutagenesis. We obtained three single-residue mutations-Phe39-->Leu (F39L), Asn135-->Ser (N135S), and Thr706-->Ile (T706I)-by random mutagenesis. Although the wild-type enzyme was completely inactivated, these mutant enzymes retained their activity even after heat treatment at 60 degrees C for 2 h. Combinations of these mutations were introduced by site-directed mutagenesis. The simultaneous mutation of two (F39L/N135S, F39L/T706I, and N135S/T706I) or three (F39L/N135S/T706I) residues further increased the thermostability of the enzyme, indicating that the effect of the replacement of the residues was cumulative. The triple-mutant enzyme, F39L/N135S/T706I, retained 50% of its original activity after heat treatment at 65 degrees C for 20 min. Further analysis indicated that enzymes with a F39L or T706I mutation were resistant to possible proteolytic degradation.
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Affiliation(s)
- Michiyo Yanase
- Biochemical Research Laboratory, Ezaki Glico Co. Ltd., 4-6-5 Utajima, Nishiyodogawa-ku, Osaka 555-8502, Japan.
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Abstract
Escherichia coli and Salmonella enterica serovar Typhimurium exhibit a remarkable versatility in the usage of different sugars as the sole source of carbon and energy, reflecting their ability to make use of the digested meals of mammalia and of the ample offerings in the wild. Degradation of sugars starts with their energy-dependent uptake through the cytoplasmic membrane and is carried on further by specific enzymes in the cytoplasm, destined finally for degradation in central metabolic pathways. As variant as the different sugars are, the biochemical strategies to act on them are few. They include phosphorylation, keto-enol isomerization, oxido/reductions, and aldol cleavage. The catabolic repertoire for using carbohydrate sources is largely the same in E. coli and in serovar Typhimurium. Nonetheless, significant differences are found, even among the strains and substrains of each species. We have grouped the sugars to be discussed according to their first step in metabolism, which is their active transport, and follow their path to glycolysis, catalyzed by the sugar-specific enzymes. We will first discuss the phosphotransferase system (PTS) sugars, then the sugars transported by ATP-binding cassette (ABC) transporters, followed by those that are taken up via proton motive force (PMF)-dependent transporters. We have focused on the catabolism and pathway regulation of hexose and pentose monosaccharides as well as the corresponding sugar alcohols but have also included disaccharides and simple glycosides while excluding polysaccharide catabolism, except for maltodextrins.
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Affiliation(s)
- Christoph Mayer
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, Fushinobu S. Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Structure 2004; 12:937-47. [PMID: 15274915 DOI: 10.1016/j.str.2004.03.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 03/08/2004] [Accepted: 03/09/2004] [Indexed: 10/26/2022]
Abstract
Vibrio proteolyticus chitobiose phosphorylase (ChBP) belongs to glycosyl transferase family 36 (GT-36), and catalyzes the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. As the first known structures of a GT-36 enzyme, we determined the crystal structure of ChBP in a ternary complex with GlcNAc and SO(4). It is also the first structures of an inverting phosphorolytic enzyme in a complex with a sugar and a sulfate ion, and reveals a pseudo-ternary complex structure of enzyme-sugar-phosphate. ChBP comprises a beta sandwich domain and an (alpha/alpha)(6) barrel domain, constituting a distinctive structure among GT families. Instead, it shows significant structural similarity with glycoside hydrolase (GH) enzymes, glucoamylases (GH-15), and maltose phosphorylase (GH-65) in clan GH-L. The structural similarity reported here, together with distant sequence similarities between ChBP and GHs, led to the reclassification of family GT-36 into a novel GH family, namely GH-94.
