1
|
Chuankhayan P, Lee RH, Guan HH, Lin CC, Chen NC, Huang YC, Yoshimura M, Nakagawa A, Chen CJ. Structural insight into the hydrolase and synthase activities of an alkaline α-galactosidase from Arabidopsis from complexes with substrate/product. Acta Crystallogr D Struct Biol 2023; 79:154-167. [PMID: 36762861 PMCID: PMC9912918 DOI: 10.1107/s2059798323000037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
The alkaline α-galactosidase AtAkαGal3 from Arabidopsis thaliana catalyzes the hydrolysis of α-D-galactose from galacto-oligosaccharides under alkaline conditions. A phylogenetic analysis based on sequence alignment classifies AtAkαGal3 as more closely related to the raffinose family of oligosaccharide (RFO) synthases than to the acidic α-galactosidases. Here, thin-layer chromatography is used to demonstrate that AtAkαGal3 exhibits a dual function and is capable of synthesizing stachyose using raffinose, instead of galactinol, as the galactose donor. Crystal structures of complexes of AtAkαGal3 and its D383A mutant with various substrates and products, including galactose, galactinol, raffinose, stachyose and sucrose, are reported as the first representative structures of an alkaline α-galactosidase. The structure of AtAkαGal3 comprises three domains: an N-terminal domain with 13 antiparallel β-strands, a catalytic domain with an (α/β)8-barrel fold and a C-terminal domain composed of β-sheets that form two Greek-key motifs. The WW box of the N-terminal domain, which comprises the conserved residues FRSK75XW77W78 in the RFO synthases, contributes Trp77 and Trp78 to the +1 subsite to contribute to the substrate-binding ability together with the (α/β)8 barrel of the catalytic domain. The C-terminal domain is presumably involved in structural stability. Structures of the D383A mutant in complex with various substrates and products, especially the natural substrate/product stachyose, reveal four complete subsites (-1 to +3) at the catalytic site. A functional loop (residues 329-352) that exists in the alkaline α-galactosidase AtAkαGal3 and possibly in RFO synthases, but not in acidic α-galactosidases, stabilizes the stachyose at the +2 and +3 subsites and extends the catalytic pocket for the transferase mechanism. Considering the similarities in amino-acid sequence, catalytic domain and activity between alkaline α-galactosidases and RFO synthases, the structure of AtAkαGal3 might also serve a model for the study of RFO synthases, structures of which are lacking.
Collapse
Affiliation(s)
- Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan
| | - Ruey-Hua Lee
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan City 701, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan
| | - Chein-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan
| | - Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan
| | - Yen-Chieh Huang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan
| | - Masato Yoshimura
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Cente, Hsinchu 30076, Taiwan,Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan,Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan,Correspondence e-mail:
| |
Collapse
|
2
|
Bakunina I, Imbs T, Likhatskaya G, Grigorchuk V, Zueva A, Malyarenko O, Ermakova S. Effect of Phlorotannins from Brown Algae Costaria costata on α- N-Acetylgalactosaminidase Produced by Duodenal Adenocarcinoma and Melanoma Cells. Mar Drugs 2022; 21:33. [PMID: 36662206 PMCID: PMC9860849 DOI: 10.3390/md21010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
The inhibitor of human α-N-acetylgalactosaminidase (α-NaGalase) was isolated from a water-ethanol extract of the brown algae Costaria costata. Currently, tumor α-NaGalase is considered to be a therapeutic target in the treatment of cancer. According to NMR spectroscopy and mass spectrometric analysis, it is a high-molecular-weight fraction of phlorethols with a degree of polymerization (DP) equaling 11-23 phloroglucinols (CcPh). It was shown that CcPh is a direct inhibitor of α-NaGalases isolated from HuTu 80 and SK-MEL-28 cells (IC50 0.14 ± 0.008 and 0.12 ± 0.004 mg/mL, respectively) and reduces the activity of this enzyme in HuTu 80 and SK-MEL-28 cells up to 50% at concentrations of 15.2 ± 9.5 and 5.7 ± 1.6 μg/mL, respectively. Molecular docking of the putative DP-15 oligophlorethol (P15OPh) and heptaphlorethol (PHPh) with human α-NaGalase (PDB ID 4DO4) showed that this compound forms a complex and interacts directly with the Asp 156 and Asp 217 catalytic residues of the enzyme in question. Thus, brown algae phlorethol CcPh is an effective marine-based natural inhibitor of the α-NaGalase of cancer cells and, therefore, has high therapeutic potential.
Collapse
Affiliation(s)
- Irina Bakunina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| | - Tatiana Imbs
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| | - Galina Likhatskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| | - Valeria Grigorchuk
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| | - Anastasya Zueva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| | - Olesya Malyarenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| | - Svetlana Ermakova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 Pr-t 100-let Vladivostoka Str., 690022 Vladivostok, Russia
| |
Collapse
|
3
|
Naidoo P, Mkhize-Kwitshana ZL. Clustered Regularly Interspaced Short Palindromic Repeats/ CRISPR associated protein 9-mediated editing of Schistosoma mansoni genes: Identifying genes for immunologically potent drug and vaccine development. Rev Soc Bras Med Trop 2022; 55:e0131. [PMID: 35976333 PMCID: PMC9405935 DOI: 10.1590/0037-8682-0131-2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/08/2022] [Indexed: 12/26/2022] Open
Abstract
Schistosomiasis is a neglected acute and chronic tropical disease caused by intestinal (Schistosoma mansoni and Schistosoma japonicum) and urogenital (Schistosoma haematobium) helminth parasites (blood flukes or digenetic trematodes). It afflicts over 250 million people worldwide, the majority of whom reside in impoverished tropical and subtropical regions in sub-Saharan Africa. Schistosomiasis is the second most common devastating parasitic disease in the world after malaria and causes over 200,000 deaths annually. Currently, there is no effective and approved vaccine available for human use, and treatment strongly relies on praziquantel drug therapy, which is ineffective in killing immature larval schistosomula stages and eggs already lodged in the tissues. The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9 (CRISPR/Cas9)-mediated gene editing tool is used to deactivate a gene of interest to scrutinize its role in health and disease, and to identify genes for vaccine and drug targeting. The present review aims to summarize the major findings from the current literature reporting the usage of CRISPR/Cas9-mediated gene editing to inactivate genes in S. mansoni (acetylcholinesterase (AChE), T2 ribonuclease omega-1 (ω1), sulfotransferase oxamniquine resistance protein (SULT-OR), and α-N-acetylgalactosaminidase (SmNAGAL)), and freshwater gastropod snails, Biomphalaria glabrata (allograft inflammatory factor (BgAIF)), an obligatory component of the life cycle of S. mansoni, to identify their roles in the pathogenesis of schistosomiasis, and to highlight the importance of such studies in identifying and developing drugs and vaccines with high therapeutic efficacy.
Collapse
Affiliation(s)
- Pragalathan Naidoo
- University of KwaZulu-Natal, College of Health Sciences, Department of Medical Microbiology, Durban, KwaZulu-Natal, South Africa.,South African Medical Research Council (SAMRC), Division of Research Capacity Development, Cape Town, Western Cape, South Africa
| | - Zilungile Lynette Mkhize-Kwitshana
- University of KwaZulu-Natal, College of Health Sciences, Department of Medical Microbiology, Durban, KwaZulu-Natal, South Africa.,South African Medical Research Council (SAMRC), Division of Research Capacity Development, Cape Town, Western Cape, South Africa
| |
Collapse
|
4
|
Schistosoma mansoni α-N-acetylgalactosaminidase (SmNAGAL) regulates coordinated parasite movement and egg production. PLoS Pathog 2022; 18:e1009828. [PMID: 35025955 PMCID: PMC8791529 DOI: 10.1371/journal.ppat.1009828] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/26/2022] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
α-galactosidase (α-GAL) and α-N-acetylgalactosaminidase (α-NAGAL) are two glycosyl hydrolases responsible for maintaining cellular homeostasis by regulating glycan substrates on proteins and lipids. Mutations in the human genes encoding either enzyme lead to neurological and neuromuscular impairments seen in both Fabry- and Schindler/Kanzaki- diseases. Here, we investigate whether the parasitic blood fluke Schistosoma mansoni, responsible for the neglected tropical disease schistosomiasis, also contains functionally important α-GAL and α-NAGAL proteins. As infection, parasite maturation and host interactions are all governed by carefully-regulated glycosylation processes, inhibiting S. mansoni's α-GAL and α-NAGAL activities could lead to the development of novel chemotherapeutics. Sequence and phylogenetic analyses of putative α-GAL/α-NAGAL protein types showed Smp_089290 to be the only S. mansoni protein to contain the functional amino acid residues necessary for α-GAL/α-NAGAL substrate cleavage. Both α-GAL and α-NAGAL enzymatic activities were higher in females compared to males (p<0.05; α-NAGAL > α-GAL), which was consistent with smp_089290's female biased expression. Spatial localisation of smp_089290 revealed accumulation in parenchymal cells, neuronal cells, and the vitellaria and mature vitellocytes of the adult schistosome. siRNA-mediated knockdown (>90%) of smp_089290 in adult worms significantly inhibited α-NAGAL activity when compared to control worms (siLuc treated males, p<0.01; siLuc treated females, p<0.05). No significant reductions in α-GAL activities were observed in the same extracts. Despite this, decreases in α-NAGAL activities correlated with a significant inhibition in adult worm motility as well as in egg production. Programmed CRISPR/Cas9 editing of smp_089290 in adult worms confirmed the egg reduction phenotype. Based on these results, Smp_089290 was determined to act predominantly as an α-NAGAL (hereafter termed SmNAGAL) in schistosome parasites where it participates in coordinating movement and oviposition processes. Further characterisation of SmNAGAL and other functionally important glycosyl hydrolases may lead to the development of a novel anthelmintic class of compounds.
