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, 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 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

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References

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23. Furtado GP, Santos CR, Cordeiro RL, Ribeiro LF, de Moraes LA, Damásio AR, Polizeli Mde L, Lourenzoni MR, Murakami MT, and Ward RJ. (2015). Enhanced xyloglucan-specific endo-β-1,4-glucanase efficiency in an engineered CBM44-XegA chimera. Appl Microbiol Biotechnol. 2015;99(12):5095-107. DOI:10.1007/s00253-014-6324-0 |
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 |