View source for User:Mario Murakami

[[Image:Murakami.jpg|250px|right]]

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]] <cite>Giuseppe2014, Crespim2016, Santos2016, Zanphorlin2016, Toyama2018, Santos2019</cite>, [[GH2]] <cite>Domingues2018</cite>, [[GH5]] <cite>Santos2012a, Santos2012b, Alvarez2013a, Santos2015, Ruiz2016, Rosa2019</cite>, [[GH7]] <cite>Segato2012</cite>, [[GH8]] <cite>Scapin2017</cite>, [[GH10]] <cite>Santos2010, Alvarez2013b, Santos2014a</cite>, [[GH11]] <cite>Murakami2005, Ribeiro2011, Hoffmam2016 </cite>, [[GH12]] <cite>Damasio2012, Furtado2015, Segato2017</cite>, [[GH16]] <cite>Cota2011, Cota2013</cite>, [[GH26]] <cite>Mandelli2020</cite>, [[GH39]] <cite>Santos2012c, Morais2020</cite>, [[GH42]] <cite>Godoy2016</cite>, [[GH43]] <cite>Santos2014b, Diogo2015, Zanphorlin2019</cite>, [[GH45]] <cite>Berto2019</cite>, [[GH51]] <cite>Souza2011, Santos2018</cite>, [[GH54]] <cite>Goncalves2012</cite>, [[GH57]] <cite>Santos2011</cite>, [[GH128]] <cite>Santos2020</cite> and [[AA10]] <cite>Correa2019</cite>. 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 <cite>Fonseca2020</cite>.

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family <cite>Santos2020</cite>, the development of a cellulase hyper-secreting strain <cite>Fonseca2020</cite>, the elucidation of the molecular basis for Man-β-1,4-GlcNAc <cite>Rosa2019</cite> and xyloglucan <cite>Santos2015</cite> specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase <cite>Santos2014a</cite>, the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases <cite>Santos2014b</cite> and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases <cite>Giuseppe2014, Santos2019</cite>.


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'''Solved structures'''

'''GH128'''

[{{PDBlink}}6UAQ PDB ID 6UAQ] - GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei

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

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

[{{PDBlink}}6UAU 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

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

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

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

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

[{{PDBlink}}6UAV PDB ID 6UAV] - GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava

[{{PDBlink}}6UAX PDB ID 6UAX] - GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum

[{{PDBlink}}6UB0 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

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

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

[{{PDBlink}}6UB1 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

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

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

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

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

[{{PDBlink}}6UB2 PDB ID 6UB2] - GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes

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

[{{PDBlink}}6UB7 PDB ID 6UB7] - GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans

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

[{{PDBlink}}6UB8 PDB ID 6UB8] - GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae

[{{PDBlink}}6UBD PDB ID 6UBD] - GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii

[{{PDBlink}}6UBC PDB ID 6UBC] - GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans

'''GH5'''

[{{PDBlink}}6MP2 PDB ID 6MP2] - BlMan5B, a Man-β-1,4-GlcNAc specific GH5 mannosidase from ''Bifidobacterium longum''

[{{PDBlink}}6MPA PDB ID 6MPA] - BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MPC PDB ID 6MPC] - E257A mutant of BlMan5B

[{{PDBlink}}6MP7 PDB ID 6MP7] - E257A mutant of BlMan5B in complex with GlcNAc (soaking)

[{{PDBlink}}6MOY PDB ID 6MOY] - E257A mutant of BlMan5B in complex with GlcNAc (co-crystallization)

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

[{{PDBlink}}5HOS PDB ID 5HOS] - GH5 endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri

[{{PDBlink}}4W7U PDB ID 4W7U] - GH5 XacCel5A in the native form

[{{PDBlink}}4W7V PDB ID 4W7V] - GH5 XacCel5A in complex with cellobiose

[{{PDBlink}}4W7W PDB ID 4W7W] - GH5 XacCel5A in complex with cellopentaose

[{{PDBlink}}4W84 PDB ID 4W84] - XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W85 PDB ID 4W85] - XEG5A in complex with glucose

[{{PDBlink}}4W86 PDB ID 4W86] - XEG5A in complex with glucose and TRIS

[{{PDBlink}}4W87 PDB ID 4W87] - XEG5A in complex with a xyloglucan oligosaccharide

[{{PDBlink}}4W88 PDB ID 4W88] - XEG5A in complex with a xyloglucan oligosaccharide and TRIS

[{{PDBlink}}4W89 PDB ID 4W89] - XEG5A   in complex with cellotriose

[{{PDBlink}}4W8A PDB ID 4W8A] - XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library

[{{PDBlink}}4W8B PDB ID 4W8B] - XEG5B in complex with XXLG

[{{PDBlink}}4M1R PDB ID 4M1R] - GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library

[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 (P212121 crystal form)

[{{PDBlink}}3PZG PDB ID 3PZG] - TpMan5A (I222 crystal form)

[{{PDBlink}}3PZM PDB ID 3PZM] - TpMan5A in complex with three glycerol molecules

[{{PDBlink}}3PZO PDB ID 3PZO] - TpMan5A in complex with three maltose molecules

[{{PDBlink}}3PZQ PDB ID 3PZQ] - TpMan5A in complex with maltose and glycerol

[{{PDBlink}}3PZI PDB ID 3PZI] - TpMan in complex with beta-D-glucose

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

[{{PDBlink}}3PZV PDB ID 3PZV] - BsCel5A (C2 crystal form)