Collapse
|
5
|
Miyazaki T, Park EY. Crystal structure of the Enterococcus faecalis α-N-acetylgalactosaminidase, a member of the glycoside hydrolase family 31. FEBS Lett 2020; 594:2282-2293. [PMID: 32367553 DOI: 10.1002/1873-3468.13804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Glycoside hydrolases catalyze the hydrolysis of glycosidic linkages in carbohydrates. The glycoside hydrolase family 31 (GH31) contains α-glucosidase, α-xylosidase, α-galactosidase, and α-transglycosylase. Recent work has expanded the diversity of substrate specificity of GH31 enzymes, and α-N-acetylgalactosaminidases (αGalNAcases) belonging to GH31 have been identified in human gut bacteria. Here, we determined the first crystal structure of a truncated form of GH31 αGalNAcase from the human gut bacterium Enterococcus faecalis. The enzyme has a similar fold to other reported GH31 enzymes and an additional fibronectin type 3-like domain. Additionally, the structure in complex with N-acetylgalactosamine reveals that conformations of the active site residues, including its catalytic nucleophile, change to recognize the ligand. Our structural analysis provides insight into the substrate recognition and catalytic mechanism of GH31 αGalNAcases.
Collapse
Affiliation(s)
- Takatsugu Miyazaki
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Japan
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Japan
| |
Collapse
|
6
|
Kytidou K, Beekwilder J, Artola M, van Meel E, Wilbers RHP, Moolenaar GF, Goosen N, Ferraz MJ, Katzy R, Voskamp P, Florea BI, Hokke CH, Overkleeft HS, Schots A, Bosch D, Pannu N, Aerts JMFG. Nicotiana benthamiana α-galactosidase A1.1 can functionally complement human α-galactosidase A deficiency associated with Fabry disease. J Biol Chem 2018; 293:10042-10058. [PMID: 29674318 PMCID: PMC6028973 DOI: 10.1074/jbc.ra118.001774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
α-Galactosidases (EC 3.2.1.22) are retaining glycosidases that cleave terminal α-linked galactose residues from glycoconjugate substrates. α-Galactosidases take part in the turnover of cell wall-associated galactomannans in plants and in the lysosomal degradation of glycosphingolipids in animals. Deficiency of human α-galactosidase A (α-Gal A) causes Fabry disease (FD), a heritable, X-linked lysosomal storage disorder, characterized by accumulation of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3). Current management of FD involves enzyme-replacement therapy (ERT). An activity-based probe (ABP) covalently labeling the catalytic nucleophile of α-Gal A has been previously designed to study α-galactosidases for use in FD therapy. Here, we report that this ABP labels proteins in Nicotiana benthamiana leaf extracts, enabling the identification and biochemical characterization of an N. benthamiana α-galactosidase we name here A1.1 (gene accession ID GJZM-1660). The transiently overexpressed and purified enzyme was a monomer lacking N-glycans and was active toward 4-methylumbelliferyl-α-d-galactopyranoside substrate (Km = 0.17 mm) over a broad pH range. A1.1 structural analysis by X-ray crystallography revealed marked similarities with human α-Gal A, even including A1.1's ability to hydrolyze Gb3 and lyso-Gb3, which are not endogenous in plants. Of note, A1.1 uptake into FD fibroblasts reduced the elevated lyso-Gb3 levels in these cells, consistent with A1.1 delivery to lysosomes as revealed by confocal microscopy. The ease of production and the features of A1.1, such as stability over a broad pH range, combined with its capacity to degrade glycosphingolipid substrates, warrant further examination of its value as a potential therapeutic agent for ERT-based FD management.
Collapse
Affiliation(s)
| | - Jules Beekwilder
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | | | | | - Ruud H P Wilbers
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Geri F Moolenaar
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | - Nora Goosen
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | | | | | | | | | - Cornelis H Hokke
- the Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - Arjen Schots
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Dirk Bosch
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | | | | |
Collapse
|
7
|
Morales-Quintana L, Faúndez C, Herrera R, Zavaleta V, Ravanal MC, Eyzaguirre J, Moya-León MA. Biochemical and structural characterization of Penicillium purpurogenum α-D galactosidase: Binding of galactose to an alternative pocket may explain enzyme inhibition. Carbohydr Res 2017. [DOI: 10.1016/j.carres.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
8
|
Rashid MHO, Sadik G, Alam AK, Tanaka T. Chemical and structural characterization of α-N-acetylgalactosaminidase I and II from starfish, asterina amurensis. BMC BIOCHEMISTRY 2017; 18:9. [PMID: 28545388 PMCID: PMC5445309 DOI: 10.1186/s12858-017-0085-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND The marine invertebrate starfish was found to contain a novel α-N-acetylgalactosaminidase, α-GalNAcase II, which catalyzes removal of terminal α-N-acetylgalactosamine (α-GalNAc), in addition to a typical α-N-acetylgalactosaminidase, α-GalNAcase I, which catalyzes removal of terminal α-N-acetylgalactosamine (α-GalNAc) and, to a lesser extent, galactose. The interrelationship between α-GalNAcase I and α-GalNAcase II and the molecular basis of their differences in substrate specificity remain unknown. RESULTS Chemical and structural comparisons between α-GalNAcase I and II using immunostaining, N-terminal amino acid sequencing and peptide analysis showed high homology to each other and also to other glycoside hydrolase family (GHF) 27 members. The amino acid sequence of peptides showed conserved residues at the active site as seen in typical α-GalNAcase. Some substitutions of conserved amino acid residues were found in α-GalNAcase II that were located near catalytic site. Among them G171 and A173, in place of C171 and W173, respectively in α-GalNAcase were identified to be responsible for lacking intrinsic α-galactosidase activity of α-GalNAcase II. Chemical modifications supported the presence of serine, aspartate and tryptophan as active site residues. Two tryptophan residues (W16 and W173) were involved in α-galactosidase activity, and one (W16) of them was involved in α-GalNAcase activity. CONCLUSIONS The results suggested that α-GalNAcase I and II are closely related with respect to primary and higher order structure and that their structural differences are responsible for difference in substrate specificities.
Collapse
Affiliation(s)
- Md Harun-Or Rashid
- Institute of Biological Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Golam Sadik
- Department of Pharmacy, University of Rajshahi, Rajshahi, 6205, Bangladesh.
| | - Ahm Khurshid Alam
- Department of Pharmacy, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Toshihisa Tanaka
- Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| |
Collapse
|
9
|
Stütz AE, Wrodnigg TM. Carbohydrate-Processing Enzymes of the Lysosome: Diseases Caused by Misfolded Mutants and Sugar Mimetics as Correcting Pharmacological Chaperones. Adv Carbohydr Chem Biochem 2016; 73:225-302. [PMID: 27816107 DOI: 10.1016/bs.accb.2016.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lysosomal storage diseases are hereditary disorders caused by mutations on genes encoding for one of the more than fifty lysosomal enzymes involved in the highly ordered degradation cascades of glycans, glycoconjugates, and other complex biomolecules in the lysosome. Several of these metabolic disorders are associated with the absence or the lack of activity of carbohydrate-processing enzymes in this cell compartment. In a recently introduced therapy concept, for susceptible mutants, small substrate-related molecules (so-called pharmacological chaperones), such as reversible inhibitors of these enzymes, may serve as templates for the correct folding and transport of the respective protein mutant, thus improving its concentration and, consequently, its enzymatic activity in the lysosome. Carbohydrate-processing enzymes in the lysosome, related lysosomal diseases, and the scope and limitations of reported reversible inhibitors as pharmacological chaperones are discussed with a view to possibly extending and improving research efforts in this area of orphan diseases.
Collapse
Affiliation(s)
- Arnold E Stütz
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Tanja M Wrodnigg
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| |
Collapse
|
10
|
McKee LS, Brumer H. Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 β-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation. PLoS One 2015; 10:e0139932. [PMID: 26448175 PMCID: PMC4598101 DOI: 10.1371/journal.pone.0139932] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/18/2015] [Indexed: 12/16/2022] Open
Abstract
The genome of the soil bacterium Chitinophaga pinensis encodes a diverse array of carbohydrate active enzymes, including nearly 200 representatives from over 50 glycoside hydrolase (GH) families, the enzymology of which is essentially unexplored. In light of this genetic potential, we reveal that C. pinensis has a broader saprophytic capacity to thrive on plant cell wall polysaccharides than previously reported, and specifically that secretion of β-l-arabinopyranosidase activity is induced during growth on arabinogalactan. We subsequently correlated this activity with the product of the Cpin_5740 gene, which encodes the sole member of glycoside hydrolase family 27 (GH27) in C. pinensis, CpArap27. Historically, GH27 is most commonly associated with α-d-galactopyranosidase and α-d-N-acetylgalactosaminidase activity. A new phylogenetic analysis of GH27 highlighted the likely importance of several conserved secondary structural features in determining substrate specificity and provides a predictive framework for identifying enzymes with the less common β-l-arabinopyranosidase activity.
