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Difference between revisions of "User:Mario Murakami"

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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 <cite>Fonseca2020</cite>. 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>.
 +
 
 +
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>.
  
−
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]] <cite>Giuseppe2012, 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, Diogo2015, 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></cite>, [[GH54]] <cite></cite>, [[GH57]] <cite></cite>, [[GH128]] <cite></cite>and [[AA9]] <cite></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></cite>.
 
  
 
----
 
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 +
'''Solved structures'''
 +
 +
'''GH128'''
 +
 +
[{{PDBlink}}6UAQ PDB ID 6UAQ] - Subgroup I endo-beta-1,3-glucanase from ''Amycolatopsis mediterranei'' (AmGH128_I)
 +
 +
[{{PDBlink}}6UAR PDB ID 6UAR] - AmGH128_I in complex with laminaritriose
 +
 +
[{{PDBlink}}6UAS PDB ID 6UAS] - AmGH128_I in complex with laminaripentaose
 +
 +
[{{PDBlink}}6UAU PDB ID 6UAU] - AmGH128_I, E102A mutant, in complex with laminaritriose and laminaribiose
 +
 +
[{{PDBlink}}6UAT PDB ID 6UAT] - AmGH128_I, E102A mutant, in complex with laminaripentaose
 +
 +
[{{PDBlink}}6UFZ PDB ID 6UFZ] - AmGH128_I, E199Q mutant
 +
 +
[{{PDBlink}}6UFL PDB ID 6UFL] - AmGH128_I, E199Q mutant, in the complex with laminarihexaose
 +
 +
[{{PDBlink}}6UAV PDB ID 6UAV] - Subgroup II long oligosaccharide-releasing endo-beta-1,3-glucanase from ''Pseudomonas viridiflava'' (PvGH128_II)
 +
 +
[{{PDBlink}}6UAW PDB ID 6UAW] - PvGH128_II in complex with laminaritriose
 +
 +
[{{PDBlink}}6UAX PDB ID 6UAX] - Subgroup II long-oligosaccharide-releasing endo-beta-1,3-glucanase from ''Sorangium cellulosum'' (ScGH128_II)
 +
 +
[{{PDBlink}}6UAY PDB ID 6UAY] - Subgroup III non-reducing-end curdlan-specific exo-beta-1,3-glucanase from ''Blastomyces gilchristii'' (BgGH128_III)
 +
 +
[{{PDBlink}}6UNV PDB ID 6UNV] - BgGH128_III in complex with glucose
 +
 +
[{{PDBlink}}6UB0 PDB ID 6UB0] - BgGH128_III in complex with laminaribiose at -2 and -1 subsites
 +
 +
[{{PDBlink}}6UB1 PDB ID 6UB1] - BgGH128_III in complex with laminaribiose at -3 and -2 subsides
 +
 +
[{{PDBlink}}6UB2 PDB ID 6UB2] - Subgroup IV atypical endo-beta-1,3-glucanase from ''Lentinula edodes'' (LeGH128_IV)
 +
 +
[{{PDBlink}}6UB4 PDB ID 6UB4] - LeGH128_IV in complex with laminaritriose (C2 crystal form)
 +
 +
[{{PDBlink}}6UB5 PDB ID 6UB5] - LeGH128_IV in complex with laminaritriose (P21 crystal form)
 +
 +
[{{PDBlink}}6UB6 PDB ID 6UB6] - LeGH128_IV in complex with laminaritetraose
 +
 +
[{{PDBlink}}6UB3 PDB ID 6UB3] - LeGH128_IV with laminaribiose at the surface-binding site
 +
 +
[{{PDBlink}}6UB7 PDB ID 6UB7] - Subgroup V glucose-releasing exo-beta-1,3-glucanase from ''Cryptococcus neoformans'' (CnGH128_V)
 +
 +
[{{PDBlink}}6UB8 PDB ID 6UB8] - Subgroup VI reducing-end L3-releasing exo-beta-1,3-glucanase from ''Aureobasidium namibiae'' (AnGH128_VI)
 +
 +
[{{PDBlink}}6UBA PDB ID 6UBA] - AnGH128_VI in complex with laminaritriose
 +
 +
[{{PDBlink}}6UBB PDB ID 6UBB] - AnGH128_VI with laminaribiose at the surface-binding site
 +
 +
[{{PDBlink}}6UBD PDB ID 6UBD] - Subgroup VII oligosaccharide-binding protein from ''Trichoderma gamsii'' (TgGH128_VII)
