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Janíčková Z, Janeček Š. Fungal α-amylases from three GH13 subfamilies: their sequence-structural features and evolutionary relationships. Int J Biol Macromol 2020; 159:763-772. [DOI: 10.1016/j.ijbiomac.2020.05.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/12/2023]
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2
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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Varshney NK, Ramasamy S, Brannigan JA, Wilkinson AJ, Suresh CG. Cloning, overexpression, crystallization and preliminary X-ray crystallographic analysis of a slow-processing mutant of penicillin G acylase from Kluyvera citrophila. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:925-9. [PMID: 23908045 PMCID: PMC3729176 DOI: 10.1107/s174430911301943x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/14/2013] [Indexed: 06/02/2023]
Abstract
Kluyvera citrophila penicillin G acylase (KcPGA) has recently attracted increased attention relative to the well studied and commonly used Escherichia coli PGA (EcPGA) because KcPGA is more resilient to harsh conditions and is easier to immobilize for the industrial hydrolysis of natural penicillins to generate the 6-aminopenicillin (6-APA) nucleus, which is the starting material for semi-synthetic antibiotic production. Like other penicillin acylases, KcPGA is synthesized as a single-chain inactive pro-PGA, which upon autocatalytic processing becomes an active heterodimer of α and β chains. Here, the cloning of the pac gene encoding KcPGA and the preparation of a slow-processing mutant precursor are reported. The purification, crystallization and preliminary X-ray analysis of crystals of this precursor protein are described. The protein crystallized in two different space groups, P1, with unit-cell parameters a = 54.0, b = 124.6, c = 135.1 Å, α = 104.1, β = 101.4, γ = 96.5°, and C2, with unit-cell parameters a = 265.1, b = 54.0, c = 249.2 Å, β = 104.4°, using the sitting-drop vapour-diffusion method. Diffraction data were collected at 100 K and the phases were determined using the molecular-replacement method. The initial maps revealed electron density for the spacer peptide.
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Affiliation(s)
- Nishant Kumar Varshney
- Division of Biochemical Sciences, CSIR – National Chemical Laboratory, Pune 411 008, Maharashtra, India
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR – National Chemical Laboratory, Pune 411 008, Maharashtra, India
- California Institute of Technology, Pasadena, USA
| | - James A. Brannigan
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, England
| | - Anthony J. Wilkinson
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, England
| | - C. G. Suresh
- Division of Biochemical Sciences, CSIR – National Chemical Laboratory, Pune 411 008, Maharashtra, India
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Goddard AD, Moir JWB, Richardson DJ, Ferguson SJ. Interdependence of two NarK domains in a fused nitrate/nitrite transporter. Mol Microbiol 2008; 70:667-81. [PMID: 18823285 DOI: 10.1111/j.1365-2958.2008.06436.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrate uptake is essential for various bacterial processes and combines with nitrite export to form the usual initial steps of denitrification, a process that reduces nitrate to dinitrogen gas. Although many bacterial species contain NarK-like transporters that are proposed to function as either nitrate/proton symporters or nitrate/nitrite antiporters based on sequence homology, these transporters remain, in general, poorly characterized. Several bacteria appear to contain a transporter that is a fusion of two NarK-like proteins, although the significance of this arrangement remains elusive. We demonstrate that NarK from Paracoccus denitrificans is expressed as a fusion of two NarK-like transporters. NarK1 and NarK2 are separately capable of supporting anaerobic denitrifying growth but with growth defects that are partially mitigated by coexpression of the two domains. NarK1 appears to be a nitrate/proton symporter with high affinity for nitrate and NarK2 a nitrate/nitrite antiporter with lower affinity for nitrate. Each transporter requires two conserved arginine residues for activity. A transporter consisting of inactivated NarK1 fused to active NarK2 has a dramatically increased affinity for nitrate compared with NarK2 alone, implying a functional interaction between the two domains. A potential model for nitrate and nitrite transport in P. denitrificans is proposed.
