User:Mario Murakami

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families GH1 [1, 2, 3, 4, 5, 6], GH2 [7], GH5 [8, 9, 10, 11, 12, 13], GH7 [14], GH8 [15], GH10 [16, 17, 18], GH11 [19, 20, 21], GH12 [22, 23], GH16 [24, 25, 26], GH26 [27], GH39 [28, 29], GH42 [30], GH43 [31, 32, 33], GH45 [34], GH51 [35, 36], GH54 [37], GH57 [38], GH128 [39] and AA9 [40]. Recently, his group rationally engineered a publicly available strain (Trichoderma reesei RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess [41].

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family [39], the development of a cellulase hyper-secreting strain [41], the molecular basis for Man-β-1,4-GlcNAc [13] and xyloglucan [11] specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase [11], the mechanistic understanding and rational design of rumen metagenome GH43 arabinanases [31] and the structural determinants for glucose tolerance in GH1 beta-glucosidases [1].

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Solved structures

GH128

PDB ID 6UAQ - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

PDB ID 6UAS - GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

PDB ID 6UAR - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei in complex with laminaritriose

PDB ID 6UAU - Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaritriose and laminaribiose

PDB ID 6UAT - GH128 (subgroup I) endo-beta-1,3-glucanase (E102A mutant) from Amycolatopsis mediterranei in complex with laminaripentaose

PDB ID 6UFZ - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei

PDB ID 6UFL - GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei in the complex with laminarihexaose

PDB ID 6UAW - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava in complex with laminaritriose

PDB ID 6UAV - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

PDB ID 6UAX - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

PDB ID 6UB0 - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -2 and -1 subsites

PDB ID 6UNV - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with glucose

PDB ID 6UAY - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii

PDB ID 6UB1 - GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii in complex with laminaribiose at -3 and -2 subsites

PDB ID 6UB4 - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritriose (C2 form)

PDB ID 6UB3 - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes with laminaribiose at the surface-binding site

PDB ID 6UB6 - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes in complex with laminaritetraose

PDB ID 6UB5 - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose (P21 form)

PDB ID 6UB2 - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

PDB ID 6UBB - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae with laminaribiose at the surface-binding site

PDB ID 6UB7 - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

PDB ID 6UBA - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae in complex with laminaritriose

PDB ID 6UB8 - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

PDB ID 6UBD - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

PDB ID 6UBC - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

GH5 PDB ID 6MP2 - GH5 BlMan5B solved by SIRAS

PDB ID 6MP7 - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

PDB ID 6MPA - BlMan5B in complex with GlcNAc (soaking)

PDB ID 6MPC - E257A mutant of BlMan5B

PDB ID 6MOY - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

PDB ID 5HNN - GH5 endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg

PDB ID 5HOS – GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

PDB ID 5HPC – GH5 XacCel5A crystallized in the space group P41212

PDB ID 4W7U – GH5 XacCel5A in the native form

PDB ID 4W7V - GH5 XacCel5A in complex with cellobiose

PDB ID 4W7W – GH5 XacCel5A in complex with cellopentaose

PDB ID 4W84 - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in the native form

PDB ID 4W8A - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in the native form

PDB ID 4W8B - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in complex with XXLG

PDB ID 4W85 - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose

PDB ID 4W86 - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose and TRIS

PDB ID 4W87 - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library, in complex with a xyloglucan oligosaccharide

PDB ID 4W88 - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with a xyloglucan oligosaccharide and TRIS

PDB ID 4W89 - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from metagenomic library in complex with cellotriose

PDB ID 4M1R GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

PDB ID 3PZ9 - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1

PDB ID 3PZM - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with three glycerol molecules

PDB ID 3PZO - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with three maltose molecules

PDB ID 3PZQ - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with maltose and glycerol

PDB ID 3PZG - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (I222 crystal form)

PDB ID 3PZI - GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with beta-D-glucose

PDB ID 3PZU – GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

PDB ID 3PZV – GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (C2 crystal form)

PDB ID 3PZT – GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 with manganese(II) ion

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References

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3. Santos CA, Zanphorlin LM, Crucello A, Tonoli CCC, Ruller R, Horta MAC, Murakami MT, and de Souza AP. (2016). Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. Biotechnol Biofuels. 2016;9:71. DOI:10.1186/s13068-016-0487-0 |
6. Santos CA, Morais MAB, Terrett OM, Lyczakowski JJ, Zanphorlin LM, Ferreira-Filho JA, Tonoli CCC, Murakami MT, Dupree P, and Souza AP. (2019). An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials. Sci Rep. 2019;9(1):4903. DOI:10.1038/s41598-019-41300-3 |
30. Godoy AS, Camilo CM, Kadowaki MA, Muniz HD, Espirito Santo M, Murakami MT, Nascimento AS, and Polikarpov I. (2016). Crystal structure of β1→6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose. FEBS J. 2016;283(22):4097-4112. DOI:10.1111/febs.13908 |
39. Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, and Murakami MT. (2020). Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol. 2020;16(8):920-929. DOI:10.1038/s41589-020-0554-5 |