Collapse
Affiliation(s)
- Lauren S. McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56–56, 100 44, Stockholm, Sweden
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56–56, 100 44, Stockholm, Sweden
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, V6T 1Z4, BC, Canada
- * E-mail:
| |
Collapse
|
11
|
Bakunina IY, Balabanova LA, Pennacchio A, Trincone A. Hooked on α-d-galactosidases: from biomedicine to enzymatic synthesis. Crit Rev Biotechnol 2015; 36:233-45. [PMID: 25394540 DOI: 10.3109/07388551.2014.949618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
α-d-Galactosidases (EC 3.2.1.22) are enzymes employed in a number of useful bio-based applications. We have depicted a comprehensive general survey of α-d-galactosidases from different origin with special emphasis on marine example(s). The structures of natural α-galactosyl containing compounds are described. In addition to 3D structures and mechanisms of action of α-d-galactosidases, different sources, natural function and genetic regulation are also covered. Finally, hydrolytic and synthetic exploitations as free or immobilized biocatalysts are reviewed. Interest in the synthetic aspects during the next years is anticipated for access to important small molecules by green technology with an emphasis on alternative selectivity of this class of enzymes from different sources.
Collapse
Affiliation(s)
- Irina Yu Bakunina
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Larissa A Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Angela Pennacchio
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
| | - Antonio Trincone
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
| |
Collapse
|
12
|
Qiu H, Honey DM, Kingsbury JS, Park A, Boudanova E, Wei RR, Pan CQ, Edmunds T. Impact of cysteine variants on the structure, activity, and stability of recombinant human α-galactosidase A. Protein Sci 2015; 24:1401-11. [PMID: 26044846 DOI: 10.1002/pro.2719] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 11/07/2022]
Abstract
Recombinant human α-galactosidase A (rhαGal) is a homodimeric glycoprotein deficient in Fabry disease, a lysosomal storage disorder. In this study, each cysteine residue in rhαGal was replaced with serine to understand the role each cysteine plays in the enzyme structure, function, and stability. Conditioned media from transfected HEK293 cells were assayed for rhαGal expression and enzymatic activity. Activity was only detected in the wild type control and in mutants substituting the free cysteine residues (C90S, C174S, and the C90S/C174S). Cysteine-to-serine substitutions at the other sites lead to the loss of expression and/or activity, consistent with their involvement in the disulfide bonds found in the crystal structure. Purification and further characterization confirmed that the C90S, C174S, and the C90S/C174S mutants are enzymatically active, structurally intact and thermodynamically stable as measured by circular dichroism and thermal denaturation. The purified inactive C142S mutant appeared to have lost part of its alpha-helix secondary structure and had a lower apparent melting temperature. Saturation mutagenesis study on Cys90 and Cys174 resulted in partial loss of activity for Cys174 mutants but multiple mutants at Cys90 with up to 87% higher enzymatic activity (C90T) compared to wild type, suggesting that the two free cysteines play differential roles and that the activity of the enzyme can be modulated by side chain interactions of the free Cys residues. These results enhanced our understanding of rhαGal structure and function, particularly the critical roles that cysteines play in structure, stability, and enzymatic activity.
Collapse
Affiliation(s)
- Huawei Qiu
- Sanofi Biotherapeutics, Framingham, Massachusetts, 01701
| | - Denise M Honey
- Sanofi Biotherapeutics, Framingham, Massachusetts, 01701
| | | | - Anna Park
- Sanofi Biotherapeutics, Framingham, Massachusetts, 01701
| | | | - Ronnie R Wei
- Sanofi Biotherapeutics, Framingham, Massachusetts, 01701
| | - Clark Q Pan
- Sanofi Biotherapeutics, Framingham, Massachusetts, 01701
| | - Tim Edmunds
- Sanofi Biotherapeutics, Framingham, Massachusetts, 01701
| |
Collapse
|
13
|
Lansky S, Salama R, Solomon HV, Feinberg H, Belrhali H, Shoham Y, Shoham G. Structure-specificity relationships in Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus T6. ACTA ACUST UNITED AC 2014; 70:2994-3012. [PMID: 25372689 DOI: 10.1107/s139900471401863x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/15/2014] [Indexed: 11/10/2022]
Abstract
L-Arabinose sugar residues are relatively abundant in plants and are found mainly in arabinan polysaccharides and in other arabinose-containing polysaccharides such as arabinoxylans and pectic arabinogalactans. The majority of the arabinose units in plants are present in the furanose form and only a small fraction of them are present in the pyranose form. The L-arabinan-utilization system in Geobacillus stearothermophilus T6, a Gram-positive thermophilic soil bacterium, has recently been characterized, and one of the key enzymes was found to be an intracellular β-L-arabinopyranosidase (Abp). Abp, a GH27 enzyme, was shown to remove β-L-arabinopyranose residues from synthetic substrates and from the native substrates sugar beet arabinan and larch arabinogalactan. The Abp monomer is made up of 448 amino acids, and based on sequence homology it was suggested that Asp197 is the catalytic nucleophile and Asp255 is the catalytic acid/base. In the current study, the detailed three-dimensional structure of wild-type Abp (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (at 2.20 Å resolution) and without (at 2.30 Å resolution) a bound L-arabinose product are reported as determined by X-ray crystallography. These structures demonstrate that the three-dimensional structure of the Abp monomer correlates with the general fold observed for GH27 proteins, consisting of two main domains: an N-terminal TIM-barrel domain and a C-terminal all-β domain. The two catalytic residues are located in the TIM-barrel domain, such that their carboxylic functional groups are about 5.9 Å from each other, consistent with a retaining mechanism. An isoleucine residue (Ile67) located at a key position in the active site is shown to play a critical role in the substrate specificity of Abp, providing a structural basis for the high preference of the enzyme towards arabinopyranoside over galactopyranoside substrates. The crystal structure demonstrates that Abp is a tetramer made up of two `open-pincers' dimers, which clamp around each other to form a central cavity. The four active sites of the Abp tetramer are situated on the inner surface of this cavity, all opening into the central space of the cavity. The biological relevance of this tetrameric structure is supported by independent results obtained from size-exclusion chromatography (SEC), dynamic light-scattering (DLS) and small-angle X-ray scattering (SAXS) experiments. These data and their comparison to the structural data of related GH27 enzymes are used for a more general discussion concerning structure-selectivity aspects in this glycoside hydrolase (GH) family.
Collapse
Affiliation(s)
- Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Hodaya V Solomon
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Hadar Feinberg
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation and the Unit for Virus Host-Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
14
|
Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold. Biosci Biotechnol Biochem 2014; 77:1363-71. [DOI: 10.1271/bbb.130183] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
15
|
Chakladar S, Shamsi Kazem Abadi S, Bennet AJ. A mechanistic study on the α-N-acetylgalactosaminidase from E. meningosepticum: a family 109 glycoside hydrolase. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00104d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies on the mechanism of action used by a GH109 enzyme.
Collapse
|
16
|
Sui XL, Meng FZ, Wang HY, Wei YX, Li RF, Wang ZY, Hu LP, Wang SH, Zhang ZX. Molecular cloning, characteristics and low temperature response of raffinose synthase gene in Cucumis sativus L. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1883-91. [PMID: 22985990 DOI: 10.1016/j.jplph.2012.07.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 07/30/2012] [Accepted: 07/30/2012] [Indexed: 05/07/2023]
Abstract
Raffinose synthase (RS, EC2.4.1.82) is one of the key enzymes that channels sucrose into the raffinose family oligosaccharides (RFOs) biosynthetic pathway. However, the gene encoding RS is poorly characterized in cucumber (Cucumis sativus L.), which is a typical RFOs-translocating plant species. Here we isolated the gene encoding RS (CsRS) from the leaves of cucumber plants. The complete cDNA of CsRS consisted of 2552 nucleotides with an open reading frame encoding a polypeptide of 784 amino acid residues. Reverse transcription-polymerase chain reaction and RNA hybridization analysis revealed that expression of CsRS was the highest in leaves followed by roots, fruits, and stems. The RS activity was up-regulated and the raffinose content was high in the leaves of transgenic tobacco with over-expression of CsRS, while both the RS activity and the raffinose content decreased in the transgenic cucumber plants with anti-sense expression of CsRS. The expression of CsRS could be induced by low temperature and exogenous phytohormone abscisic acid (ABA). In cucumber growing under low temperature stress, CsRS expression, RS activity and raffinose content increased gradually in the leaves, the fruits, the stems and the roots. The most notable increase was observed in the leaves. Similarly, the expression of CsRS was induced in cucumber leaves and fruits with 200 μM and 150 μM ABA treatments, respectively.
Collapse
Affiliation(s)
- Xiao-lei Sui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Schindler/Kanzaki disease is an inherited metabolic disease with no current treatment options. This neurologic disease results from a defect in the lysosomal α-N-acetylgalactosaminidase (α-NAGAL) enzyme. In this report, we show evidence that the iminosugar DGJNAc can inhibit, stabilize, and chaperone human α-NAGAL both in vitro and in vivo. We demonstrate that a related iminosugar DGJ (currently in phase III clinical trials for another metabolic disorder, Fabry disease) can also chaperone human α-NAGAL in Schindler/Kanzaki disease. The 1.4- and 1.5-Å crystal structures of human α-NAGAL complexes reveal the different binding modes of iminosugars compared with glycosides. We show how differences in two functional groups result in >9 kcal/mol of additional binding energy and explain the molecular interactions responsible for the unexpectedly high affinity of the pharmacological chaperones. These results open two avenues for treatment of Schindler/Kanzaki disease and elucidate the atomic basis for pharmacological chaperoning in the entire family of lysosomal storage diseases.