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Affiliation(s)
- Masafumi Hidaka
- Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Yep A, Ballicora MA, Preiss J. The active site of the Escherichia coli glycogen synthase is similar to the active site of retaining GT-B glycosyltransferases. Biochem Biophys Res Commun 2004; 316:960-6. [PMID: 15033495 DOI: 10.1016/j.bbrc.2004.02.136] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Indexed: 10/26/2022]
Abstract
Bacterial glycogen synthases transfer a glucosyl unit, retaining the anomeric configuration, from ADP-glucose to the non-reducing end of glycogen. We modeled the Escherichia coli glycogen synthase based on three glycosyltransferases with a GT-B fold. Comparison between the model and the structure of the active site of crystallized retaining GT-B glycosyltransferases identified conserved residues with the same topology. To confirm the importance of these residues predicted by the model, we studied them in E. coli glycogen synthase by site-directed mutagenesis. Mutations D137A, R300A, K305A, and H161A decreased the specific activity 8100-, 2600-, 1200-, and 710-fold, respectively. None of these mutations increased the Km for glycogen and only H161A and R300A had a higher Km for ADP-Glc of 11- and 8-fold, respectively. These residues were essential, validating the model that shows a strong similarity between the active site of E. coli glycogen synthase and the other retaining GT-B glycosyltransferases known to date.
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Affiliation(s)
- Alejandra Yep
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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35
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Geremia S, Campagnolo M, Schinzel R, Johnson LN. Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase. J Mol Biol 2002; 322:413-23. [PMID: 12217700 DOI: 10.1016/s0022-2836(02)00771-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The bacterial enzyme maltodextrin phosphorylase (MalP) catalyses the phosphorolysis of an alpha-1,4-glycosidic bond in maltodextrins, removing the non-reducing glucosyl residues of linear oligosaccharides as glucose-1-phosphate (Glc1P). In contrast to the well-studied muscle glycogen phosphorylase (GP), MalP exhibits no allosteric properties and has a higher affinity for linear oligosaccharides than GP. We have used MalP as a model system to study catalysis in the crystal in the direction of maltodextrin synthesis. The 2.0A crystal structure of the MalP/Glc1P binary complex shows that the Glc1P substrate adopts a conformation seen previously with both inactive and active forms of mammalian GP, with the phosphate group not in close contact with the 5'-phosphate group of the essential pyridoxal phosphate (PLP) cofactor. In the active MalP enzyme, the residue Arg569 stabilizes the negative-charged Glc1P, whereas in the inactive form of GP this key residue is held away from the catalytic site by loop 280s and an allosteric transition of the mammalian enzyme is required for activation. The comparison between MalP structures shows that His377, through a hydrogen bond with the 6-hydroxyl group of Glc1P substrate, triggers a conformational change of the 380s loop. This mobile region folds over the catalytic site and contributes to the specific recognition of the oligosaccharide and to the synergism between substrates in promoting the formation of the MalP ternary complex. The structures solved after the diffusion of oligosaccharides (either maltotetraose, G4 or maltopentaose, G5) into MalP/Glc1P crystals show the formation of phosphate and elongation of the oligosaccharide chain. These structures, refined at 1.8A and at 2.2A, confirm that only when an oligosaccharide is bound to the catalytic site will Glc1P bend its phosphate group down so it can contact the PLP 5' phosphate group and promote catalysis. The relatively large oligosaccharide substrates can diffuse quickly into the MalP/Glc1P crystals and the enzymatic reaction can occur without significant crystal damage. These structures obtained before and after catalysis have been used as frames of a molecular movie. This movie reveals the relative positions of substrates in the catalytic channel and shows a minimal movement of the protein, involving mainly Arg569, which tracks the substrate phosphate group.
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Affiliation(s)
- S Geremia
- CEB--Centre of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy.
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36
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MacGregor EA. Possible structure and active site residues of starch, glycogen, and sucrose synthases. JOURNAL OF PROTEIN CHEMISTRY 2002; 21:297-306. [PMID: 12168700 DOI: 10.1023/a:1019701621256] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A group of enzymes that include muscle glycogen phosphorylase and sugar transferases involved in, for example, the glucosylation of DNA and the synthesis of peptidoglycan are known to possess the same basic three-dimensional fold. Here the possibility is examined that other monosaccharide transferases, those that catalyze synthesis of starch, glycogen, and the disaccharide sucrose, resemble the phosphorylase-type enzymes in structure. In particular, a clear relationship is shown, for the first time, between mammalian glycogen synthases and the phosphorylase structural group of proteins. Domain architecture and secondary structure are discussed, and the possible role of several conserved amino acids at the active site is explored.
