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 [18], the mechanistic understanding and rational redesign 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

GH1 PDB ID 6EFU - Double mutant L167W / P172L of the beta-glucosidase from Trichoderma harzianum

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

PDB ID 5BWF - GH1 beta-glucosidase from Trichoderma harzianum

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

PDB ID 5DT7 - GH1 beta-glucosidase from Exiguobacterium antarcticum B7 (C2221 form)

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

PDB ID 4MDP - GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

GH43

PDB ID 6MS3 - GH43 protein BlXynB mutant (K247S) from Bacillus licheniformis

PDB ID 6MS2 - GH43 BlXynB protein from Bacillus licheniformis 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

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

GH2 PDB ID 6BYE - GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri in complex with mannose PDB ID 6BYG - nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri PDB ID 6BYI - Acid/Base mutant (E477A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

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

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

PDB ID 3N98 - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

PDB ID 3N92 - TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, 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 - GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri

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

GH42

PDB ID 4UZS - Bifidobacterium bifidum GH42 beta-galactosidase PDB ID 4UCF - Bifidobacterium bifidum GH42 beta-galactosidase in complex with alpha-galactose

GH16

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

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

GH8

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

GH12 PDB ID 4NPR - GH12 Xyloglucanase from Aspergillus niveus

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

CBM3 PDB ID 2L8A – a CBM3 lacking the calcium-binding site from Bacillus subtilis

