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Dhagat U, Endo S, Mamiya H, Hara A, El-Kabbani O. Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:198-204. [PMID: 20124700 DOI: 10.1107/s0907444909051464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Accepted: 11/29/2009] [Indexed: 11/10/2022]
Abstract
Mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) is the only aldo-keto reductase that catalyzes the stereospecific reduction of 3- and 17-ketosteroids to the corresponding 3(17)alpha-hydroxysteroids. The Y224D mutation of AKR1C21 reduced the K(m) value for NADP(H) by up to 80-fold and completely reversed the 17alpha stereospecificity of the enzyme. The crystal structure of the Y224D mutant at 2.3 A resolution revealed that the mutation resulted in a change in the conformation of the flexible loop B, including the V-shaped groove, which is a unique feature of the active-site architecture of wild-type AKR1C21 and is formed by the side chains of Tyr224 and Trp227. Furthermore, mutations (Y224F and Q222N) of residues involved in forming the safety belt for binding of the coenzyme showed similar alterations in kinetic constants for 3alpha-hydroxy/3-ketosteroids and 17-hydroxy/ketosteroids compared with the wild type.
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Affiliation(s)
- Urmi Dhagat
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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2
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Ramasubbu N, Ragunath C, Mishra PJ, Thomas LM, Gyémánt G, Kandra L. Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity. ACTA ACUST UNITED AC 2004; 271:2517-29. [PMID: 15182367 DOI: 10.1111/j.1432-1033.2004.04182.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nonreducing end of the substrate-binding site of human salivary alpha-amylase contains two residues Trp58 and Trp59, which belong to beta2-alpha2 loop of the catalytic (beta/alpha)(8) barrel. While Trp59 stacks onto the substrate, the exact role of Trp58 is unknown. To investigate its role in enzyme activity the residue Trp58 was mutated to Ala, Leu or Tyr. Kinetic analysis of the wild-type and mutant enzymes was carried out with starch and oligosaccharides as substrates. All three mutants exhibited a reduction in specific activity (150-180-fold lower than the wild type) with starch as substrate. With oligosaccharides as substrates, a reduction in k(cat), an increase in K(m) and distinct differences in the cleavage pattern were observed for the mutants W58A and W58L compared with the wild type. Glucose was the smallest product generated by these two mutants in the hydrolysis oligosaccharides; in contrast, wild-type enzyme generated maltose as the smallest product. The production of glucose by W58L was confirmed from both reducing and nonreducing ends of CNP-labeled oligosaccharide substrates. The mutant W58L exhibited lower binding affinity at subsites -2, -3 and +2 and showed an increase in transglycosylation activity compared with the wild type. The lowered affinity at subsites -2 and -3 due to the mutation was also inferred from the electron density at these subsites in the structure of W58A in complex with acarbose-derived pseudooligosaccharide. Collectively, these results suggest that the residue Trp58 plays a critical role in substrate binding and hydrolytic activity of human salivary alpha-amylase.
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Affiliation(s)
- Narayanan Ramasubbu
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA.
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3
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Nichols BL, Avery S, Sen P, Swallow DM, Hahn D, Sterchi E. The maltase-glucoamylase gene: common ancestry to sucrase-isomaltase with complementary starch digestion activities. Proc Natl Acad Sci U S A 2003; 100:1432-7. [PMID: 12547908 PMCID: PMC298790 DOI: 10.1073/pnas.0237170100] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Brush-border maltase-glucoamylase (MGA) activity serves as the final step of small intestinal digestion of linear regions of dietary starch to glucose. Brush-border sucrase-isomaltase (SI) activity is complementary, through digestion of branched starch linkages. Here we report the cloning and sequencing of human MGA gene and demonstrate its close evolutionary relationship to SI. The gene is approximately 82,000 bp long and located at chromosome 7q34. Forty-eight exons were identified. The 5' gene product, when expressed as the N-terminal protein sequence, hydrolyzes maltose and starch, but not sucrose, and is thus distinct from SI. The catalytic residue was identified by mutation of an aspartic acid and was found to be identical with that described for SI. The exon structures of MGA and SI were identical. This homology of genomic structure is even more impressive than the previously reported 59% amino acid sequence identity. The shared exon structures and peptide domains, including proton donors, suggest that MGA and SI evolved by duplication of an ancestral gene, which itself had already undergone tandem gene duplication. The complementary human enzyme activities allow digestion of the starches of plant origin that make up two-thirds of most diets.
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Affiliation(s)
- Buford L Nichols
- U.S. Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030-2600, USA.
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4
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Zarembinski TI, Kim Y, Peterson K, Christendat D, Dharamsi A, Arrowsmith CH, Edwards AM, Joachimiak A. Deep trefoil knot implicated in RNA binding found in an archaebacterial protein. Proteins 2003; 50:177-83. [PMID: 12486711 PMCID: PMC2792022 DOI: 10.1002/prot.10311] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas I. Zarembinski
- Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois
| | - Youngchang Kim
- Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois
| | - Kelly Peterson
- Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois
| | - Dinesh Christendat
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Akil Dharamsi
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H. Arrowsmith
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aled M. Edwards
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Andrzej Joachimiak
- Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois
- Correspondence to Andrzej Joachimiak, Biosciences Division, Structural Biology Center, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439.