Collapse
|
18
|
Merceron R, Foucault M, Haser R, Mattes R, Watzlawick H, Gouet P. The molecular mechanism of thermostable α-galactosidases AgaA and AgaB explained by x-ray crystallography and mutational studies. J Biol Chem 2012; 287:39642-52. [PMID: 23012371 DOI: 10.1074/jbc.m112.394114] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The α-galactosidase AgaA from the thermophilic microorganism Geobacillus stearothermophilus has great industrial potential because it is fully active at 338 K against raffinose and can increase the yield of manufactured sucrose. AgaB has lower affinity for its natural substrates but is a powerful tool for the enzymatic synthesis of disaccharides by transglycosylation. These two enzymes have 97% identity and belong to the glycoside hydrolase (GH) family GH36 for which few structures are available. To understand the structural basis underlying the differences between these two enzymes, we determined the crystal structures of AgaA and AgaB by molecular replacement at 3.2- and 1.8 Å-resolution, respectively. We also solved a 2.8-Å structure of the AgaA(A355E) mutant, which has enzymatic properties similar to those of AgaB. We observe that residue 355 is located 20 Å away from the active site and that the A355E substitution causes structural rearrangements resulting in a significant displacement of the invariant Trp(336) at catalytic subsite -1. Hence, the active cleft of AgaA is narrowed in comparison with AgaB, and AgaA is more efficient than AgaB against its natural substrates. The structure of AgaA(A355E) complexed with 1-deoxygalactonojirimycin reveals an induced fit movement; there is a rupture of the electrostatic interaction between Glu(355) and Asn(335) and a return of Trp(336) to an optimal position for ligand stacking. The structures of two catalytic mutants of AgaA(A355E) complexed with raffinose and stachyose show that the binding interactions are stronger at subsite -1 to enable the binding of various α-galactosides.
Collapse
Affiliation(s)
- Romain Merceron
- Biocrystallography and Structural Biology of Therapeutic Targets, Bases Moléculaires et Structurales des Systèmes Infectieux-Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | | | | | | | | | | |
Collapse
|
19
|
Bruel L, Sulzenbacher G, Cervera Tison M, Pujol A, Nicoletti C, Perrier J, Galinier A, Ropartz D, Fons M, Pompeo F, Giardina T. α-Galactosidase/sucrose kinase (AgaSK), a novel bifunctional enzyme from the human microbiome coupling galactosidase and kinase activities. J Biol Chem 2011; 286:40814-23. [PMID: 21931163 PMCID: PMC3220449 DOI: 10.1074/jbc.m111.286039] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/03/2011] [Indexed: 11/06/2022] Open
Abstract
α-Galactosides are non-digestible carbohydrates widely distributed in plants. They are a potential source of energy in our daily food, and their assimilation by microbiota may play a role in obesity. In the intestinal tract, they are degraded by microbial glycosidases, which are often modular enzymes with catalytic domains linked to carbohydrate-binding modules. Here we introduce a bifunctional enzyme from the human intestinal bacterium Ruminococcus gnavus E1, α-galactosidase/sucrose kinase (AgaSK). Sequence analysis showed that AgaSK is composed of two domains: one closely related to α-galactosidases from glycoside hydrolase family GH36 and the other containing a nucleotide-binding motif. Its biochemical characterization showed that AgaSK is able to hydrolyze melibiose and raffinose to galactose and either glucose or sucrose, respectively, and to specifically phosphorylate sucrose on the C6 position of glucose in the presence of ATP. The production of sucrose-6-P directly from raffinose points toward a glycolytic pathway in bacteria, not described so far. The crystal structures of the galactosidase domain in the apo form and in complex with the product shed light onto the reaction and substrate recognition mechanisms and highlight an oligomeric state necessary for efficient substrate binding and suggesting a cross-talk between the galactose and kinase domains.
Collapse
Affiliation(s)
- Laëtitia Bruel
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
- the IMM/Laboratoire de Chimie Bactérienne, UPR CNRS 9043, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, and
| | - Gerlind Sulzenbacher
- the Architecture et Fonction des Macromolécules Biologiques UMR CNRS 6098, Université Aix-Marseille, Campus Luminy, Case 932, F-13288 Marseille Cedex 09
| | - Marine Cervera Tison
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
| | - Ange Pujol
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
| | - Cendrine Nicoletti
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
| | - Josette Perrier
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
| | - Anne Galinier
- the IMM/Laboratoire de Chimie Bactérienne, UPR CNRS 9043, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, and
| | - David Ropartz
- the Laboratoire de Spectrométrie de Masse, Plate-forme Biopolymères-Biologie Structurale, INRA UR1268 Biopolymères Interactions Assemblages, Rue de la Géraudière, B.P. 71627, F-44316 Nantes cedex 3, France
| | - Michel Fons
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
| | - Frédérique Pompeo
- the IMM/Laboratoire de Chimie Bactérienne, UPR CNRS 9043, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, and
| | - Thierry Giardina
- From the Faculté des Sciences et Techniques Saint-Jérôme, Université Paul Cézanne, ISM2/BiosCiences UMR CNRS 6263, service 342, 13397 Marseille Cedex 20
| |
Collapse
|
20
|
Naumoff DG, Stepuschenko OO. Endo-α-1,4-polygalactosaminidases and their homologs: Structure and evolution. Mol Biol 2011. [DOI: 10.1134/s0026893311030113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
21
|
Fernández-Leiro R, Pereira-Rodríguez Á, Cerdán ME, Becerra M, Sanz-Aparicio J. Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases. J Biol Chem 2010; 285:28020-33. [PMID: 20592022 PMCID: PMC2934667 DOI: 10.1074/jbc.m110.144584] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 06/17/2010] [Indexed: 11/06/2022] Open
Abstract
Alpha-galactosidases catalyze the hydrolysis of terminal alpha-1,6-galactosyl units from galacto-oligosaccharides and polymeric galactomannans. The crystal structures of tetrameric Saccharomyces cerevisiae alpha-galactosidase and its complexes with the substrates melibiose and raffinose have been determined to 1.95, 2.40, and 2.70 A resolution. The monomer folds into a catalytic (alpha/beta)(8) barrel and a C-terminal beta-sandwich domain with unassigned function. This pattern is conserved with other family 27 glycosidases, but this enzyme presents a unique 45-residue insertion in the beta-sandwich domain that folds over the barrel protecting it from the solvent and likely explaining its high stability. The structure of the complexes and the mutational analysis show that oligomerization is a key factor in substrate binding, as the substrates are located in a deep cavity making direct interactions with the adjacent subunit. Furthermore, docking analysis suggests that the supplementary domain could be involved in binding sugar units distal from the scissile bond, therefore ascribing a role in fine-tuning substrate specificity to this domain. It may also have a role in promoting association with the polymeric substrate because of the ordered arrangement that the four domains present in one face of the tetramer. Our analysis extends to other family 27 glycosidases, where some traits regarding specificity and oligomerization can be formulated on the basis of their sequence and the structures available. These results improve our knowledge on the activity of this important family of enzymes and give a deeper insight into the structural features that rule modularity and protein-carbohydrate interactions.
Collapse
Affiliation(s)
- Rafael Fernández-Leiro
- From the Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071-A Coruña and
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Ángel Pereira-Rodríguez
- From the Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071-A Coruña and
| | - M. Esperanza Cerdán
- From the Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071-A Coruña and
| | - Manuel Becerra
- From the Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071-A Coruña and
| | - Juliana Sanz-Aparicio
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| |
Collapse
|
22
|
Nakai H, Baumann MJ, Petersen BO, Westphal Y, Hachem MA, Dilokpimol A, Duus JØ, Schols HA, Svensson B. Aspergillus nidulans alpha-galactosidase of glycoside hydrolase family 36 catalyses the formation of alpha-galacto-oligosaccharides by transglycosylation. FEBS J 2010; 277:3538-51. [PMID: 20681989 DOI: 10.1111/j.1742-4658.2010.07763.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The alpha-galactosidase from Aspergillus nidulans (AglC) belongs to a phylogenetic cluster containing eukaryotic alpha-galactosidases and alpha-galacto-oligosaccharide synthases of glycoside hydrolase family 36 (GH36). The recombinant AglC, produced in high yield (0.65 g.L(-1) culture) as His-tag fusion in Escherichia coli, catalysed efficient transglycosylation with alpha-(1-->6) regioselectivity from 40 mm 4-nitrophenol alpha-d-galactopyranoside, melibiose or raffinose, resulting in a 37-74% yield of 4-nitrophenol alpha-D-Galp-(1-->6)-D-Galp, alpha-D-Galp-(1-->6)-alpha-D-Galp-(1-->6)-D-Glcp and alpha-D-Galp-(1-->6)-alpha-D-Galp-(1-->6)-D-Glcp-(alpha1-->beta2)-d-Fruf (stachyose), respectively. Furthermore, among 10 monosaccharide acceptor candidates (400 mm) and the donor 4-nitrophenol alpha-D-galactopyranoside (40 mm), alpha-(1-->6) linked galactodisaccharides were also obtained with galactose, glucose and mannose in high yields of 39-58%. AglC did not transglycosylate monosaccharides without the 6-hydroxymethyl group, i.e. xylose, L-arabinose, L-fucose and L-rhamnose, or with axial 3-OH, i.e. gulose, allose, altrose and L-rhamnose. Structural modelling using Thermotoga maritima GH36 alpha-galactosidase as the template and superimposition of melibiose from the complex with human GH27 alpha-galactosidase supported that recognition at subsite +1 in AglC presumably requires a hydrogen bond between 3-OH and Trp358 and a hydrophobic environment around the C-6 hydroxymethyl group. In addition, successful transglycosylation of eight of 10 disaccharides (400 mm), except xylobiose and arabinobiose, indicated broad specificity for interaction with the +2 subsite. AglC thus transferred alpha-galactosyl to 6-OH of the terminal residue in the alpha-linked melibiose, maltose, trehalose, sucrose and turanose in 6-46% yield and the beta-linked lactose, lactulose and cellobiose in 28-38% yield. The product structures were identified using NMR and ESI-MS and five of the 13 identified products were novel, i.e. alpha-D-Galp-(1-->6)-D-Manp; alpha-D-Galp-(1-->6)-beta-D-Glcp-(1-->4)-D-Glcp; alpha-D-Galp-(1-->6)-beta-D-Galp-(1-->4)-D-Fruf; alpha-D-Galp-(1-->6)-D-Glcp-(alpha1-->alpha1)-D-Glcp; and alpha-D-Galp-(1-->6)-alpha-D-Glcp-(1-->3)-D-Fruf.