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Affiliation(s)
- Alan D Goddard
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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Ballschmiter M, Armbrecht M, Ivanova K, Antranikian G, Liebl W. AmyA, an alpha-amylase with beta-cyclodextrin-forming activity, and AmyB from the thermoalkaliphilic organism Anaerobranca gottschalkii: two alpha-amylases adapted to their different cellular localizations. Appl Environ Microbiol 2005; 71:3709-15. [PMID: 16000780 PMCID: PMC1169011 DOI: 10.1128/aem.71.7.3709-3715.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 01/15/2005] [Indexed: 11/20/2022] Open
Abstract
Two alpha-amylase genes from the thermophilic alkaliphile Anaerobranca gottschalkii were cloned, and the corresponding enzymes, AmyA and AmyB, were investigated after purification of the recombinant proteins. Based on their amino acid sequences, AmyA is proposed to be a lipoprotein with extracellular localization and thus is exposed to the alkaline milieu, while AmyB apparently represents a cytoplasmic enzyme. The amino acid sequences of both enzymes bear high similarity to those of GHF13 proteins. The different cellular localizations of AmyA and AmyB are reflected in their physicochemical properties. The alkaline pH optimum (pH 8), as well as the broad pH range, of AmyA activity (more than 50% activity between pH 6 and pH 9.5) mirrors the conditions that are encountered by an extracellular enzyme exposed to the medium of A. gottschalkii, which grows between pH 6 and pH 10.5. AmyB, on the other hand, has a narrow pH range with a slightly acidic pH optimum at 6 to 6.5, which is presumably close to the pH in the cytoplasm. Also, the intracellular AmyB is less tolerant of high temperatures than the extracellular AmyA. While AmyA has a half-life of 48 h at 70 degrees C, AmyB has a half-life of only about 10 min at that temperature, perhaps due to the lack of stabilizing constituents of the cytoplasm. AmyA and AmyB were very similar with respect to their substrate specificity profiles, clearly preferring amylose over amylopectin, pullulan, and glycogen. Both enzymes also hydrolyzed alpha-, beta-, and gamma-cyclodextrin. Very interestingly, AmyA, but not AmyB, displayed high transglycosylation activity on maltooligosaccharides and also had significant beta-cyclodextrin glycosyltransferase (CGTase) activity. CGTase activity has not been reported for typical alpha-amylases before. The mechanism of cyclodextrin formation by AmyA is unknown.
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Affiliation(s)
- Meike Ballschmiter
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Sumitani J, Tottori T, Kawaguchi T, Arai M. New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading. Biochem J 2000; 350 Pt 2:477-84. [PMID: 10947962 PMCID: PMC1221275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The alpha-amylase from Bacillus sp. no. 195 (BAA) consists of two domains: one is the catalytic domain similar to alpha-amylases from animals and Streptomyces in the N-terminal region; the other is the functionally unknown domain composed of an approx. 90-residue direct repeat in the C-terminal region. The gene coding for BAA was expressed in Streptomyces lividans TK24. Three active forms of the gene products were found. The pH and thermal profiles of BAAs, and their catalytic activities for p-nitrophenyl maltopentaoside and soluble starch, showed almost the same behaviours. The largest, 69 kDa, form (BAA-alpha) was of the same molecular mass as that of the mature protein estimated from the nucleotide sequence, and had raw-starch-binding and -degrading abilities. The second largest, 60 kDa, form (BAA-beta), whose molecular mass was the same as that of the natural enzyme from Bacillus sp. no. 195, was generated by proteolytic processing between the two repeat sequences in the C-terminal region, and had lower activities for raw starch binding and degrading than those of BAA-alpha. The smallest, 50 kDa, form (BAA-gamma) contained only the N-terminal catalytic domain as a result of removal of the C-terminal repeat sequence, which led to loss of binding and degradation of insoluble starches. Thus the starch adsorption capacity and raw-starch-degrading activity of BAAs depends on the existence of the repeat sequence in the C-terminal region. BAA-alpha was specifically adsorbed on starch or dextran (alpha-1,4 or alpha-1,6 glucan), and specifically desorbed with maltose or beta-cyclodextrin. These observations indicated that the repeat sequence of the enzyme was functional in the starch-binding domain (SBD). We propose the designation of the homologues to the SBD of glucoamylase from Aspergillus niger as family I SBDs, the homologues to that of glucoamylase from Rhizopus oryzae as family II, and the homologues of this repeat sequence of BAA as family III.