[{{PDBlink}}3PZT PDB ID 3PZT] - BsCel5A in complex with manganese(II) ion

'''GH1'''

[{{PDBlink}}5BWF PDB ID 5BWF] - GH1 beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}6EFU PDB ID 6EFU] - Double mutant L167W/P172L of the beta-glucosidase from Trichoderma harzianum

[{{PDBlink}}5WKA PDB ID 5WKA] - GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake

[{{PDBlink}}5DT5 PDB ID 5DT5] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (P21 crystal form)

[{{PDBlink}}5DT7 PDB ID 5DT7] - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 crystal form)

[{{PDBlink}}4MDO PDB ID 4MDO] - GH1 beta-glucosidase from the fungus Humicola insolens

[{{PDBlink}}4MDP PDB ID 4MDP] - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

'''GH43'''

[{{PDBlink}}6MS2 PDB ID 6MS2] - BlXynB, an inactive GH43 member from Bacillus licheniformis

[{{PDBlink}}6MS3 PDB ID 6MS3] - Active BlXynB mutant (K247S) from Bacillus licheniformis

[{{PDBlink}}4KCA PDB ID 4KCA] - Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KCB PDB ID 4KCB] - Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library

[{{PDBlink}}4KC7 PDB ID 4KC7] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1

[{{PDBlink}}4KC8 PDB ID 4KC8] - Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

'''GH2'''

[{{PDBlink}}6BYC PDB ID 6BYC] - XacMan2A, a GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}6BYE PDB ID 6BYE] - XacMan2A in complex with mannose

[{{PDBlink}}6BYG PDB ID 6BYG] - Nucleophile mutant (E575A) of XacMan2A

[{{PDBlink}}6BYI PDB ID 6BYI] - Acid/Base mutant (E477A) of XacMan2A

'''GH57'''

[{{PDBlink}}3N8T PDB ID 3N8T] - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

[{{PDBlink}}3N98 PDB ID 3N98] - TK1436 in complex with glucose and additives

[{{PDBlink}}3N92 PDB ID 3N92] - TK1436 in complex with glucose

'''GH22'''

[{{PDBlink}}6B7U PDB ID 6B7U] - Hen egg-white lysozyme without high-pressure pre-treatment

[{{PDBlink}}6B7V PDB ID 6B7V] - Hen egg-white lysozyme pre-treated with high-pressure homogenization at 120 MPa

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

'''GH51'''

[{{PDBlink}}6D25 PDB ID 6D25] - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

[{{PDBlink}}3S2C PDB ID 3S2C] - Thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1

'''GH42'''

[{{PDBlink}}4UZS PDB ID 4UZS] - Bifidobacterium bifidum GH42 beta-galactosidase

[{{PDBlink}}4UCF PDB ID 4UCF] - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

'''GH39'''  

[{{PDBlink}}4M29 PDB ID 4M29] - GH39 beta-xylosidase from Caulobacter crescentus

'''GH26'''

[{{PDBlink}}6UEH PDB ID 6UEH] - Ruminal GH26 endo-beta-1,4-mannanase

'''GH16'''

[{{PDBlink}}3O5S PDB ID 3O5S] - endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)

'''GH8'''

[{{PDBlink}}5CZL PDB ID 5CZL] - GH8 endo-beta-1,4-glucanase from an Achatina fulica gut metagenomic library

'''GH12'''

[{{PDBlink}}4NPR PDB ID 4NPR] - GH12 Xyloglucanase from Aspergillus niveus

'''GH11'''

[{{PDBlink}}1XXN PDB ID 1XXN] - GH11 xylanase A from Bacillus subtilis 1A1

'''AA10'''

[{{PDBlink}}6NDQ PDB ID 6NDQ] - an AA10 LPMO from Kitasatospora papulosa

'''CBM3'''

[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from Bacillus subtilis

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'''References'''
<biblio>

#Giuseppe2014 pmid=24914974
#Crespim2016 pmid=26475230
#Santos2016 pmid=27006690
#Zanphorlin2016 pmid=27029646
#Toyama2018 pmid=29454992
#Santos2019 pmid=30894609
#Domingues2018 pmid=29997257
#Santos2012a pmid=22155669
#Santos2012b pmid=21880019
#Alvarez2013a pmid=24358302
#Santos2015 pmid=25714929
#Ruiz2016 pmid=27334041
#Rosa2019 pmid=30641082
#Segato2012 pmid=22494694
#Scapin2017 pmid=28448629
#Santos2010 pmid=21070746
#Alvarez2013b pmid=23922891
#Santos2014a pmid=25266726
#Murakami2005 pmid=16289057
#Ribeiro2011 pmid=22006920
#Hoffmam2016 pmid=26923808
#Damasio2012 pmid=22230786
#Furtado2015 pmid=25605422
#Segato2017 pmid=28088615
#Cota2011 pmid=21352806
#Cota2013 pmid=23459129
#Mandelli2020 pmid=32139511
#Santos2012c pmid=22993088
#Morais2020 pmid=32500063
#Godoy2016 pmid=27685756
#Santos2014b pmid=24469445
#Diogo2015 pmid=25640722
#Zanphorlin2019 pmid=30556897
#Berto2019 pmid=30396396
#Souza2011 pmid=21796714
#Santos2018 pmid=30127853
#Goncalves2012 pmid=22750495
#Santos2011 pmid=21104698
#Santos2020 pmid=32451508
#Correa2019 pmid=31168322 
#Fonseca2020 pmid=32461765

</biblio>

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[[Category:Contributors|Murakami,Mario]]