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 coagulation cascade and mechanochemical 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 structural and functional 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, 24], GH16 [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 AA10 [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 elucidation of 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 [18], the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases [31] and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases [1, 6].

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Solved structures

GH128

PDB ID 6UAQ - Subgroup I endo-beta-1,3-glucanase from Amycolatopsis mediterranei (AmGH128_I)

PDB ID 6UAR - AmGH128_I in complex with laminaritriose

PDB ID 6UAS - AmGH128_I in complex with laminaripentaose

PDB ID 6UAU - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose

PDB ID 6UAT - AmGH128_I, E102A mutant, in complex with laminaripentaose

PDB ID 6UFZ - AmGH128_I, E199Q mutant

PDB ID 6UFL - AmGH128_I, E199Q mutant, in the complex with laminarihexaose

PDB ID 6UAV - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II)

PDB ID 6UAW - PvGH128_II in complex with laminaritriose

PDB ID 6UAX - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from Sorangium cellulosum (ScGH128_II)

PDB ID 6UAY - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii (BgGH128_III)

PDB ID 6UNV - BgGH128_III in complex with glucose

PDB ID 6UB0 - BgGH128_III in complex with laminaribiose at -2 and -1 subsites

PDB ID 6UB1 - BgGH128_III in complex with laminaribiose at -3 and -2 subsides

PDB ID 6UB2 - Subgroup IV atypical endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV)

PDB ID 6UB4 - LeGH128_IV in complex with laminaritriose (C2 crystal form)

PDB ID 6UB5 - LeGH128_IV in complex with laminaritriose (P21 crystal form)

PDB ID 6UB6 - LeGH128_IV in complex with laminaritetraose

PDB ID 6UB3 - LeGH128_IV with laminaribiose at the surface-binding site

PDB ID 6UB7 - Subgroup V glucose-releasing exo-beta-1,3-glucanase from Cryptococcus neoformans (CnGH128_V)

PDB ID 6UB8 - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI)

PDB ID 6UBA - AnGH128_VI in complex with laminaritriose

PDB ID 6UBB - AnGH128_VI with laminaribiose at the surface-binding site

PDB ID 6UBD - Subgroup VII oligosaccharide-binding protein from Trichoderma gamsii (TgGH128_VII)

PDB ID 6UBC - Subgroup VII oligosaccharide-binding protein from Cryptococcus neoformans (CnGH128_VII)

GH5

PDB ID 6MP2 - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from Bifidobacterium longum

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

PDB ID 6MPC - BlMan5B, E257A mutant

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

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

PDB ID 4W7U - Xac0030, a GH5 endo-beta-1,4-glucanase from Xanthomonas axonopodis pv. citri

PDB ID 4W7V - Xac0030 in complex with cellobiose

PDB ID 4W7W - Xac0030 in complex with cellopentaose

PDB ID 5HNN - Xac0030, triple mutation H174W, Y211A and K227R

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

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

PDB ID 4W85 - XEG5A in complex with glucose

PDB ID 4W86 - XEG5A in complex with glucose and TRIS

PDB ID 4W89 - XEG5A in complex with cellotriose

PDB ID 4W87 - XEG5A in complex with a xyloglucan oligosaccharide

PDB ID 4W88 - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

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

PDB ID 4W8B - XEG5B in complex with XXLG

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

PDB ID 3PZ9 - TpMan5A, a GH5 endo-1,4-beta-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

PDB ID 3PZG - TpMan5A (I222 crystal form)

PDB ID 3PZM - TpMan5A in complex with three glycerol molecules

PDB ID 3PZO - TpMan5A in complex with three maltose molecules

PDB ID 3PZQ - TpMan5A in complex with maltose and glycerol

PDB ID 3PZI - TpMan5A in complex with glucose

PDB ID 3PZU - BsCel5A, a GH5 endo-1,4-beta-glucanase from Bacillus subtilis 168 (P212121 crystal form)

PDB ID 3PZV - BsCel5A (C2 crystal form)

PDB ID 3PZT - BsCel5A in complex with manganese(II) ion

GH1

PDB ID 5BWF - ThBgl, a GH1 beta-glucosidase from Trichoderma harzianum

PDB ID 6EFU - ThBgl, double mutant L167W/P172L

PDB ID 5WKA - a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

PDB ID 5DT5 - EaBgl, GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

PDB ID 5DT7 - EaBgl (C2221 crystal form)

PDB ID 4MDO - HiBG, a GH1 beta-glucosidase from the fungus Humicola insolens

PDB ID 4MDP - HiBG in complex with glucose

GH43

PDB ID 6MS2 - BlXynB, an inactive GH43 member from Bacillus licheniformis

PDB ID 6MS3 - Active BlXynB mutant (K247S)

PDB ID 4KCA - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

PDB ID 4KCB - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

PDB ID 4KC7 - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

GH2

PDB ID 6BYC - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

PDB ID 6BYE - XacMan2A in complex with mannose

PDB ID 6BYG - XacMan2A, nucleophile mutant (E575A)

PDB ID 6BYI - XacMan2A, Acid/Base mutant (E477A)

GH57

PDB ID 3N8T - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

PDB ID 3N98 - TK1436 in complex with glucose and additives

PDB ID 3N92 - TK1436 in complex with glucose

GH22

PDB ID 6B7U - Hen egg-white lysozyme without high-pressure pre-treatment

PDB ID 6B7V - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

PDB ID 6B7W - Hen egg-white lysozyme pre-treated with high pressure (600 MPa) under isobaric condition

GH51

PDB ID 6D25 - XacAbf51, a GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

PDB ID 3S2C - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

GH42

PDB ID 4UZS - BbgII, a GH42 beta-galactosidase from Bifidobacterium bifidum

PDB ID 4UCF - BbgII in complex with alpha-galactose

GH39

PDB ID 4M29 - GH39 beta-xylosidase from Caulobacter crescentus

GH26

PDB ID 6UEH - Ruminal GH26 endo-beta-1,4-mannanase

GH16

PDB ID 3O5S - Endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

GH8

PDB ID 5CZL - A GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

GH12

PDB ID 4NPR - A GH12 Xyloglucanase from Aspergillus niveus

GH11

PDB ID 1XXN - A GH11 xylanase A from Bacillus subtilis 1A1

AA10

PDB ID 6NDQ - KpLPMO10A, a AA10 LPMO from Kitasatospora papulosa

CBM3

PDB ID 2L8A - CBM3 domain from BsCel5A from Bacillus subtilis

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References

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27. Mandelli F, de Morais MAB, de Lima EA, Oliveira L, Persinoti GF, and Murakami MT. (2020). Spatially remote motifs cooperatively affect substrate preference of a ruminal GH26-type endo-β-1,4-mannanase. J Biol Chem. 2020;295(15):5012-5021. DOI:10.1074/jbc.RA120.012583 |
29. de Morais MAB, Polo CC, Domingues MN, Persinoti GF, Pirolla RAS, de Souza FHM, Correa JBL, Dos Santos CR, and Murakami MT. (2020). Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases. Front Bioeng Biotechnol. 2020;8:419. DOI:10.3389/fbioe.2020.00419 |
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 |