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Affiliation(s)
- E Ann MacGregor
- Department of Chemistry, University of Manitoba, Winnipeg, Canada.
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Oikonomakos NG, Kosmopoulou M, Zographos SE, Leonidas DD, Chrysina ED, Somsák L, Nagy V, Praly JP, Docsa T, Tóth B, Gergely P. Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1684-96. [PMID: 11895439 DOI: 10.1046/j.1432-1327.2002.02813.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two substituted ureas of beta-D-glucose, N-acetyl-N'-beta-D-glucopyranosyl urea (Acurea) and N-benzoyl-N'-beta-D-glucopyranosyl urea (Bzurea), have been identified as inhibitors of glycogen phosphorylase, a potential target for therapeutic intervention in type 2 diabetes. To elucidate the structural basis of inhibition, we determined the structure of muscle glycogen phosphorylase b (GPb) complexed with the two compounds at 2.0 A and 1.8 A resolution, respectively. The structure of the GPb-Acurea complex reveals that the inhibitor can be accommodated in the catalytic site of T-state GPb with very little change in the tertiary structure. The glucopyranose moiety makes the standard hydrogen bonds and van der Waals contacts as observed in the GPb-glucose complex, while the acetyl urea moiety is in a favourable electrostatic environment and makes additional polar contacts with the protein. The structure of the GPb-Bzurea complex shows that Bzurea binds tightly at the catalytic site and induces substantial conformational changes in the vicinity of the catalytic site. In particular, the loop of the polypeptide chain containing residues 282-287 shifts 1.3-3.7 A (Calpha atoms) to accommodate Bzurea. Bzurea can also occupy the new allosteric site, some 33 A from the catalytic site, which is currently the target for the design of antidiabetic drugs.
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Affiliation(s)
- Nikos G Oikonomakos
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, Athens, Greece.
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Denesyuk AI, Denessiouk KA, Korpela T, Johnson MS. Functional attributes of the phosphate group binding cup of pyridoxal phosphate-dependent enzymes. J Mol Biol 2002; 316:155-72. [PMID: 11829510 DOI: 10.1006/jmbi.2001.5310] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Twenty-four structures of pyridoxal-5'-phosphate (PLP)-dependent enzymes that represent five different folds are shown to share a common recognition pattern for the phosphate group of their PLP-ligands. All atoms that interact with the phosphate group of PLP in these proteins are organized within a two-layer structure so that the first interacting layer contains from five to seven atoms and parallel with this is a second layer containing from three to seven interacting atoms. In order to identify features of the phosphate-binding site common to PLP-dependent enzymes, a simple procedure is described that assigns relative positions to all interacting atoms unambiguously, such that the networks of interactions for different proteins can be compared. On the basis of these diagrams for 24 enzyme-cofactor complexes, a detailed comparison of the two-layer structures of PLP-dependent enzymes, with both similar and different folds, was made. A majority of the structurally defined PLP-dependent proteins use the same atom types in analogous "key" positions to bind their PLP-ligands. In some instances, proteins use water molecules when a key position is unoccupied. A similar two-layer recognition pattern extends to protein recognition of at least one other, non-PLP ligand, glucosamine 6-phosphate. We refer to this three-dimensional recognition pattern as the phosphate-binding cup. In general, the phosphate-binding cup provides a very stable anchoring point for PLP. When numerous water molecules occur within the cup, however, then the phosphate group of PLP participates directly in the enzymatic reactions with inorganic phosphate replacing the water molecules of the cup. With glucosamine-6-phosphate synthase, the water molecules of the phosphate-binding cup facilitate the entry of substrate and the exit of product.