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Affiliation(s)
- J Sumitani
- Department of Applied Biological Chemistry, College of Agriculture, and Research Institute of Applied Science and Technology, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Osaka, Japan
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Pujadas G, Ramírez FM, Valero R, Palau J. Evolution of β-amylase: Patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(199608)25:4<456::aid-prot6>3.0.co;2-b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Yin XH, Gerbaud C, Francou FX, Guérineau M, Virolle MJ. amlC, another amylolytic gene maps close to the amlB locus in Streptomyces lividans TK24. Gene 1998; 215:171-80. [PMID: 9666116 DOI: 10.1016/s0378-1119(98)00265-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The region located upstream of the alpha-amylase gene (amlB) of Streptomyces lividans TK24 (Yin et al., 1997) contains a 2978-bp-long ORF divergent from amlB, and designated amlC. amlC Encodes a 993amino acid (aa) protein with a calculated molecular weight of 107.054kDa. On the basis of sequence similarity as well as enzymatic activity, AmlC is likely to belong to the 1, 4-alpha-D-glucan glucanohydrolase family. amlC is transcribed as a unique 3kb leaderless monocistronic mRNA. Primer extension experiments allowed the identification of promoter sequences that do not resemble the typical eubacterial promoter sequences. amlC was successfully disrupted and was mapped at approx. 700kb from a chromosomal end of S. lividans TK24, 100kb on the right of the amplifiable unit AUD1 (Volff et al., 1996). Nevertheless, amlC disruption seemed to be accompanied by extensive rearrangements of the 2500-kb DraI-II fragment of the chromosome.
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Affiliation(s)
- X H Yin
- Laboratoire de Biologie et Génétique Moléculaire, Institut de Génétique et Microbiologie, CNRS URA D2225 Bâtiment 400, Université Paris-Sud, F-91405, Orsay, Cedex, France
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9
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Sumitani JI, Nagae H, Kawaguchi T, Arai M. Bacillus animal type α-amylase: Cloning and sequencing of the gene, and comparison of the deduced amino acid sequence with that of other amylases. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0922-338x(98)80088-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Janecek S. alpha-Amylase family: molecular biology and evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1997; 67:67-97. [PMID: 9401418 DOI: 10.1016/s0079-6107(97)00015-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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11
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Pujadas G, Ramírez FM, Valero R, Palau J. Evolution of beta-amylase: patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms. Proteins 1996; 25:456-72. [PMID: 8865341 DOI: 10.1002/prot.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Soybean and sweet potato beta-amylases are structured as alpha/beta barrels and the same kind of folding may account for all known beta-amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of beta-amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known beta-amylases. Our approach combines the identification of the putative eightfold structural core formed by beta-strands with a complete multi-alignment analysis of all known sequences. Comparing putative beta-amylase (alpha/beta)8 cores from plants and microorganisms, two differentiated versions of residues at the packing sites, and a unique set of eight identical residues at the C-terminal catalytical site are observed, indicating early evolutionary divergence and absence of localized three-dimensional evolution, respectively. A new analytical approach has been developed in order to work out conserved motifs for beta-amylases, mostly related with the enzyme activity. This approach appears useful as a new routine to find sets of motifs (each set being known as a fingerprint) in protein families. We demonstrate that the evolutionary mechanism for beta-amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and alpha-helix-containing loops.
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Affiliation(s)
- G Pujadas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Catalonia, Spain
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12
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Three chitinase genes (chiA, chiC and chiD) comprise the chitinase system of Bacillus circulans WL-12. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0922-338x(96)89450-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Abstract
Diverse functional roles of multifunctional proteins arise from either their independent functional domains or dual activities mediated through a single active site. Presence of multifunctional proteins significantly enhances the metabolic efficiency of a cell. Microorganisms utilising complex substrates with extensive microheterogeneities, such as carbohydrates evolved batteries of multifunctional glucanases, facilitating parsimonious utilisation of these substrates. Various attempts have since been made to artificially construct these glucanases. Analysis of information on various glucanases would be helpful in understanding the evolutionary interrelationship between this class of enzymes and will give an insight into the structural features controlling different unrelated activities. This review examines the genesis, evolution and structural features of multifunctional glucanases.