Collapse
Affiliation(s)
- Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Tomasic IB, Metcalf MC, Guce AI, Clark NE, Garman SC. Interconversion of the specificities of human lysosomal enzymes associated with Fabry and Schindler diseases. J Biol Chem 2010; 285:21560-6. [PMID: 20444686 PMCID: PMC2898384 DOI: 10.1074/jbc.m110.118588] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/23/2010] [Indexed: 11/06/2022] Open
Abstract
The human lysosomal enzymes alpha-galactosidase (alpha-GAL, EC 3.2.1.22) and alpha-N-acetylgalactosaminidase (alpha-NAGAL, EC 3.2.1.49) share 46% amino acid sequence identity and have similar folds. The active sites of the two enzymes share 11 of 13 amino acids, differing only where they interact with the 2-position of the substrates. Using a rational protein engineering approach, we interconverted the enzymatic specificity of alpha- GAL and alpha-NAGAL. The engineered alpha-GAL (which we call alpha-GAL(SA)) retains the antigenicity of alpha-GAL but has acquired the enzymatic specificity of alpha-NAGAL. Conversely, the engineered alpha-NAGAL (which we call alpha-NAGAL(EL)) retains the antigenicity of alpha-NAGAL but has acquired the enzymatic specificity of the alpha-GAL enzyme. Comparison of the crystal structures of the designed enzyme alpha-GAL(SA) to the wild-type enzymes shows that active sites of alpha-GAL(SA) and alpha-NAGAL superimpose well, indicating success of the rational design. The designed enzymes might be useful as non-immunogenic alternatives in enzyme replacement therapy for treatment of lysosomal storage disorders such as Fabry disease.
Collapse
Affiliation(s)
- Ivan B. Tomasic
- From the Departments of Biochemistry & Molecular Biology and
| | | | - Abigail I. Guce
- Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | | | - Scott C. Garman
- From the Departments of Biochemistry & Molecular Biology and
- Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| |
Collapse
|
24
|
The -galactosidase type A gene aglA from Aspergillus niger encodes a fully functional -N-acetylgalactosaminidase. Glycobiology 2010; 20:1410-9. [DOI: 10.1093/glycob/cwq105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
25
|
Fernández-Leiro R, Pereira-Rodríguez Á, Cerdán ME, Becerra M, Sanz-Aparicio J. Crystallization and preliminary X-ray diffraction data of alpha-galactosidase from Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:44-7. [PMID: 20057068 PMCID: PMC2805534 DOI: 10.1107/s1744309109047794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 11/11/2009] [Indexed: 11/10/2022]
Abstract
Saccharomyces cerevisiae alpha-galactosidase is a highly glycosylated extracellular protein that catalyzes the hydrolysis of alpha-galactosidic linkages in various glucids. Its enzymatic activity is of interest in many food-related industries and has biotechnological applications. Glycosylated and in vitro deglycosylated protein samples were both assayed for crystallization, but only the latter gave good-quality crystals that were suitable for X-ray crystallography. The crystals belonged to space group P42(1)2, with unit-cell parameters a = b = 101.24, c = 111.52 A. A complete diffraction data set was collected to 1.95 A resolution using a synchrotron source.
Collapse
Affiliation(s)
- Rafael Fernández-Leiro
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071 A Coruña, Spain
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Ángel Pereira-Rodríguez
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071 A Coruña, Spain
| | - M. Esperanza Cerdán
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071 A Coruña, Spain
| | - Manuel Becerra
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n 15071 A Coruña, Spain
| | - Juliana Sanz-Aparicio
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| |
Collapse
|
26
|
Sakamoto T, Tsujitani Y, Fukamachi K, Taniguchi Y, Ihara H. Identification of two GH27 bifunctional proteins with β-L-arabinopyranosidase/α-D-galactopyranosidase activities from Fusarium oxysporum. Appl Microbiol Biotechnol 2009; 86:1115-24. [DOI: 10.1007/s00253-009-2344-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 11/25/2022]
|
27
|
Tajima Y, Kawashima I, Tsukimura T, Sugawara K, Kuroda M, Suzuki T, Togawa T, Chiba Y, Jigami Y, Ohno K, Fukushige T, Kanekura T, Itoh K, Ohashi T, Sakuraba H. Use of a modified alpha-N-acetylgalactosaminidase in the development of enzyme replacement therapy for Fabry disease. Am J Hum Genet 2009; 85:569-80. [PMID: 19853240 DOI: 10.1016/j.ajhg.2009.09.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 09/17/2009] [Accepted: 09/24/2009] [Indexed: 11/16/2022] Open
Abstract
A modified alpha-N-acetylgalactosaminidase (NAGA) with alpha-galactosidase A (GLA)-like substrate specificity was designed on the basis of structural studies and was produced in Chinese hamster ovary cells. The enzyme acquired the ability to catalyze the degradation of 4-methylumbelliferyl-alpha-D-galactopyranoside. It retained the original NAGA's stability in plasma and N-glycans containing many mannose 6-phosphate (M6P) residues, which are advantageous for uptake by cells via M6P receptors. There was no immunological cross-reactivity between the modified NAGA and GLA, and the modified NAGA did not react to serum from a patient with Fabry disease recurrently treated with a recombinant GLA. The enzyme cleaved globotriaosylceramide (Gb3) accumulated in cultured fibroblasts from a patient with Fabry disease. Furthermore, like recombinant GLA proteins presently used for enzyme replacement therapy (ERT) for Fabry disease, the enzyme intravenously injected into Fabry model mice prevented Gb3 storage in the liver, kidneys, and heart and improved the pathological changes in these organs. Because this modified NAGA is hardly expected to cause an allergic reaction in Fabry disease patients, it is highly promising as a new and safe enzyme for ERT for Fabry disease.
Collapse
Affiliation(s)
- Youichi Tajima
- Department of Clinical Genetics, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Clark NE, Garman SC. The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases. J Mol Biol 2009; 393:435-47. [PMID: 19683538 PMCID: PMC2771859 DOI: 10.1016/j.jmb.2009.08.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/30/2009] [Accepted: 08/04/2009] [Indexed: 01/07/2023]
Abstract
alpha-N-acetylgalactosaminidase (alpha-NAGAL; E.C. 3.2.1.49) is a lysosomal exoglycosidase that cleaves terminal alpha-N-acetylgalactosamine residues from glycopeptides and glycolipids. In humans, a deficiency of alpha-NAGAL activity results in the lysosomal storage disorders Schindler disease and Kanzaki disease. To better understand the molecular defects in the diseases, we determined the crystal structure of human alpha-NAGAL after expressing wild-type and glycosylation-deficient glycoproteins in recombinant insect cell expression systems. We measured the enzymatic parameters of our purified wild-type and mutant enzymes, establishing their enzymatic equivalence. To investigate the binding specificity and catalytic mechanism of the human alpha-NAGAL enzyme, we determined three crystallographic complexes with different catalytic products bound in the active site of the enzyme. To better understand how individual defects in the alpha-NAGAL glycoprotein lead to Schindler disease, we analyzed the effect of disease-causing mutations on the three-dimensional structure.