 +
 +
[{{PDBlink}}6UBC PDB ID 6UBC] - Subgroup VII oligosaccharide-binding protein from ''Cryptococcus neoformans'' (CnGH128_VII)
 +
 +
'''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] - BlMan5B, E257A mutant
 +
 +
[{{PDBlink}}6MP7 PDB ID 6MP7] - BlMan5B, E257A mutant, in complex with GlcNAc (soaking)
 +
 +
[{{PDBlink}}6MOY PDB ID 6MOY] - BlMan5B, E257A mutant, in complex with GlcNAc (co-crystallization)
 +
 +
[{{PDBlink}}4W7U PDB ID 4W7U] - Xac0030, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri
 +
 +
[{{PDBlink}}4W7V PDB ID 4W7V] - Xac0030 in complex with cellobiose
 +
 +
[{{PDBlink}}4W7W PDB ID 4W7W] - Xac0030 in complex with cellopentaose
 +
 +
[{{PDBlink}}5HNN PDB ID 5HNN] - Xac0030, triple mutation H174W, Y211A and K227R
 +
 +
[{{PDBlink}}5HOS PDB ID 5HOS] - Xac0029, a GH5 endo-beta-1,4-glucanase from ''Xanthomonas axonopodis'' pv. citri
 +
 +
[{{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}}4W89 PDB ID 4W89] - XEG5A in complex with cellotriose
 +
 +
[{{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}}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] - A GH5 endo-beta-1,4-glucanase from a sugarcane soil metagenomic library
 +
 +
[{{PDBlink}}3PZ9 PDB ID 3PZ9] - TpMan5A, a GH5 endo-1,4-beta-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] - TpMan5A in complex with 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] - ThBgl, a GH1 beta-glucosidase from ''Trichoderma harzianum''
 +
 +
[{{PDBlink}}6EFU PDB ID 6EFU] - ThBgl, double mutant L167W/P172L
 +
 +
[{{PDBlink}}5WKA PDB ID 5WKA] - a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake
 +
 +
[{{PDBlink}}5DT5 PDB ID 5DT5] - EaBgl, GH1 beta-glucosidase from ''Exiguobacterium antarcticum'' B7 (P21 crystal form)
 +
 +
[{{PDBlink}}5DT7 PDB ID 5DT7] - EaBgl (C2221 crystal form)
 +
 +
[{{PDBlink}}4MDO PDB ID 4MDO] - HiBG, a GH1 beta-glucosidase from the fungus ''Humicola insolens''
 +
 +
[{{PDBlink}}4MDP PDB ID 4MDP] - HiBG 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)
 +
 +
[{{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
 +
 +
'''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] - XacMan2A, nucleophile mutant (E575A)
 +
 +
[{{PDBlink}}6BYI PDB ID 6BYI] - XacMan2A, Acid/Base mutant (E477A)
 +
 +
'''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] - XacAbf51, a 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] - BbgII, a GH42 beta-galactosidase from ''Bifidobacterium bifidum''
 +
 +
[{{PDBlink}}4UCF PDB ID 4UCF] - BbgII 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] - A GH8 endo-beta-1,4-glucanase from an ''Achatina fulica'' gut metagenomic library
 +
 +
'''GH12'''
 +
 +
[{{PDBlink}}4NPR PDB ID 4NPR] - A GH12 Xyloglucanase from ''Aspergillus niveus''
 +
 +
'''GH11'''
 +
 +
[{{PDBlink}}1XXN PDB ID 1XXN] - A GH11 xylanase A from ''Bacillus subtilis'' 1A1
 +
 +
'''AA10'''
 +
 +
[{{PDBlink}}6NDQ PDB ID 6NDQ] - KpLPMO10A, a AA10 LPMO from ''Kitasatospora papulosa''
 +
 +
'''CBM3'''
 +
 +
[{{PDBlink}}2L8A PDB ID 2L8A] - CBM3 domain from BsCel5A from ''Bacillus subtilis''
 +
 +
----
 +
 +
'''References'''
 
<biblio>
 
<biblio>
  
−
#Giuseppe2012 pmid=24914974
+
#Giuseppe2014 pmid=24914974
 
#Crespim2016 pmid=26475230
 
#Crespim2016 pmid=26475230
 
#Santos2016 pmid=27006690
 
#Santos2016 pmid=27006690
Line 27: Line 243:
 