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Affiliation(s)
- N N Kumar
- Molecular Biology Research Laboratory, Department of Zoology, University of Pune, Pune-411 007, India
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Little E, Bork P, Doolittle RF. Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. J Mol Evol 1994; 39:631-43. [PMID: 7528812 DOI: 10.1007/bf00160409] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The evolutionary spread of 22 fibronectin type III (Fn3) sequences among a dozen bacterial enzymes has been traced by searching databases with the non-Fn3 parts of the enzyme sequences. Numerous homologues were found that lacked the Fn3 domains. In each case the related sequences were aligned, phylogenetic trees were constructed, and the occurrences of Fn3 units on the trees were noted. Comparison with phylogenetic trees prepared from the Fn3 segments themselves allowed inferences to be made about when the Fn3 units were shuffled into their present positions.
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Affiliation(s)
- E Little
- Center for Molecular Genetics, University of California, San Diego, La Jolla 92093-0634
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15
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Hofemeister B, König S, Hoang V, Engel J, Mayer G, Hansen G, Hofemeister J. The gene amyE(TV1) codes for a nonglucogenic alpha-amylase from Thermoactinomyces vulgaris 94-2A in Bacillus subtilis. Appl Environ Microbiol 1994; 60:3381-9. [PMID: 7944369 PMCID: PMC201813 DOI: 10.1128/aem.60.9.3381-3389.1994] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We isolated the gene amyE(TV1) from Thermoactinomyces vulgaris 94-2A encoding a nonglucogenic alpha-amylase (AmyTV1). A chromosomal DNA fragment of 2,247 bp contained an open reading frame of 483 codons, which was expressed in Escherichia coli and Bacillus subtilis. The deduced amino acid sequence of the AmyTV1 protein was confirmed by sequencing of several peptides derived from the enzyme isolated from a T. vulgaris 94-2A culture. The amino acid sequence was aligned with several known alpha-amylase sequences. We found 83% homology with the 48-kDa alpha-amylase part of the Bacillus polymyxa beta-alpha-amylase polyprotein and 50% homology with Taka amylase A of Aspergillus oryzae but only 45% homology with another T. vulgaris amylase (neopullulanase, TVA II) recently cloned from strain R-47. The putative promoter region was characterized with primer extension and deletion experiments and by expression studies with B. subtilis. Multiple promoter sites (P3, P2, and P1) were found; P1 alone drives about 1/10 of the AmyTV1 expression directed by the native tandem configuration P3P2P1. The expression levels in B. subtilis could be enhanced by fusion of the amyE(TV1) coding region to the promoter of the Bacillus amyloliquefaciens alpha-amylase gene.
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Affiliation(s)
- B Hofemeister
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
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Hansen G, Heese O, Höhne WE, Hofemeister B. alpha-Amylases from Thermoactinomyces vulgaris: characteristics, primary structure and structure prediction. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 44:245-52. [PMID: 7822101 DOI: 10.1111/j.1399-3011.1994.tb00167.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two amylolytic active protein fractions (named alpha-amylase 1 and alpha-amylase 2) were isolated from the bacterium Thermoactinomyces vulgaris strain 94-2A. alpha-Amylase 1 had a molecular mass of 51.6 kDa, whereas alpha-amylase 2 consists of two fragments which have molecular masses of 17.0 and 34.6 kDa, respectively. These two fragments are products from a proteolytic cleavage of alpha-amylase 1 at amino acid position 303 (tryptophan) by a serine protease (thermitase) which is also produced by T. vulgaris. The purified alpha-amylase 1 and 2 follow the Michaelis-Menten kinetics in the presence of starch as substrate with Km values of 1.37 +/- 0.07 and 1.29 +/- 0.18 mg/mL, respectively. In effect they differ in their stability characteristics. The amino acid sequence of alpha-amylase from T. vulgaris derived from DNA sequence (1) was compared with those of other alpha-amylases. It reveals high homologies to alpha-amylases from other microorganisms (e.g. B. polymyxa, A. oryzae, S. occidentalis and S. fibuligera). A three-dimensional structure model for alpha-amylase 1 on the basis of the 3 A X-ray structure of Taka-amylase was constructed.