Collapse
Affiliation(s)
- Nathaniel E Clark
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, 01003, USA
| | | |
Collapse
|
29
|
Garman SC. Structural studies on α-GAL and α-NAGAL: The atomic basis of Fabry and Schindler diseases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420600598194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
30
|
Weignerová L, Simerská P, Křen V. α-Galactosidases and their applications in biotransformations. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420802583416] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
31
|
Kumar A, Singhal NK, Ramanujam B, Mitra A, Rameshwaram NR, Nadimpalli SK, Rao CP. C(1)-/C(2)-aromatic-imino-glyco-conjugates: experimental and computational studies of binding, inhibition and docking aspects towards glycosidases isolated from soybean and jack bean. Glycoconj J 2009; 26:495-510. [PMID: 18953653 DOI: 10.1007/s10719-008-9199-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 09/24/2008] [Accepted: 10/01/2008] [Indexed: 11/28/2022]
Abstract
Several C(1)-imino conjugates of D: -galactose, D: -lactose and D: -ribose, where the nitrogen center was substituted by the salicylidene or naphthylidene, were synthesized and characterized. Similar C(2)-imino conjugates of D: -glucose have also been synthesized. All the glyco-imino-conjugates, which are transition state analogues, exhibited 100% inhibition of the activity towards glycosidases extracted from soybean and jack bean meal. Among these, a galactosyl-napthyl-imine-conjugate (1c) showed 50% inhibition of the activity of pure alpha-mannosidase from jack bean at 22 +/- 2.5 microM, and a ribosyl-naphthyl-imine-conjugate (3c) showed at 31 +/- 5.5 microM and hence these conjugates are potent inhibitors of glycosidases. The kinetic studies suggested non-competitive inhibition by these conjugates. The studies are also suggestive of the involvement of aromatic, imine and carbohydrate moieties of the glyco-imino-conjugates in the effective inhibition. The binding of glyco-imino-conjugate has been established by extensive studies carried out using fluorescence emission and isothermal titration calorimetry. The conformational changes resulted in the enzyme upon interaction of these derivatives has been established by studying the fluorescence quench of the enzyme by KI as well as from the secondary structural changes noticed in CD spectra. All these studies revealed the difference in the binding strengths of the naphthylidene vs. salicylidene as well as galactosyl vs. lactosyl moieties present in these conjugates. The differential inhibition of these glyco-conjugates has been addressed by quantifying the specific interactions present between the glyco-conjugates and the enzyme by using rigid docking studies.
Collapse
Affiliation(s)
- Amit Kumar
- Bioinorganic Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, India
| | | | | | | | | | | | | |
Collapse
|
32
|
Stubbs K, Macauley M, Vocadlo D. A Selective Inhibitor Gal-PUGNAc of Human Lysosomal β-Hexosaminidases Modulates Levels of the Ganglioside GM2 in Neuroblastoma Cells. Angew Chem Int Ed Engl 2009; 48:1300-3. [DOI: 10.1002/anie.200804583] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
33
|
Stubbs K, Macauley M, Vocadlo D. A Selective Inhibitor Gal-PUGNAc of Human Lysosomal β-Hexosaminidases Modulates Levels of the Ganglioside GM2 in Neuroblastoma Cells. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
34
|
Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J Biol Chem 2008; 283:36328-37. [PMID: 18981178 PMCID: PMC2662298 DOI: 10.1074/jbc.m806115200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/03/2008] [Indexed: 11/06/2022] Open
Abstract
SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu532 is positioned to provide protonic assistance to leaving group departure, with Glu439 and Glu508 both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.
Collapse
Affiliation(s)
- Momoyo Kitamura
- Faculty of Advanced Life Science, Graduate School of Agriculture, Hokkaido University, Sapporo 060-0810, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. ACTA ACUST UNITED AC 2008; 15:1058-67. [PMID: 18848471 PMCID: PMC2670981 DOI: 10.1016/j.chembiol.2008.09.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/01/2008] [Accepted: 09/11/2008] [Indexed: 11/26/2022]
Abstract
Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining α-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron α-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining α-galactosidase.
Collapse
Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK.
| | | | | | | | | |
Collapse
|
36
|
Weignerová L, Filipi T, Manglová D, Křen V. Induction, purification and characterization of α-N-acetylgalactosaminidase from Aspergillus Niger. Appl Microbiol Biotechnol 2008; 79:769-74. [DOI: 10.1007/s00253-008-1485-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 03/31/2008] [Accepted: 03/31/2008] [Indexed: 11/24/2022]
|
37
|
Minai R, Matsuo Y, Onuki H, Hirota H. Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins 2008; 72:367-81. [DOI: 10.1002/prot.21933] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
38
|
Ahuja R, Singhal NK, Ramanujam B, Ravikumar M, Rao CP. Experimental and Computational Studies of the Recognition of Amino Acids by Galactosyl-imine and -amine Derivatives: An Attempt to Understand the Lectin−Carbohydrate Interactions. J Org Chem 2007; 72:3430-42. [PMID: 17394358 DOI: 10.1021/jo0700979] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A galactosyl-naphthyl-imine-based derivative, 1-(beta-D-galactopyranosyl-1'-deoxy-1'-iminomethyl)-2-hydroxynaphthalene (GNI), and a galactosyl-naphthyl-amine-based derivative, 1-(galactopyranosyl-1'-deoxy-1'-aminomethyl)-2-hydroxynaphthalene (GNA), possessing an ONO binding core were studied for their recognition of naturally occurring amino acids using fluorescence and absorption spectroscopy, and the corresponding association constants were derived for the complexes formed. The complexes formed between GNI/GNA and amino acids were supported by electrospray ionization mass spectrometry (ESI/MS). The structures of the complexes were optimized by computational studies using density functional theory, and stabilization energies were computed for the complexes to substantiate the interactions present between GNI/GNA and amino acid. The interactions were found to be primarily hydrogen bonding in nature. These interactions are reminiscent of those present in the lectin-carbohydrate and glycosidase substrate. Thus, the carbohydrate moiety present in GNI shows high specificity toward the -COOH group of the amino acid, which may be relevant to such interactions present between the carbohydrates and the polypeptides.
Collapse
Affiliation(s)
- Rohit Ahuja
- Bioinorganic Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, India
| | | | | | | | | |
Collapse
|
39
|
Li S, Li T, Kim WD, Kitaoka M, Yoshida S, Nakajima M, Kobayashi H. Characterization of raffinose synthase from rice (Oryza sativa L. var. Nipponbare). Biotechnol Lett 2007; 29:635-40. [PMID: 17206375 DOI: 10.1007/s10529-006-9268-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 11/24/2006] [Indexed: 11/25/2022]
Abstract
The putative raffinose synthase gene from rice was cloned and expressed in Escherichia coli. The enzyme displayed an optimum activity at 45 degrees C and pH 7.0, and a sulfhydryl group was required for its activity. The enzyme was specific for galactinol and p-nitrophenyl-alpha-D-galactoside as galactosyl donors, and sucrose, lactose, 4-beta-galactobiose, N-acetyl-D-lactosamine, trehalose and lacto-N-biose were recognized as galactosyl acceptors.
Collapse
Affiliation(s)
- Suhong Li
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | | | | | | | | | | |
Collapse
|
40
|
Shabbeer J, Yasuda M, Benson SD, Desnick RJ. Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations. Hum Genomics 2006; 2:297-309. [PMID: 16595074 PMCID: PMC3500179 DOI: 10.1186/1479-7364-2-5-297] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Fabry disease, an X-linked recessive inborn error of glycosphingolipid catabolism, results from the deficient activity of the lysosomal exoglycohydrolase, α-galactosidase A (EC 3.2.1.22; α-Gal A). The molecular lesions in the α-Gal A gene causing the classic phenotype of Fabry disease in 66 unrelated families were determined. In 49 families, 50 new mutations were identified, including: 29 missense mutations (N34K, T41I, D93V, R112S, L166G, G171D, M187T, S201Y, S201F, D234E, W236R, D264Y, M267R, V269M, G271S, G271V, S276G, Q283P, A285P, A285D, M290I, P293T, Q312H, Q321R, G328V, E338K, A348P, E358A, Q386P); nine nonsense mutations (C56X, E79X, K127X, Y151X, Y173X, L177X, W262X, Q306X, E338X); five splicing defects (IVS4-1G > A, IVS5-2A > G, IVS5 + 3A > G, IVS5 + 4A > G, IVS6-1G > C); four small deletions (18delA, 457delGAC, 567delG, 1096delACCAT); one small insertion (996insC); one 3.1 kilobase Alu-Alu deletion (which included exon 2); and one complex mutation (K374R, 1124delGAG). In 18 families, 17 previously reported mutations were identified, with R112C occurring in two families. In two classically affected families, affected males were identified with two mutations: one with two novel mutations, D264Y and V269M and the other with one novel (Q312H) and one previously reported (A143T) mutation. Transient expression of the individual mutations revealed that D264Y and Q312H were localised in the endoplasmic reticulum and had no detectable or markedly reduced activity, whereas V269M and A143T were localised in lysosomes and had approximately 10 per cent and approximately 35 per cent of expressed wild-type activity, respectively. Structural analyses based on the enzyme's three-dimensional structure predicted the effect of the 29 novel missense mutations on the mutant glycoprotein's structure. Of note, three novel mutations (approximately 10 per cent) were predicted not to significantly alter the glycoprotein's structure; however, they were disease causing. These studies further define the molecular heterogeneity of the α-Gal A mutations in classical Fabry disease, permit precise heterozygote detection and prenatal diagnosis, and provide insights into the structural alterations of the mutant enzymes that cause the classic phenotype.