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Affiliation(s)
- Alexander I Denesyuk
- Finnish-Russian Joint Biotechnology Laboratory, University of Turku, BioCity 6A, Turku, FIN-20520, Finland
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39
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Steegborn C, Danot O, Huber R, Clausen T. Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization. Structure 2001; 9:1051-60. [PMID: 11709169 DOI: 10.1016/s0969-2126(01)00665-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND MalT from Escherichia coli, the best-studied member of the MalT family of ATP-dependent transcriptional activators, regulates the genes for malto-oligosaccharide utilization. The active form of this 4 domain protein is a homooligomer, and its multimerization is induced by the binding of maltotriose. Domains II and III of MalT were suggested to mediate the oligomerization process, but its molecular mechanism and the specific functions of these domains remain to be identified. RESULTS We solved the crystal structure of MalT domain III at 1.45 A resolution by multiple isomorphous replacement phasing. The structure reveals eight copies of a two-helix bundle motif arranged in a novel, right-handed superhelix fold with closed walls, followed by a small C-terminal subdomain. The MalT superhelix contains a potential maltotriose binding site and forms a large hydrophobic protein-protein interaction interface that mediates the contact between two MalT domain III molecules. Structure-based analysis of the two-helix bundle motifs revealed a novel degenerated sequence pattern, and repeats of this pattern could be identified in other regulator proteins. CONCLUSIONS MalT domain III contains a novel superhelix fold. Its protein-protein interaction interface, however, resembles protein binding sites of other superhelical proteins, suggesting a model with domain III mediating MalT oligomerization. Maltotriose seems to modulate the interaction interface and MalT oligomerization by occupying the ligand binding site inside the superhelix. Similar structural and mechanistic features in other MalT protein-family members and unrelated regulator proteins are indicated by the reappearance of a novel sequence motif derived from the MalT domain III structure.
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Affiliation(s)
- C Steegborn
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, 82152, Planegg-Martinsried, Germany.
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Buchbinder JL, Rath VL, Fletterick RJ. Structural relationships among regulated and unregulated phosphorylases. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:191-209. [PMID: 11340058 DOI: 10.1146/annurev.biophys.30.1.191] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Species and tissue-specific isozymes of phosphorylase display differences in regulatory properties consistent with their distinct roles in particular organisms and tissues. In this review, we compare crystallographic structures of regulated and unregulated phosphorylases, including maltodextrin phosphorylase (MalP) from Escherichia coli, glycogen phosphorylase from yeast, and mammalian isozymes from muscle and liver tissues. Mutagenesis and functional studies supplement the structural work and provide insights into the structural basis for allosteric control mechanisms. MalP, a simple, unregulated enzyme, is contrasted with the more complicated yeast and mammalian phosphorylases that have evolved regulatory sites onto the basic catalytic architecture. The human liver and muscle isozymes show differences structurally in their means of invoking allosteric activation. Phosphorylation, though common to both the yeast and mammalian enzymes, occurs at different sites and activates the enzymes by surprisingly different mechanisms.
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Affiliation(s)
- J L Buchbinder
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143, USA.
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41
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Abstract
Oligosaccharides in which at least one glycosidic oxygen atom is replaced with a sulfur atom can be routinely synthesized and act as competitive inhibitors of various glycoside hydrolases. Recent studies using both X-ray crystallography and other biophysical techniques provide structural insight into binding, recognition, and the catalytic mechanism of action of these enzymes.
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Affiliation(s)
- H Driguez
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), Affiliated with Université Joseph Fourier, Grenoble B.P. 53, 38041 Grenoble cedex 9, France.
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42
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Griessler R, D'Auria S, Tanfani F, Nidetzky B. Thermal denaturation pathway of starch phosphorylase from Corynebacterium callunae: oxyanion binding provides the glue that efficiently stabilizes the dimer structure of the protein. Protein Sci 2000; 9:1149-61. [PMID: 10892808 PMCID: PMC2144666 DOI: 10.1110/ps.9.6.1149] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Starch phosphorylase from Corynebacterium callunae is a dimeric protein in which each mol of 90 kDa subunit contains 1 mol pyridoxal 5'-phosphate as an active-site cofactor. To determine the mechanism by which phosphate or sulfate ions bring about a greater than 500-fold stabilization against irreversible inactivation at elevated temperatures (> or = 50 degrees C), enzyme/oxyanion interactions and their role during thermal denaturation of phosphorylase have been studied. By binding to a protein site distinguishable from the catalytic site with dissociation constants of Ksulfate = 4.5 mM and Kphosphate approximately 16 mM, dianionic oxyanions induce formation of a more compact structure of phosphorylase, manifested by (a) an increase by about 5% in the relative composition of the alpha-helical secondary structure, (b) reduced 1H/2H exchange, and (c) protection of a cofactor fluorescence against quenching by iodide. Irreversible loss of enzyme activity is triggered by the release into solution of pyridoxal 5'-phosphate, and results from subsequent intermolecular aggregation driven by hydrophobic interactions between phosphorylase subunits that display a temperature-dependent degree of melting of secondary structure. By specifically increasing the stability of the dimer structure of phosphorylase (probably due to tightened intersubunit contacts), phosphate, and sulfate, this indirectly (1) preserves a functional active site up to approximately 50 degrees C, and (2) stabilizes the covalent protein cofactor linkage up to approximately 70 degrees C. The effect on thermostability shows a sigmoidal and saturatable dependence on the concentration of phosphate, with an apparent binding constant at 50 degrees C of approximately 25 mM. The extra stability conferred by oxyanion-ligand binding to starch phosphorylase is expressed as a dramatic shift of the entire denaturation pathway to a approximately 20 degrees C higher value on the temperature scale.