#Murakami2005 pmid=16289057
 
#Murakami2005 pmid=16289057
 
#Ribeiro2011 pmid=22006920
 
#Ribeiro2011 pmid=22006920
−
#Diogo2015 pmid=25640722
 
 
#Hoffmam2016 pmid=26923808
 
#Hoffmam2016 pmid=26923808
 
#Damasio2012 pmid=22230786
 
#Damasio2012 pmid=22230786
Line 42: Line 257:
 
#Zanphorlin2019 pmid=30556897
 
#Zanphorlin2019 pmid=30556897
 
#Berto2019 pmid=30396396
 
#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>
 
</biblio>

Latest revision as of 05:10, 22 June 2020

Murakami.jpg

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 [1]. He has contributed to structural and functional studies of CAZymes from families GH1 [2, 3, 4, 5, 6, 7], GH2 [8], GH5 [9, 10, 11, 12, 13, 14], GH7 [15], GH8 [16], GH10 [17, 18, 19], GH11 [20, 21, 22], GH12 [23, 24, 25], GH16 [26, 27], GH26 [28], GH39 [29, 30], GH42 [31], GH43 [32, 33, 34], GH45 [35], GH51 [36, 37], GH54 [38], GH57 [39], GH128 [40] and AA10 [41].

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family [40], the development of a cellulase hyper-secreting strain [1], the elucidation of the molecular basis for Man-β-1,4-GlcNAc [14] and xyloglucan [12] specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase [19], the mechanistic understanding and rational redesign of rumen metagenome GH43 arabinanases [32] and the uncovering of the structural determinants for glucose tolerance in GH1 beta-glucosidases [2, 7].


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

References

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  1. Error fetching PMID 32461765: [Fonseca2020]
  2. Error fetching PMID 24914974: [Giuseppe2014]
  3. Error fetching PMID 26475230: [Crespim2016]
  4. Error fetching PMID 27006690: [Santos2016]
  5. Error fetching PMID 27029646: [Zanphorlin2016]
  6. Error fetching PMID 29454992: [Toyama2018]
  7. Error fetching PMID 30894609: [Santos2019]
  8. Error fetching PMID 29997257: [Domingues2018]
  9. Error fetching PMID 22155669: [Santos2012a]
  10. Error fetching PMID 21880019: [Santos2012b]
  11. Error fetching PMID 24358302: [Alvarez2013a]
  12. Error fetching PMID 25714929: [Santos2015]
  13. Error fetching PMID 27334041: [Ruiz2016]
  14. Error fetching PMID 30641082: [Rosa2019]
  15. Error fetching PMID 22494694: [Segato2012]
  16. Error fetching PMID 28448629: [Scapin2017]
  17. Error fetching PMID 21070746: [Santos2010]
  18. Error fetching PMID 23922891: [Alvarez2013b]
  19. Error fetching PMID 25266726: [Santos2014a]
  20. Error fetching PMID 16289057: [Murakami2005]
  21. Error fetching PMID 22006920: [Ribeiro2011]
  22. Error fetching PMID 26923808: [Hoffmam2016]
  23. Error fetching PMID 22230786: [Damasio2012]
  24. Error fetching PMID 25605422: [Furtado2015]
  25. Error fetching PMID 28088615: [Segato2017]
  26. Error fetching PMID 21352806: [Cota2011]
  27. Error fetching PMID 23459129: [Cota2013]
  28. Error fetching PMID 32139511: [Mandelli2020]
  29. Error fetching PMID 22993088: [Santos2012c]
  30. Error fetching PMID 32500063: [Morais2020]
  31. 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 | PubMed ID:27685756 [Godoy2016]
  32. Error fetching PMID 24469445: [Santos2014b]
  33. Error fetching PMID 25640722: [Diogo2015]
  34. Error fetching PMID 30556897: [Zanphorlin2019]
  35. Error fetching PMID 30396396: [Berto2019]
  36. Error fetching PMID 21796714: [Souza2011]
  37. Error fetching PMID 30127853: [Santos2018]
  38. Error fetching PMID 22750495: [Goncalves2012]
  39. 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 | PubMed ID:21104698 [Santos2011]
  40. 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 | PubMed ID:32451508 [Santos2020]
  41. Error fetching PMID 31168322: [Correa2019]

All Medline abstracts: PubMed

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