Collapse
Affiliation(s)
- Junaid Shabbeer
- Department of Human Genetics, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA
| | - Makiko Yasuda
- Department of Human Genetics, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA
| | - Stacy D Benson
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert J Desnick
- Department of Human Genetics, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA
| |
Collapse
|
41
|
Brouns SJJ, Smits N, Wu H, Snijders APL, Wright PC, de Vos WM, van der Oost J. Identification of a novel alpha-galactosidase from the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol 2006; 188:2392-9. [PMID: 16547025 PMCID: PMC1428385 DOI: 10.1128/jb.188.7.2392-2399.2006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sulfolobus solfataricus is an aerobic crenarchaeon that thrives in acidic volcanic pools. In this study, we have purified and characterized a thermostable alpha-galactosidase from cell extracts of S. solfataricus P2 grown on the trisaccharide raffinose. The enzyme, designated GalS, is highly specific for alpha-linked galactosides, which are optimally hydrolyzed at pH 5 and 90 degrees C. The protein consists of 74.7-kDa subunits and has been identified as the gene product of open reading frame Sso3127. Its primary sequence is most related to plant enzymes of glycoside hydrolase family 36, which are involved in the synthesis and degradation of raffinose and stachyose. Both the galS gene from S. solfataricus P2 and an orthologous gene from Sulfolobus tokodaii have been cloned and functionally expressed in Escherichia coli, and their activity was confirmed. At present, these Sulfolobus enzymes not only constitute a distinct type of thermostable alpha-galactosidases within glycoside hydrolase clan D but also represent the first members from the Archaea.
Collapse
Affiliation(s)
- Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
42
|
Ernst HA, Lo Leggio L, Willemoës M, Leonard G, Blum P, Larsen S. Structure of the Sulfolobus solfataricus alpha-glucosidase: implications for domain conservation and substrate recognition in GH31. J Mol Biol 2006; 358:1106-24. [PMID: 16580018 DOI: 10.1016/j.jmb.2006.02.056] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 02/21/2006] [Accepted: 02/22/2006] [Indexed: 11/26/2022]
Abstract
The crystal structure of alpha-glucosidase MalA from Sulfolobus solfataricus has been determined at 2.5Angstrom resolution. It provides a structural model for enzymes representing the major specificity in glycoside hydrolase family 31 (GH31), including alpha-glucosidases from higher organisms, involved in glycogen degradation and glycoprotein processing. The structure of MalA shows clear differences from the only other structure known from GH31, alpha-xylosidase YicI. MalA and YicI share only 23% sequence identity. Although the two enzymes display a similar domain structure and both form hexamers, their structures differ significantly in quaternary organization: MalA is a dimer of trimers, YicI a trimer of dimers. MalA and YicI also differ in their substrate specificities, as shown by kinetic measurements on model chromogenic substrates. In addition, MalA has a clear preference for maltose (Glc-alpha1,4-Glc), whereas YicI prefers isoprimeverose (Xyl-alpha1,6-Glc). The structural origin of this difference occurs in the -1 subsite where MalA residues Asp251 and Trp284 could interact with OH6 of the substrate. The structure of MalA in complex with beta-octyl-glucopyranoside has been determined. It reveals Arg400, Asp87, Trp284, Met321 and Phe327 as invariant residues forming the +1 subsite in the GH31 alpha-glucosidases. Structural comparisons with other GH families suggest that the GH31 enzymes belong to clan GH-D.
Collapse
Affiliation(s)
- Heidi A Ernst
- Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | | | | | | | | |
Collapse
|
43
|
Foucault M, Watzlawick H, Mattes R, Haser R, Gouet P. Crystallization and preliminary X-ray diffraction studies of two thermostable alpha-galactosidases from glycoside hydrolase family 36. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:100-3. [PMID: 16511274 PMCID: PMC2150962 DOI: 10.1107/s1744309105042582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Accepted: 12/20/2005] [Indexed: 11/10/2022]
Abstract
alpha-Galactosidases from thermophilic organisms have gained interest owing to their applications in the sugar industry. The alpha-galactosidases AgaA, AgaB and AgaA A355E mutant from Geobacillus stearothermophilus have been overexpressed in Escherichia coli. Crystals of AgaB and AgaA A355E have been obtained by the vapour-diffusion method and synchrotron data have been collected to 2.0 and 2.8 A resolution, respectively. Crystals of AgaB belong to space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 87.5, b = 113.3, c = 161.6 A. Crystals of AgaA A355E belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 150.1, c = 233.2 A.
Collapse
Affiliation(s)
- M. Foucault
- Institut de Biologie et Chimie des Protéines, CNRS–UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07, France
| | - H. Watzlawick
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | - R. Mattes
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
| | - R. Haser
- Institut de Biologie et Chimie des Protéines, CNRS–UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07, France
| | - P. Gouet
- Institut de Biologie et Chimie des Protéines, CNRS–UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07, France
- Correspondence e-mail:
| |
Collapse
|
44
|
Hinz SWA, Doeswijk-Voragen CHL, Schipperus R, van den Broek LAM, Vincken JP, Voragen AGJ. Increasing the transglycosylation activity of α-galactosidase fromBifidobacterium adolescentisDSM 20083 by site-directed mutagenesis. Biotechnol Bioeng 2006; 93:122-31. [PMID: 16320365 DOI: 10.1002/bit.20713] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The alpha-galactosidase (AGA) from Bifidobacterium adolescentis DSM 20083 has a high transglycosylation activity. The optimal conditions for this activity are pH 8, and 37 degrees C. At high melibiose concentration (600 mM), approximately 64% of the enzyme-substrate encounters resulted in transglycosylation. Examination of the acceptor specificity showed that AGA required a hydroxyl group at C-6 for transglycosylation. Pentoses, hexuronic acids, deoxyhexoses, and alditols did not serve as acceptor molecules. Disaccharides were found to be good acceptors. A putative 3D-structure of the catalytic site of AGA was obtained by homology modeling. Based on this structure and amino acid sequence alignments, site-directed mutagenesis was performed to increase the transglycosylation efficiency of the enzyme, which resulted in four positive mutants. The positive single mutations were combined, resulting in six double mutants. The mutant H497M had an increase in transglycosylation of 16%, whereas most of the single mutations showed an increase of 2%-5% compared to the wild-type AGA. The double mutants G382C-Y500L, and H497M-Y500L had an increase in transglycosylation activity of 10%-16%, compared to the wild-type enzyme, whereas the increase for the other double mutants was low (4%-7%). The results show that with a single mutation (H497M) the transglycosylation efficiency can be increased from 64% to 75% of all enzyme-substrate encounters. Combining successful single mutants in double mutations did not necessarily result in an extra increase in transglycosylation efficiency. The donor and acceptor specificity did not change in the mutants, whereas the thermostability of the mutants with G382C decreased drastically.
Collapse
Affiliation(s)
- Sandra W A Hinz
- Laboratory of Food Chemistry, Wageningen University, PO Box 8129, The Netherlands
| | | | | | | | | | | |
Collapse
|
45
|
Naumoff DG. GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. BMC Genomics 2005; 6:112. [PMID: 16131397 PMCID: PMC1249566 DOI: 10.1186/1471-2164-6-112] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 08/30/2005] [Indexed: 11/29/2022] Open
Abstract
Background As a rule, about 1% of genes in a given genome encode glycoside hydrolases and their homologues. On the basis of sequence similarity they have been grouped into more than ninety GH families during the last 15 years. The GH97 family has been established very recently and initially included only 18 bacterial proteins. However, the evolutionary relationship of the genes encoding proteins of this family remains unclear, as well as their distribution among main groups of the living organisms. Results The extensive search of the current databases allowed us to double the number of GH97 family proteins. Five subfamilies were distinguished on the basis of pairwise sequence comparison and phylogenetic analysis. Iterative sequence analysis revealed the relationship of the GH97 family with the GH27, GH31, and GH36 families of glycosidases, which belong to the α-galactosidase superfamily, as well as a more distant relationship with some other glycosidase families (GH13 and GH20). Conclusion The results of this study show an unexpected sequence similarity of GH97 family proteins with glycoside hydrolases from several other families, that have (β/α)8-barrel fold of the catalytic domain and a retaining mechanism of the glycoside bond hydrolysis. These data suggest a common evolutionary origin of glycosidases representing different families and clans.
Collapse
Affiliation(s)
- Daniil G Naumoff
- State Institute for Genetics and Selection of Industrial Microorganisms, I-Dorozhny proezd, 1, Moscow 117545, Russia.