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Affiliation(s)
- R Griessler
- Division of Biochemical Engineering, Institute of Food Technology, Universität für Bodenkultur Wien (BOKU), Austria
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43
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Abstract
Pyridoxal-5'-phosphate (vitamin B6) binding enzymes form a large superfamily that contains at least five different folds. The availability of an increasing number of known three-dimensional structures for members of this superfamily has allowed a detailed structural classification. Most progress has been made with the fold type I or aspartate aminotransferase family.
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Affiliation(s)
- G Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, S-171 77, Sweden.
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44
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Abstract
Although glycogen and other alpha-1,4-D-glucan storage polysaccharides are present in many bacteria, only few glucan phosphorylases from bacteria have been identified and characterised on the protein or gene level. All bacterial phosphorylases follow the same catalytic mechanisms as their plant and vertebrate counterparts, but differ considerably in terms of their substrate specificity and regulation. The catalytic domains are highly conserved while the regulatory sites are only poorly conserved. The degree of conservation between bacterial and mammalian phosphorylases is comparable to that of other non-mammalian and mammalian alpha-glucan phosphorylases. Only for maltodextrin phosphorylase from E. coli the physiological role of the enzyme in the utilisation of maltodextrins is known in detail; that of all other phosphorylases remains still unclear. Roles in regulation of endogenous glycogen metabolism in periods of starvation, and sporulation, stress response or quick adaptation to changing environments are imaginable.
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Affiliation(s)
- R Schinzel
- Theodor-Boveri-Institut, Biozentrum, Universität Würzburg, Germany.
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45
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Gregoriou M, Noble ME, Watson KA, Garman EF, Krulle TM, de la Fuente C, Fleet GW, Oikonomakos NG, Johnson LN. The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding. Protein Sci 1998; 7:915-27. [PMID: 9568898 PMCID: PMC2143971 DOI: 10.1002/pro.5560070409] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that contribute to the binding, the structures of GPb in the native T state conformation and in complex with glucopyranose spirohydantoin have been determined at 100 K to 2.0 A and 1.8 A resolution, respectively, and refined to crystallographic R values of 0.197 (R[free] 0.248) and 0.182 (R[free] 0.229), respectively. The low temperature structure of GPb is almost identical to that of the previously determined room temperature structure, apart from a decrease in overall atomic temperature factors ((B) room temperature GPb = 34.9 A2; (B) 100 K GPb = 23.4 A2). The glucopyranose spirohydantoin inhibitor (Ki = 3.0 microM) binds at the catalytic site and induces small changes in two key regions of the protein: the 280s loop (residues 281-286) that results in a decrease in mobility of this region, and the 380s loop (residues 377-385) that undergoes more significant shifts in order to optimize contact to the ligand. The hydantoin group, that is responsible for increasing the affinity of the glucose compound by a factor of 10(3), makes only one hydrogen bond to the protein, from one of its NH groups to the main chain oxygen of His377. The other polar groups of the hydantoin group form hydrogen bonds to five water molecules. These waters are involved in extensive networks of hydrogen bonds and appear to be an integral part of the protein structure. Analysis of the water structure at the catalytic site of the native enzyme, shows that five waters are displaced by ligand binding and that there is a significant decrease in mobility of the remaining waters on formation of the GPb-hydantoin complex. The ability of the inhibitor to exploit existing waters, to displace waters and to recruit new waters appears to be important for the high affinity of the inhibitor.