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

AA10

PDB ID 6NDQ – an AA10 LPMO from Kitasatospora papulosa

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References

1. de Giuseppe PO, Souza Tde A, Souza FH, Zanphorlin LM, Machado CB, Ward RJ, Jorge JA, Furriel Rdos P, and Murakami MT. (2014). Structural basis for glucose tolerance in GH1 β-glucosidases. Acta Crystallogr D Biol Crystallogr. 2014;70(Pt 6):1631-9. DOI:10.1107/S1399004714006920 |
2. Crespim E, Zanphorlin LM, de Souza FH, Diogo JA, Gazolla AC, Machado CB, Figueiredo F, Sousa AS, Nóbrega F, Pellizari VH, Murakami MT, and Ruller R. (2016). A novel cold-adapted and glucose-tolerant GH1 β-glucosidase from Exiguobacterium antarcticum B7. Int J Biol Macromol. 2016;82:375-80. DOI:10.1016/j.ijbiomac.2015.09.018 |
3. Santos CA, Zanphorlin LM, Crucello A, Tonoli CCC, Ruller R, Horta MAC, Murakami MT, and de Souza AP. (2016). Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. Biotechnol Biofuels. 2016;9:71. DOI:10.1186/s13068-016-0487-0 |
4. Zanphorlin LM, de Giuseppe PO, Honorato RV, Tonoli CC, Fattori J, Crespim E, de Oliveira PS, Ruller R, and Murakami MT. (2016). Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. Sci Rep. 2016;6:23776. DOI:10.1038/srep23776 |
5. Toyama D, de Morais MAB, Ramos FC, Zanphorlin LM, Tonoli CCC, Balula AF, de Miranda FP, Almeida VM, Marana SR, Ruller R, Murakami MT, and Henrique-Silva F. (2018). A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil). Biochim Biophys Acta Proteins Proteom. 2018;1866(4):569-579. DOI:10.1016/j.bbapap.2018.02.001 |
6. Santos CA, Morais MAB, Terrett OM, Lyczakowski JJ, Zanphorlin LM, Ferreira-Filho JA, Tonoli CCC, Murakami MT, Dupree P, and Souza AP. (2019). An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials. Sci Rep. 2019;9(1):4903. DOI:10.1038/s41598-019-41300-3 |
7. Domingues MN, Souza FHM, Vieira PS, de Morais MAB, Zanphorlin LM, Dos Santos CR, Pirolla RAS, Honorato RV, de Oliveira PSL, Gozzo FC, and Murakami MT. (2018). Structural basis of exo-β-mannanase activity in the GH2 family. J Biol Chem. 2018;293(35):13636-13649. DOI:10.1074/jbc.RA118.002374 |
8. dos Santos CR, Paiva JH, Meza AN, Cota J, Alvarez TM, Ruller R, Prade RA, Squina FM, and Murakami MT. (2012). Molecular insights into substrate specificity and thermal stability of a bacterial GH5-CBM27 endo-1,4-β-D-mannanase. J Struct Biol. 2012;177(2):469-76. DOI:10.1016/j.jsb.2011.11.021 |
9. Santos CR, Paiva JH, Sforça ML, Neves JL, Navarro RZ, Cota J, Akao PK, Hoffmam ZB, Meza AN, Smetana JH, Nogueira ML, Polikarpov I, Xavier-Neto J, Squina FM, Ward RJ, Ruller R, Zeri AC, and Murakami MT. (2012). Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168. Biochem J. 2012;441(1):95-104. DOI:10.1042/BJ20110869 |
10. Alvarez TM, Paiva JH, Ruiz DM, Cairo JP, Pereira IO, Paixão DA, de Almeida RF, Tonoli CC, Ruller R, Santos CR, Squina FM, and Murakami MT. (2013). Structure and function of a novel cellulase 5 from sugarcane soil metagenome. PLoS One. 2013;8(12):e83635. DOI:10.1371/journal.pone.0083635 |
11. Dos Santos CR, Cordeiro RL, Wong DW, and Murakami MT. (2015). Structural basis for xyloglucan specificity and α-d-Xylp(1 → 6)-D-Glcp recognition at the -1 subsite within the GH5 family. Biochemistry. 2015;54(10):1930-42. DOI:10.1021/acs.biochem.5b00011 |
12. Ruiz DM, Turowski VR, and Murakami MT. (2016). Effects of the linker region on the structure and function of modular GH5 cellulases. Sci Rep. 2016;6:28504. DOI:10.1038/srep28504 |
13. Cordeiro RL, Pirolla RAS, Persinoti GF, Gozzo FC, de Giuseppe PO, and Murakami MT. (2019). N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist β-Mannosidase. J Mol Biol. 2019;431(4):732-747. DOI:10.1016/j.jmb.2018.12.017 |
14. Segato F, Damasio AR, Gonçalves TA, Murakami MT, Squina FM, Polizeli M, Mort AJ, and Prade RA. (2012). Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber. Biotechnol Biofuels. 2012;5:21. DOI:10.1186/1754-6834-5-21 |
15. Scapin SMN, Souza FHM, Zanphorlin LM, de Almeida TS, Sade YB, Cardoso AM, Pinheiro GL, and Murakami MT. (2017). Structure and function of a novel GH8 endoglucanase from the bacterial cellulose synthase complex of Raoultella ornithinolytica. PLoS One. 2017;12(4):e0176550. DOI:10.1371/journal.pone.0176550 |
16. Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, and Murakami MT. (2010). Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1. Biochem Biophys Res Commun. 2010;403(2):214-9. DOI:10.1016/j.bbrc.2010.11.010 |