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Uitdehaag JC, Dijkstra BW, Dijkhuizen L. Engineering of cyclodextrin glycosyltransferase reaction and product specificity. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1543:336-360. [PMID: 11150613 DOI: 10.1016/s0167-4838(00)00233-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Nielsen JE, Borchert TV. Protein engineering of bacterial alpha-amylases. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1543:253-274. [PMID: 11150610 DOI: 10.1016/s0167-4838(00)00240-5] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
alpha-Amylases constitute a very diverse family of glycosyl hydrolases that cleave alpha1-->4 linkages in amylose and related polymers. Recent structural and mutagenic studies of archeael, mammalian and bacterial alpha-amylases have resulted in a wealth of information on the catalytic mechanism and on the structural features of this enzyme class. Because of their high thermo-stability, the Bacillus alpha-amylases have found widespread use in industrial processes, and much attention has been devoted to optimising these enzymes for the very harsh conditions encountered there. Stability has been a major area of focus in this respect, and several remarkably stable bacterial alpha-amylases have been produced by bioengineering techniques. Protein engineering studies of pH-activity profiles and of substrate specificities have also been initiated, although without much success. In the coming years it is likely, however, that the focus of alpha-amylase engineering will shift from engineering stability to these new areas.
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Affiliation(s)
- J E Nielsen
- EMBL, Meyerhofstrasse 1, 69117 Heidelber, Germany
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Copley RR, Bork P. Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. J Mol Biol 2000; 303:627-41. [PMID: 11054297 DOI: 10.1006/jmbi.2000.4152] [Citation(s) in RCA: 163] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We provide statistically reliable sequence evidence indicating that at least 12 of 23 SCOP (betaalpha)(8) (TIM) barrel superfamilies share a common origin. This includes all but one of the known and predicted TIM barrels found in central metabolism. The statistical evidence is complemented by an examination of the details of protein structure, with certain structural locations favouring catalytic residues even though the nature of their molecular function may change. The combined analysis of sequence, structure and function also enables us to propose a phylogeny of TIM barrels. Based on these data, we are able to examine differing theories of pathway and enzyme evolution, by mapping known TIM barrel folds to the pathways of central metabolism. The results favour widespread recruitment of enzymes between pathways, rather than a "backwards evolution" model, and support the idea that modern proteins may have arisen from common ancestors that bound key metabolites.
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Affiliation(s)
- R R Copley
- Biocomputing, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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Souchet M, Legave M, Jullian N, Bertrand HO, Bril A, Berrebi-Bertrand I. Structure of the human glycogen-associated protein phosphatase 1 regulatory subunit hGM: homology modeling revealed an (alpha/beta)8-barrel-like fold in the multidomain protein. Protein Sci 1999; 8:2570-9. [PMID: 10631972 PMCID: PMC2144220 DOI: 10.1110/ps.8.12.2570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Protein phosphatase 1 (PP1) is widely distributed among tissues and species and acts as a regulator of many important cellular processes. By targeting the catalytic part of PP1 (PP1C) toward particular loci and substrates, regulatory subunits constitute key elements conferring specificity to the holoenzyme. Here, we report the identification of an (alpha/beta)8-barrel-like structure within the N-ter stretch of the human PP1 regulatory subunit hGM, which is part of the family of diverse proteins associated with glycogen metabolism. Protein homology modeling gave rise to a three-dimensional (3D) model for the 381 N-ter residue stretch of hGM, based on sequence similarity with Streptomyces olivochromogenes xylose isomerase, identified by using FASTA. The alignment was subsequently extended by using hydrophobic cluster analysis. The homology-derived model includes the putative glycogen binding area located within the 142-230 domain of hGM as well as a structural characterization of the PP1C interacting domain (segment 51-67). Refinement of the latter by molecular dynamics afforded a topology that is in agreement with previous X-ray studies (Egloff et al., 1997). Finite difference Poisson-Boltzmann calculations performed on the interacting domains of PP1C and hGM confirm the complementarity of the local electrostatic potentials of the two partners. This work highlights the presence of a conserved fold among distant species (mammalian, Caenorhabditis elegans, yeast) and, thus, emphasizes the involvement of PP1 in crucial basic cellular functions.
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Affiliation(s)
- M Souchet
- SmithKline-Beecham Laboratoires Pharmaceutiques, Saint Grégoire, France.