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Affiliation(s)
- M Gregoriou
- Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, University of Oxford, United Kingdom
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46
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Boos W, Shuman H. Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation. Microbiol Mol Biol Rev 1998; 62:204-29. [PMID: 9529892 PMCID: PMC98911 DOI: 10.1128/mmbr.62.1.204-229.1998] [Citation(s) in RCA: 465] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The maltose system of Escherichia coli offers an unusually rich set of enzymes, transporters, and regulators as objects of study. This system is responsible for the uptake and metabolism of glucose polymers (maltodextrins), which must be a preferred class of nutrients for E. coli in both mammalian hosts and in the environment. Because the metabolism of glucose polymers must be coordinated with both the anabolic and catabolic uses of glucose and glycogen, an intricate set of regulatory mechanisms controls the expression of mal genes, the activity of the maltose transporter, and the activities of the maltose/maltodextrin catabolic enzymes. The ease of isolating many of the mal gene products has contributed greatly to the understanding of the structures and functions of several classes of proteins. Not only was the outer membrane maltoporin, LamB, or the phage lambda receptor, the first virus receptor to be isolated, but also its three-dimensional structure, together with extensive knowledge of functional sites for ligand binding as well as for phage lambda binding, has led to a relatively complete description of this sugar-specific aqueous channel. The periplasmic maltose binding protein (MBP) has been studied with respect to its role in both maltose transport and maltose taxis. Again, the combination of structural and functional information has led to a significant understanding of how this soluble receptor participates in signaling the presence of sugar to the chemosensory apparatus as well as how it participates in sugar transport. The maltose transporter belongs to the ATP binding cassette family, and although its structure is not yet known at atomic resolution, there is some insight into the structures of several functional sites, including those that are involved in interactions with MBP and recognition of substrates and ATP. A particularly astonishing discovery is the direct participation of the transporter in transcriptional control of the mal regulon. The MalT protein activates transcription at all mal promoters. A subset also requires the cyclic AMP receptor protein for transcription. The MalT protein requires maltotriose and ATP as ligands for binding to a dodecanucleotide MalT box that appears in multiple copies upstream of all mal promoters. Recent data indicate that the ATP binding cassette transporter subunit MalK can directly inhibit MalT when the transporter is inactive due to the absence of substrate. Despite this wealth of knowledge, there are still basic issues that require clarification concerning the mechanism of MalT-mediated activation, repression by the transporter, biosynthesis and assembly of the outer membrane and inner membrane transporter proteins, and interrelationships between the mal enzymes and those of glucose and glycogen metabolism.
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Affiliation(s)
- W Boos
- Department of Biology, University of Konstanz, Germany.
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47
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Abstract
Tumour necrosis factor (TNF) receptor family members regulate processes that range from cell proliferation to programmed cell death. The extracellular, ligand-binding domains of these proteins consist of small, cysteine-rich subdomains, first observed in the three-dimensional structures of the type I TNF receptor. A structure-based alignment of TNFR family members indicates that the extracellular domains are constructed primarily of two small polypeptide modules. These modules play distinctive structural roles in the architecture of the domains. Analogues of at least one of these modules can be found in the domains of other receptors and extracellular proteins. Variations in their sequence and order of assembly are expected to account for differences in shape, flexibility and ligand specificity.
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Affiliation(s)
- J H Naismith
- Centre for Biomolecular Sciences, University, St Andrews, Scotland, UK.