| |
Collapse
|
46
|
Hujová J, Sikora J, Dobrovolný R, Poupětová H, Ledvinová J, Kostrouchová M, Hřebíček M. Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate alpha-galactosidase and alpha-N-acetylgalactosaminidase. BMC Cell Biol 2005; 6:5. [PMID: 15676072 PMCID: PMC548690 DOI: 10.1186/1471-2121-6-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Accepted: 01/27/2005] [Indexed: 11/10/2022] Open
Abstract
Background Human α-galactosidase A (α-GAL) and α-N-acetylgalactosaminidase (α-NAGA) are presumed to share a common ancestor. Deficiencies of these enzymes cause two well-characterized human lysosomal storage disorders (LSD) – Fabry (α-GAL deficiency) and Schindler (α-NAGA deficiency) diseases. Caenorhabditis elegans was previously shown to be a relevant model organism for several late endosomal/lysosomal membrane proteins associated with LSDs. The aim of this study was to identify and characterize C. elegans orthologs to both human lysosomal luminal proteins α-GAL and α-NAGA. Results BlastP searches for orthologs of human α-GAL and α-NAGA revealed a single C. elegans gene (R07B7.11) with homology to both human genes (α-galactosidase and α-N-acetylgalactosaminidase) – gana-1. We cloned and sequenced the complete gana-1 cDNA and elucidated the gene organization. Phylogenetic analyses and homology modeling of GANA-1 based on the 3D structure of chicken α-NAGA, rice α-GAL and human α-GAL suggest a close evolutionary relationship of GANA-1 to both human α-GAL and α-NAGA. Both α-GAL and α-NAGA enzymatic activities were detected in C. elegans mixed culture homogenates. However, α-GAL activity on an artificial substrate was completely inhibited by the α-NAGA inhibitor, N-acetyl-D-galactosamine. A GANA-1::GFP fusion protein expressed from a transgene, containing the complete gana-1 coding region and 3 kb of its hypothetical promoter, was not detectable under the standard laboratory conditions. The GFP signal was observed solely in a vesicular compartment of coelomocytes of the animals treated with Concanamycin A (CON A) or NH4Cl, agents that increase the pH of the cellular acidic compartment. Immunofluorescence detection of the fusion protein using polyclonal anti-GFP antibody showed a broader and coarsely granular cytoplasmic expression pattern in body wall muscle cells, intestinal cells, and a vesicular compartment of coelomocytes. Inhibition of gana-1 by RNA interference resulted in a decrease of both α-GAL and α-NAGA activities measured in mixed stage culture homogenates but did not cause any obvious phenotype. Conclusions GANA-1 is a single C. elegans ortholog of both human α-GAL and α-NAGA proteins. Phylogenetic, homology modeling, biochemical and GFP expression analyses support the hypothesis that GANA-1 has dual enzymatic activity and is localized in an acidic cellular compartment.
Collapse
Affiliation(s)
- Jana Hujová
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| | - Jakub Sikora
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| | - Robert Dobrovolný
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| | - Helena Poupětová
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| | - Jana Ledvinová
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| | - Marta Kostrouchová
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| | - Martin Hřebíček
- Institute of Inherited Metabolic Disorders, Charles University, 1Medical Faculty, Prague, Czech Republic
| |
Collapse
|
47
|
Kanekura T, Sakuraba H, Matsuzawa F, Aikawa S, Doi H, Hirabayashi Y, Yoshii N, Fukushige T, Kanzaki T. Three dimensional structural studies of alpha-N-acetylgalactosaminidase (alpha-NAGA) in alpha-NAGA deficiency (Kanzaki disease): different gene mutations cause peculiar structural changes in alpha-NAGAs resulting in different substrate specificities and clinical phenotypes. J Dermatol Sci 2004; 37:15-20. [PMID: 15619430 DOI: 10.1016/j.jdermsci.2004.09.005] [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: 06/24/2004] [Revised: 09/17/2004] [Accepted: 09/22/2004] [Indexed: 11/22/2022]
Abstract
BACKGROUND Kanzaki disease (OMIM#104170) is attributable to a deficiency in alpha-N-acetylgalactosaminidase (alpha-NAGA; E.C.3.2.1.49), which hydrolyzes GalNAcalpha1-O-Ser/Thr. Missense mutations, R329W or R329Q were identified in two Japanese Kanzaki patients. Although they are on the same codon, the clinical manifestation was more severe in R329W because an amino acid substitution led to protein instability resulting in structural change, which is greater in R329W than in R329Q. OBJECTIVE To examine whether the different clinical phenotypes are attributable to the two mutations. METHODS Plasma alpha-NAGA activity and urinary excreted glycopeptides were measured and three-dimensional models of human alpha-NAGA and its complexes with GalNAcalpha1-O-Ser and GalNAcalpha1-O-Thr were constructed by homology modeling. RESULTS Residual enzyme activity was significantly higher in the R329Q- than the R329W mutant (0.022+/-0.005 versus 0.005+/-0.001 nmol/h/ml: p<0.05); the urinary ratios of GalNAcalpha1-O-Ser:GalNAcalpha1-O-Thr were 2:10 and 8:10, respectively. GalNAcalpha1-O-Ser/Thr fit tightly in a narrow space of the active site pocket of alpha-NAGA. GalNAcalpha1-O-Thr requires a larger space to associate with alpha-NAGA because of the side chain (CH3) of the threonine residue. CONCLUSION Our findings suggest that the association of alpha-NAGA with its substrates is strongly affected by the amino acid substitution at R329 and that the association with GalNAcalpha1-O-Thr is more highly susceptible to structural changes. The residual mutant enzyme in R329W could not associate with GalNAcalpha1-O-Thr and GalNAcalpha1-O-Ser. However, the residual mutant enzyme in R329Q catalyzed GalNAcalpha1-O-Ser to some extent. Therefore, the urinary ratio of GalNAcalpha1-O-Ser:GalNAcalpha1-O-Thr was lower and the clinical phenotype was milder in the R329Q mutation. Structural analysis revealed biochemical and phenotypic differences in these Kanzaki patients with the R329Q and R329W mutation.
Collapse
Affiliation(s)
- Takuro Kanekura
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8520, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Golubev AM, Nagem RAP, Brandão Neto JR, Neustroev KN, Eneyskaya EV, Kulminskaya AA, Shabalin KA, Savel'ev AN, Polikarpov I. Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism. J Mol Biol 2004; 339:413-22. [PMID: 15136043 DOI: 10.1016/j.jmb.2004.03.062] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 03/15/2004] [Accepted: 03/23/2004] [Indexed: 11/18/2022]
Abstract
The crystal structures of alpha-galactosidase from the mesophilic fungus Trichoderma reesei and its complex with the competitive inhibitor, beta-d-galactose, have been determined at 1.54 A and 2.0 A resolution, respectively. The alpha-galactosidase structure was solved by the quick cryo-soaking method using a single Cs derivative. The refined crystallographic model of the alpha-galactosidase consists of two domains, an N-terminal catalytic domain of the (beta/alpha)8 barrel topology and a C-terminal domain which is formed by an antiparallel beta-structure. The protein contains four N-glycosylation sites located in the catalytic domain. Some of the oligosaccharides were found to participate in inter-domain contacts. The galactose molecule binds to the active site pocket located in the center of the barrel of the catalytic domain. Analysis of the alpha-galactosidase- galactose complex reveals the residues of the active site and offers a structural basis for identification of the putative mechanism of the enzymatic reaction. The structure of the alpha-galactosidase closely resembles those of the glycoside hydrolase family 27. The conservation of two catalytic Asp residues, identified for this family, is consistent with a double-displacement reaction mechanism for the alpha-galactosidase. Modeling of possible substrates into the active site reveals specific hydrogen bonds and hydrophobic interactions that could explain peculiarities of the enzyme kinetics.
Collapse
Affiliation(s)
- A M Golubev
- Petersburg Nuclear Physics Institute, Gatchina, St Petersburg, 188300, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Bodamer OA, Ratschmann R, Paschke E, Voigtländer T, Stöckler-Ipsiroglu S. Recurrent acroparaesthesia during febrile infections. Lancet 2004; 363:1698. [PMID: 15158631 DOI: 10.1016/s0140-6736(04)16254-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- O A Bodamer
- Department of General Pediatrics, University Children's Hospital, Vienna, A-1090 Austria.
| | | | | | | | | |
Collapse
|
50
|
Lee RH, Lin MC, Chen SCG. A novel alkaline alpha-galactosidase gene is involved in rice leaf senescence. PLANT MOLECULAR BIOLOGY 2004; 55:281-95. [PMID: 15604681 DOI: 10.1007/s11103-004-0641-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We previously isolated and identified numerous senescence-associated genes (SAGs) in rice leaves. Here we characterized the structure and function of an SAG- Osh69 encoding alkaline alpha-galactosidase that belongs to a novel family of glycosyl hydrolases. Osh69 is a single-copy gene composed of 13 exons located on rice chromosome 8. The expression level of Osh69 is not only up-regulated during natural leaf senescence but also induced rapidly by darkness, hormones (methyl jasmonic acid, salicylic acid), and stresses (H2O2 and wounding). The recombinant Osh69 protein over-expressed in Escherichia coli has displayed optimal alpha-galactosidase activity at pH 8.0. The enzyme showed good hydrolytic activities towards alpha-1,6-galactosyl oligosaccharides and galactolipid digalactosyl diacylglycerol. Immunoelectron microscopic analysis demonstrates that Osh69 is specifically localized in the chloroplasts of senescing leaves. These findings strongly suggest an important role for Osh69 in the degradation of chloroplast galactolipids during leaf senescence.
Collapse
MESH Headings
- Amino Acid Sequence
- Blotting, Western
- Chloroplasts/enzymology
- Chloroplasts/ultrastructure
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Gene Expression Regulation, Developmental/drug effects
- Gene Expression Regulation, Enzymologic/drug effects
- Gene Expression Regulation, Plant/drug effects
- Hydrogen Peroxide/pharmacology
- Hydrogen-Ion Concentration
- Microscopy, Immunoelectron
- Molecular Sequence Data
- Oryza/enzymology
- Oryza/genetics
- Oryza/physiology
- Phylogeny
- Plant Growth Regulators/pharmacology
- Plant Leaves/genetics
- Plant Leaves/physiology
- Plant Leaves/ultrastructure
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Stress, Mechanical
- Substrate Specificity
- alpha-Galactosidase/genetics
- alpha-Galactosidase/metabolism
Collapse
Affiliation(s)
- Ruey-Hua Lee
- Institute of Botany, Academia Sinica, Taipei, Taiwan
| | | | | |
Collapse
|