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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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10
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Devulapalle KS, Goodman SD, Gao Q, Hemsley A, Mooser G. Knowledge-based model of a glucosyltransferase from the oral bacterial group of mutans streptococci. Protein Sci 1997; 6:2489-93. [PMID: 9416598 PMCID: PMC2143619 DOI: 10.1002/pro.5560061201] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mutans streptococci glucosyltransferases catalyze glucosyl transfer from sucrose to a glucan chain. We previously identified an aspartyl residue that participates in stabilizing the glucosyl transition state. The sequence surrounding the aspartate was found to have substantial sequence similarity with members of alpha-amylase family. Because little is known of the protein structure beyond the amino acid sequence, we used a knowledge-based interactive algorithm, MACAW, which provided significant level of homology with alpha-amylases and glucosyltransferase from Streptococcus downei gtfI (GTF). The significance of GTF similarity is underlined by GTF/alpha-amylase residues conserved in all but one alpha-amylase invariant residues. Site-directed mutagenesis of the three GTF catalytic residues are homologous with the alpha-amylase catalytic triad. The glucosyltransferases are members of the 4/7-superfamily that have a (beta/alpha)8-barrel structure and belong to family 13 of the glycohydralases.
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Affiliation(s)
- K S Devulapalle
- Department of Basic Sciences, School of Dentistry, University of Southern California, Los Angeles 90089-0641, USA
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Janecek S. Sequence similarity between xylose isomerase and replicase: another TIM-barrel in the replicase structure? Int J Biol Macromol 1997; 21:277-80. [PMID: 9352374 DOI: 10.1016/s0141-8130(97)00067-6] [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] [Indexed: 02/05/2023]
Abstract
The BLAST search using the strand beta 2 (46_GAHGVTFHDDDLIP) of the (alpha/beta)8-barrel of xylose isomerase from Streptomyces olivochromogenes resulted in retrieving the sequentially similar segment of replicase from garlic latent virus (692_GGHGIGFHRDD). The detailed analysis of the entire amino acid sequences of both xylose isomerase and replicase suggested that the polypeptide segment 644-1046 of replicase (the entire length of this enzyme is 1924 residues) could share the structure of xylose isomerase (20.7% identity using the entire sequence of xylose isomerase). The relatedness of replicase and xylose isomerase is supported by the fact that the sequence similarity can be observed along the whole sequence of xylose isomerase (386 amino acid residues). The sequence of replicase exhibits moreover the similarity with that of lycopene cyclase, an enzyme implicated in the beta-carotene biosynthesis, that was previously found to share similarity with xylose isomerase. Thus the relevant segment of replicase is predicted to adopt an (alpha/beta)8-barrel topology similar to that of xylose isomerase.
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Affiliation(s)
- S Janecek
- Institute of Microbiology, Slovak Academy of Sciences, Bratislava, Slovak Republic.
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12
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Jez JM, Bennett MJ, Schlegel BP, Lewis M, Penning TM. Comparative anatomy of the aldo-keto reductase superfamily. Biochem J 1997; 326 ( Pt 3):625-36. [PMID: 9307009 PMCID: PMC1218714 DOI: 10.1042/bj3260625] [Citation(s) in RCA: 452] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The aldo-keto reductases metabolize a wide range of substrates and are potential drug targets. This protein superfamily includes aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases and dihydrodiol dehydrogenases. By combining multiple sequence alignments with known three-dimensional structures and the results of site-directed mutagenesis studies, we have developed a structure/function analysis of this superfamily. Our studies suggest that the (alpha/beta)8-barrel fold provides a common scaffold for an NAD(P)(H)-dependent catalytic activity, with substrate specificity determined by variation of loops on the C-terminal side of the barrel. All the aldo-keto reductases are dependent on nicotinamide cofactors for catalysis and retain a similar cofactor binding site, even among proteins with less than 30% amino acid sequence identity. Likewise, the aldo-keto reductase active site is highly conserved. However, our alignments indicate that variation ofa single residue in the active site may alter the reaction mechanism from carbonyl oxidoreduction to carbon-carbon double-bond reduction, as in the 3-oxo-5beta-steroid 4-dehydrogenases (Delta4-3-ketosteroid 5beta-reductases) of the superfamily. Comparison of the proposed substrate binding pocket suggests residues 54 and 118, near the active site, as possible discriminators between sugar and steroid substrates. In addition, sequence alignment and subsequent homology modelling of mouse liver 17beta-hydroxysteroid dehydrogenase and rat ovary 20alpha-hydroxysteroid dehydrogenase indicate that three loops on the C-terminal side of the barrel play potential roles in determining the positional and stereo-specificity of the hydroxysteroid dehydrogenases. Finally, we propose that the aldo-keto reductase superfamily may represent an example of divergent evolution from an ancestral multifunctional oxidoreductase and an example of convergent evolution to the same active-site constellation as the short-chain dehydrogenase/reductase superfamily.
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Affiliation(s)
- J M Jez
- Department of Biochemistry & Biophysics, University of Pennsylvania Medical School, 3620Hamilton Walk, Philadelphia, PA 19104, USA
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