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Affiliation(s)
- G Hansen
- Institute for Biochemistry, Charité University Clinic, Humboldt University of Berlin, Germany
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17
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Matsui I, Yoneda S, Ishikawa K, Miyairi S, Fukui S, Umeyama H, Honda K. Roles of the aromatic residues conserved in the active center of Saccharomycopsis alpha-amylase for transglycosylation and hydrolysis activity. Biochemistry 1994; 33:451-8. [PMID: 8286375 DOI: 10.1021/bi00168a009] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The molecular structure of Saccharomycopsis fibuligera alpha-amylase was predicted by a homology-based modeling technique, and the amino acid residues composing the active site were displayed with color codes according to their order of conservation. We noticed two highly conserved aromatic residues located in the active center, tyrosine 83 (Y83) and tryptophan 84 (W84), and examined their roles in catalytic activity by site-directed mutagenesis. The W, leucine (L), and asparagine (N) mutants at Y83 and the L mutant at W84 showed remarkable enhancement of transglycosylation activity and complementary decreases in native hydrolysis activity. The phenylalanine (F) mutant at Y83 and the F and Y mutants at W84 only decreased hydrolysis activity. Mechanistic and kinetic studies of these mutants using a reducing-end-blocked substrate and a hydrolysis-specific substrate revealed a probable transglycosylation mechanism and critical contributions of the 83rd and 84th aromatic residues to efficient hydrolysis. Given that aromatic residues stack against the faces of sugars, we assumed that Y83 and, presumably, W84 play roles in the binding of oligosaccharide substrates through the stacking interaction and in the indirect fixation of the catalytic water molecule through hydrogen bonding with the hydroxyl of the bound substrates. Mutations to nonaromatic residues could cause slight changes in the binding topology of substrates to favor transglycosylation over hydrolysis.
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Affiliation(s)
- I Matsui
- National Institute of Bioscience and Human-Technology, Ibaraki, Japan
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18
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Affiliation(s)
- N Uozumi
- Department of Biotechnology, Faculty of Engineering, Nagoya University, Japan
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19
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UOZUMI NOBUYUKI. Functional Roles of Active Site Residues of Bacillus polymyxa ?-Amylase. Ann N Y Acad Sci 1992. [DOI: 10.1111/j.1749-6632.1992.tb35598.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Abstract
Polyproteins have been found only recently in prokaryotes. The four known examples of single bacterial genes encoding precursors that are posttranslationally processed into two mature proteins are addressed here with respect to (i) their genomic arrangement, (ii) the sites of proteolytic processing, (iii) the relevant proteases, (iv) their maturation pathway, and (v) the function of the mature proteins. How these polyproteins may have evolved is also discussed.
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Affiliation(s)
- L Thöny-Meyer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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21
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Romaguera A, Menge U, Breves R, Diekmann H. Chitinases of Streptomyces olivaceoviridis and significance of processing for multiplicity. J Bacteriol 1992; 174:3450-4. [PMID: 1592803 PMCID: PMC206026 DOI: 10.1128/jb.174.11.3450-3454.1992] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Five extracellular chitinases of 20.5, 30, 47, 70, and 92 kDa purified from the culture filtrate of Streptomyces olivaceoviridis ATCC 11238 differed in their sequences at the amino termini of the protein chains. In the native state, the chitinases were found to be resistant to proteolysis by trypsin, papain, and Staphylococcus aureus V8 protease. The latter produced several fragments of identical molecular mass from chitinases denaturated with sodium dodecyl sulfate. Five proteases were detected in the protein concentrate from the culture filtrate, and two of them showing ability to cleave chitinases in the native state were purified. One, a protease of 42 kDa, released a 30-kDa protein from the 70-kDa chitinase that reacts with anti-30 kDa chitinase antibodies; the other, a protease of 29 kDa, split the 30-kDa chitinase into 20.5-, 18-, and 16-kDa fragments. From these results, it was deduced that the 70-kDa chitinase is the precursor protein of the 30- and 20.5-kDa chitinases.
