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 - BlMan5B, a Man-β-1,4-GlcNAc GH5 mannosidase from Bifidobacterium longum

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

PDB ID 6MPC - E257A mutant of BlMan5B

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

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 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

PDB ID 4W85 - XEG5A in complex with glucose

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

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

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

PDB ID 4W89 - XEG5A in complex with cellotriose

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

PDB ID 3PZ9 - TpMan5A, a GH5 endo-1,4-beta-D-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 - TpMan in complex with beta-D-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

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References

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38. Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, and Murakami MT. (2011). Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Proteins. 2011;79(2):547-57. DOI:10.1002/prot.22902 |