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48
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Forst D, Welte W, Wacker T, Diederichs K. Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. NATURE STRUCTURAL BIOLOGY 1998; 5:37-46. [PMID: 9437428 DOI: 10.1038/nsb0198-37] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The X-ray structure of a sucrose-specific porin (ScrY) from Salmonella typhimurium has been determined by multiple isomorphous replacement at 2.4 A resolution both in its uncomplexed form and with bound sucrose. ScrY is a noncrystallographic trimer of identical subunits, each with 413 structurally well-defined amino acids. A monomer is built up of 18 anti-parallel beta-strands surrounding a hydrophilic pore, with a topology closely similar to that of maltoporin. Two non-overlapping sucrose-binding sites were identified in difference Fourier maps. The higher permeability for sucrose of ScrY as compared to maltoporin is mainly accounted for by differences in their pore-lining residues.
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Affiliation(s)
- D Forst
- Institut für Biophysik und Strahlenbiologie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany
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49
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Eis C, Griessler R, Maier M, Weinhäusel A, Bock B, Kulbe KD, Haltrich D, Schinzel R, Nidetzky B. Efficient downstream processing of maltodextrin phosphorylase from Escherichia coli and stabilization of the enzyme by immobilization onto hydroxyapatite. J Biotechnol 1997; 58:157-66. [PMID: 9470221 DOI: 10.1016/s0168-1656(97)00145-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Downstream processing by biospecific chromatography of maltodextrin phosphorylase from Escherichia coli, overexpressed in E. coli, was substantially improved by a novel approach using ceramic hydroxyapatite. Wild-type and a less active mutant enzyme were purified from crude bacterial cell extracts in one efficient separation step that yielded phosphorylase in purity > 95% in at least 90% recoveries. At pH 6.9 and 25 degrees C, wild-type and mutant phosphorylases eluted from the hydroxyapatite column at a phosphate concentration of 0.4 M whereas calcium ions failed to displace the enzymes. The dynamic capacity for phosphorylase binding in the presence of bulk proteins was approximately 3 mg enzyme ml-1 matrix. The interaction of E. coli phosphorylase with hydroxyapatite seems to be mediated by surface amino groups, so that the bound enzyme retained almost full catalytic activity. Compared to the soluble enzyme, immobilization onto hydroxyapatite resulted in a more than 30-fold stabilization of wild-type phosphorylase against thermal and proteolytic inactivation and thus could improve the operational stability of phosphorylase during conversion of polysaccharide to glucose 1-phosphate.
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Affiliation(s)
- C Eis
- Institut für Lebensmitteltechnologie, Universität für Bodenkultur Wien (BOKU), Wein, Austria
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50
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Weinhäusel A, Griessler R, Krebs A, Zipper P, Haltrich D, Kulbe KD, Nidetzky B. alpha-1,4-D-glucan phosphorylase of gram-positive Corynebacterium callunae: isolation, biochemical properties and molecular shape of the enzyme from solution X-ray scattering. Biochem J 1997; 326 ( Pt 3):773-83. [PMID: 9307027 PMCID: PMC1218732 DOI: 10.1042/bj3260773] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The alpha-1,4-D-glucan phosphorylase from gram-positive Corynebacterium callunae has been isolated and characterized. The enzyme is inducible approx. 2-fold by maltose, but remarkably not repressed by D-glucose. The phosphorylase is a homodimer with a stoichiometric content of the cofactor pyridoxal 5'-phosphate per 88-kDa protein subunit. The specificity constants (kcat/Km, glucan) in the directions of glucan synthesis and degradation are used for the classification of the enzyme as the first bacterial starch phosphorylase. A preference for large over small substrates is determined by variations in the apparent binding constants rather than catalytic-centre activities. The contribution of substrate chain length to binding energy is explained assuming two glucan binding sites in C. callunae phosphorylase: an oligosaccharide binding site composed of five subsites and a high-affinity polysaccharide site separated from the active site. A structural model of the molecular shape of the phosphorylase was obtained from small-angle solution X-ray scattering measurements. A flat, slightly elongated, ellipsoidal model with the three axes related to each other as 1:(0.87-0.95):0.43 showed scattering equivalence with the enzyme molecule. The model of C. callunae phosphorylase differs from the structurally well-characterized rabbit-muscle phosphorylase in size and axial dimensions.
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Affiliation(s)
- A Weinhäusel
- Division of Biochemical Engineering, Institute of Food Technology, Universität für Bodenkultur (BOKU), Muthgasse 18, A-1190 Vienna, Austria
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