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Affiliation(s)
- A Romaguera
- Institut für Mikrobiologie, Universität Hannover, Germany
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22
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Sudhakaran V, Deshpande B, Ambedkar S, Shewale J. Molecular aspects of penicillin and cephalosporin acylases. Process Biochem 1992. [DOI: 10.1016/0032-9592(92)87001-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Schneider E, Freundlieb S, Tapio S, Boos W. Molecular characterization of the MalT-dependent periplasmic alpha-amylase of Escherichia coli encoded by malS. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42743-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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24
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Simul taneous production of alpha and beta amylases byBacillus subtilis MIR-5 in batch and continuous culture. Biotechnol Lett 1992. [DOI: 10.1007/bf01030913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Jespersen HM, MacGregor EA, Sierks MR, Svensson B. Comparison of the domain-level organization of starch hydrolases and related enzymes. Biochem J 1991; 280 ( Pt 1):51-5. [PMID: 1741756 PMCID: PMC1130598 DOI: 10.1042/bj2800051] [Citation(s) in RCA: 142] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Structure-prediction and hydrophobic-cluster analysis of several starch hydrolases and related enzymes indicated the organization of eleven domain types. Most enzymes possess a catalytic (beta/alpha)8-barrel and a smaller C-terminal domain as seen in crystal structures of alpha-amylase and cyclodextrin glucanotransferase. Some also have a starch-granule-binding domain. Enzymes breaking or forming endo-alpha-1,6 linkages contain domains N-terminal to the (beta/alpha)8-barrel.
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Affiliation(s)
- H M Jespersen
- Department of Chemistry, Carlsberg Laboratory, Copenhagen Valby, Denmark
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26
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Takekawa S, Uozumi N, Tsukagoshi N, Udaka S. Proteases involved in generation of beta- and alpha-amylases from a large amylase precursor in Bacillus polymyxa. J Bacteriol 1991; 173:6820-5. [PMID: 1834632 PMCID: PMC209033 DOI: 10.1128/jb.173.21.6820-6825.1991] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genes for extracellular neutral protease (Npr) and intracellular serine protease (Isp) were cloned from Bacillus polymyxa in order to elucidate the process involved in the generation of multiple beta-amylases and an alpha-amylase from a large amylase precursor. The npr gene was composed of 1,770 bp and 570 amino acids, while the isp gene was composed of 978 bp and 326 amino acids. Both proteases produced by E. coli cleaved the amylase precursor to generate beta- and alpha-amylases. Furthermore, several other proteases produced the same products from the precursor. A 130-kDa amylase precursor has two large domain structures responsible for the generation of beta- and alpha-amylases. The junction region of approximately 200 amino acids may be exposed on the surface of the molecule and susceptible to proteolytic enzymes, which results in the formation of multiple amylases.
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Affiliation(s)
- S Takekawa
- Department of Food Science and Technology, Faculty of Agriculture, Nagoya University, Japan
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27
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Rumbak E, Rawlings DE, Lindsey GG, Woods DR. Cloning, nucleotide sequence, and enzymatic characterization of an alpha-amylase from the ruminal bacterium Butyrivibrio fibrisolvens H17c. J Bacteriol 1991; 173:4203-11. [PMID: 2061294 PMCID: PMC208071 DOI: 10.1128/jb.173.13.4203-4211.1991] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A Butyrivibrio fibrisolvens amylase gene was cloned and expressed by using its own promoter on the recombinant plasmid pBAMY100 in Escherichia coli. The amylase gene consisted of an open reading frame of 2,931 bp encoding a protein of 976 amino acids with a calculated Mr of 106,964. In E. coli(pBAMY100), more than 86% of the active amylase was located in the periplasm, and TnphoA fusion experiments showed that the enzyme had a functional signal peptide. The B. fibrisolvens amylase is a calcium metalloenzyme, and three conserved putative calcium-binding residues were identified. The amylase showed high sequence homology with other alpha-amylases in the three highly conserved regions which constitute the active centers. These and other conserved regions were located in the N-terminal half, and no similarity with any other amylase was detected in the remainder of the protein. Deletion of approximately 40% of the C-terminal portion of the amylase did not result in loss of amylolytic activity. The B. fibrisolvens amylase was identified as an endo-alpha-amylase by hydrolysis of the Phadebas amylase substrate, hydrolysis of gamma-cyclodextrin to maltotriose, maltose, and glucose and the characteristic shape of the blue value and reducing sugar curves. Maltotriose was the major initial hydrolysis product from starch, although extended incubation resulted in its hydrolysis to maltose and glucose.
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Affiliation(s)
- E Rumbak
- Department of Microbiology, University of Cape Town, South Africa
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28
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Thöny-Meyer L, James P, Hennecke H. From one gene to two proteins: the biogenesis of cytochromes b and c1 in Bradyrhizobium japonicum. Proc Natl Acad Sci U S A 1991; 88:5001-5. [PMID: 1647023 PMCID: PMC51795 DOI: 10.1073/pnas.88.11.5001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genes coding for polyproteins that are cleaved posttranslationally into two or more functional proteins are rarely found in prokaryotes. One example concerns the biogenesis of the Bradyrhizobium japonicum cytochromes b and c1, two of the three constituent subunits of ubiquinol-cytochrome-c reductase (ubiquinol:ferricytochrome-c oxidoreductase, EC 1.10.2.2); the respective apoproteins for these subunits are encoded by the 5' and 3' halves of a single gene, fbcH. These two halves are linked by an extra piece of DNA encoding a characteristic signal peptide for protein translocation across the cytoplasmic membrane. Processing of the fbcH gene product is shown to occur at a typical signal peptidase recognition site. This reaction is reminiscent of that catalyzed by the regular bacterial signal peptidase that normally cleaves off presequences from the N termini of translocated proteins. Mutational alteration of the signal peptidase recognition site within FbcH results in the appearance of an uncleaved bc1 fusion protein in the membrane. Additionally, a functional heme-binding site in the apocytochrome c1 section of FbcH is shown to be a necessary prerequisite for the formation of the bc1 complex.
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Affiliation(s)
- L Thöny-Meyer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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29
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Garcia-Gonzalez MD, Martin JF, Vigal T, Liras P. Characterization, expression in Streptomyces lividans, and processing of the amylase of Streptomyces griseus IMRU 3570: two different amylases are derived from the same gene by an intracellular processing mechanism. J Bacteriol 1991; 173:2451-8. [PMID: 1707411 PMCID: PMC207807 DOI: 10.1128/jb.173.8.2451-2458.1991] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Extracellular amylase in Streptomyces lividans was undetectable in starch-supplemented medium. However, S. lividans produced fivefold-higher levels of amylase than Streptomyces griseus IMRU 3570 when transformed with the S. griseus amy gene. Two major proteins of 57 and 50 kDa with amylase activity accumulated in the culture broths of the donor S. griseus and S. lividans transformed with the amy gene. Both proteins were also present in protoplast lysates in the same relative proportion; they gave a positive reaction with antibodies against the 57-kDa amylase. They did not differ in substrate specificity or enzyme kinetics. The two amylases were purified to homogeneity by a two-step procedure. Both proteins showed the same amino-terminal sequence of amino acids, suggesting that both proteins are derived from the same gene. The deduced signal peptide has 28 amino acids with two positively charged arginines near the amino-terminal end. When an internal NcoI fragment was removed from the amy gene, the resulting S. lividans transformants did not synthesize any of the two amylase proteins and showed no reaction in immunoblotting. Formation of the 50-kDa protein was observed when pure 57-kDa amylase was treated with supernatants of protoplast lysates but not when it was treated with membrane preparations, indicating that the native 57-kDa amylase could be processed intracellularly.
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Affiliation(s)
- M D Garcia-Gonzalez
- Department of Ecology, Genetics and Microbiology, Faculty of Biology, University of León, Spain
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30
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Sizmann D, Keilmann C, Böck A. Primary structure requirements for the maturation in vivo of penicillin acylase from Escherichia coli ATCC 11105. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 192:143-51. [PMID: 2205499 DOI: 10.1111/j.1432-1033.1990.tb19207.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The two constituent subunits of the enzyme penicillin acylase from Escherichia coli strain ATCC 11105 are derived from a single precursor polypeptide by post-translational processing. Mutant penicillin acylase precursors were constructed carrying insertions and deletions in various domains and they were analysed for their processing behaviour. It was found that an endopeptide region of appropriate size and an intact C-terminus were absolutely necessary for the maturation process. Internal deletions within the beta-subunit domain also prevented post-translational cleavage. Processing competence, therefore, was not merely determined by the amino acid sequence in the vicinity of the processing sites but relied on a correct overall conformation of the protein. The processing pathway in vivo proceeds via an intermediate comprising the alpha subunits plus endopeptide and is thus identical to the pathway which has been determined previously by in vitro analysis. The post-translational modification of the precursor is probably not carried out by a specific processing enzyme(s) as the heterologous expression of the penicillin acylase (pac) structural gene yielded processed and active enzyme in different enterobacteria and in a Pseudomonas species.
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Affiliation(s)
- D Sizmann
- Lehrstuhl für Mikrobiologie, Universität München, Federal Republic of Germany
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31
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Weickert MJ, Chambliss GH. Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilis. Proc Natl Acad Sci U S A 1990; 87:6238-42. [PMID: 2117276 PMCID: PMC54508 DOI: 10.1073/pnas.87.16.6238] [Citation(s) in RCA: 224] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Catabolite repression of the Bacillus subtilis alpha-amylase gene (amyE) involves an operator sequence located just downstream of the promoter (amyR), overlapping the transcription start site. Oligonucleotide site-directed mutagenesis of this sequence identified bases required for catabolite repression. Two mutations increased both the 2-fold symmetry of the operator and the repression ratio. Although many mutations reduced the repression ratio 3- to 11-fold, some also caused a 2-fold or greater increase in amylase production. Others caused hyperproduction without affecting catabolite repression. Homologous sequences in other catabolite-repressed B. subtilis promoters suggest a common regulatory site may be involved in catabolite repression.
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Affiliation(s)
- M J Weickert
- Department of Genetics, University of Wisconsin, Madison 53706
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32
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Candussio A, Schmid G, Böck A. Biochemical and genetic analysis of a maltopentaose-producing amylase from an alkaliphilic gram-positive bacterium. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 191:177-85. [PMID: 1696201 DOI: 10.1111/j.1432-1033.1990.tb19108.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Two amylases have been purified from the culture fluid of an alkaliphilic bacterium. Amylase A-60 consists of a single type of polypeptide chain of 60 kDa and exhibits an alpha-amylase-type of starch cleavage. Amylase A-180 is approximately 180 kDa in size, represents the largest exoenzyme so far identified in prokaryotes and in the initial enzyme reaction cleaves starch exclusively to maltopentaose. A-60 and A-180 are immunologically unrelated enzymes. The structural gene for amylase A-180 has been cloned and its nucleotide sequence was determined. An open reading frame was identified for a putative protein of 182 kDa whose amino-terminal sequence, deduced from the nucleotide sequence, was identical in 23 out of 25 positions to that determined for the protein. The amino-terminus of the mature protein, at the gene level, is preceded by a sequence segment showing all the characteristics of a signal peptide from Gram-positive bacteria. Analysis of the deduced amino acid sequence revealed that the 70-kDa N-terminal part is similar to classical alpha-amylases. The C-terminal part contains three repeated sequence blocks of 99 amino acid residues each which are also present in two bacterial beta-amylases. It appears, therefore, that A-180 has arisen by gene fusion events.
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Affiliation(s)
- A Candussio
- Lehrstuhl für Mikrobiologie der Universität München, Federal Republic of Germany
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33
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Udaka S, Tsukagoshi N, Yamagata H. Bacillus brevis, a host bacterium for efficient extracellular production of useful proteins. Biotechnol Genet Eng Rev 1989; 7:113-46. [PMID: 2696470 DOI: 10.1080/02648725.1989.10647857] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- S Udaka
- Faculty of Agriculture, Nagoya University, Japan
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