17. Alvarez TM, Goldbeck R, dos Santos CR, Paixão DA, Gonçalves TA, Franco Cairo JP, Almeida RF, de Oliveira Pereira I, Jackson G, Cota J, Büchli F, Citadini AP, Ruller R, Polo CC, de Oliveira Neto M, Murakami MT, and Squina FM. (2013). Development and biotechnological application of a novel endoxylanase family GH10 identified from sugarcane soil metagenome. PLoS One. 2013;8(7):e70014. DOI:10.1371/journal.pone.0070014 |
18. Santos CR, Hoffmam ZB, de Matos Martins VP, Zanphorlin LM, de Paula Assis LH, Honorato RV, Lopes de Oliveira PS, Ruller R, and Murakami MT. (2014). Molecular mechanisms associated with xylan degradation by Xanthomonas plant pathogens. J Biol Chem. 2014;289(46):32186-32200. DOI:10.1074/jbc.M114.605105 |
19. Murakami MT, Arni RK, Vieira DS, Degrève L, Ruller R, and Ward RJ. (2005). Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1). FEBS Lett. 2005;579(28):6505-10. DOI:10.1016/j.febslet.2005.10.039 |
20. Ribeiro LF, Furtado GP, Lourenzoni MR, Costa-Filho AJ, Santos CR, Nogueira SC, Betini JA, Polizeli Mde L, Murakami MT, and Ward RJ. (2011). Engineering bifunctional laccase-xylanase chimeras for improved catalytic performance. J Biol Chem. 2011;286(50):43026-38. DOI:10.1074/jbc.M111.253419 |
21. Hoffmam ZB, Zanphorlin LM, Cota J, Diogo JA, Almeida GB, Damásio AR, Squina F, Murakami MT, and Ruller R. (2016). Xylan-specific carbohydrate-binding module belonging to family 6 enhances the catalytic performance of a GH11 endo-xylanase. N Biotechnol. 2016;33(4):467-72. DOI:10.1016/j.nbt.2016.02.006 |
22. Damásio AR, Ribeiro LF, Ribeiro LF, Furtado GP, Segato F, Almeida FB, Crivellari AC, Buckeridge MS, Souza TA, Murakami MT, Ward RJ, Prade RA, and Polizeli ML. (2012). Functional characterization and oligomerization of a recombinant xyloglucan-specific endo-β-1,4-glucanase (GH12) from Aspergillus niveus. Biochim Biophys Acta. 2012;1824(3):461-7. DOI:10.1016/j.bbapap.2011.12.005 |
23. Segato F, Dias B, Berto GL, de Oliveira DM, De Souza FHM, Citadini AP, Murakami MT, Damásio ARL, Squina FM, and Polikarpov I. (2017). Cloning, heterologous expression and biochemical characterization of a non-specific endoglucanase family 12 from Aspergillus terreus NIH2624. Biochim Biophys Acta Proteins Proteom. 2017;1865(4):395-403. DOI:10.1016/j.bbapap.2017.01.003 |
24. Cota J, Alvarez TM, Citadini AP, Santos CR, de Oliveira Neto M, Oliveira RR, Pastore GM, Ruller R, Prade RA, Murakami MT, and Squina FM. (2011). Mode of operation and low-resolution structure of a multi-domain and hyperthermophilic endo-β-1,3-glucanase from Thermotoga petrophila. Biochem Biophys Res Commun. 2011;406(4):590-4. DOI:10.1016/j.bbrc.2011.02.098 |
25. Cota J, Oliveira LC, Damásio AR, Citadini AP, Hoffmam ZB, Alvarez TM, Codima CA, Leite VB, Pastore G, de Oliveira-Neto M, Murakami MT, Ruller R, and Squina FM. (2013). Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations. Biochim Biophys Acta. 2013;1834(8):1492-500. DOI:10.1016/j.bbapap.2013.02.030 |
26. 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 |
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 |
28. Santos CR, Polo CC, Corrêa JM, Simão Rde C, Seixas FA, and Murakami MT. (2012). The accessory domain changes the accessibility and molecular topography of the catalytic interface in monomeric GH39 β-xylosidases. Acta Crystallogr D Biol Crystallogr. 2012;68(Pt 10):1339-45. DOI:10.1107/S0907444912028491 |
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 |
30. 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 |
31. Santos CR, Polo CC, Costa MC, Nascimento AF, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PS, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DW, and Murakami MT. (2014). Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem. 2014;289(11):7362-73. DOI:10.1074/jbc.M113.537167 |
32. Diogo JA, Hoffmam ZB, Zanphorlin LM, Cota J, Machado CB, Wolf LD, Squina F, Damásio AR, Murakami MT, and Ruller R. (2015). Development of a chimeric hemicellulase to enhance the xylose production and thermotolerance. Enzyme Microb Technol. 2015;69:31-7. DOI:10.1016/j.enzmictec.2014.11.006 |
33. Zanphorlin LM, de Morais MAB, Diogo JA, Domingues MN, de Souza FHM, Ruller R, and Murakami MT. (2019). Structure-guided design combined with evolutionary diversity led to the discovery of the xylose-releasing exo-xylanase activity in the glycoside hydrolase family 43. Biotechnol Bioeng. 2019;116(4):734-744. DOI:10.1002/bit.26899 |
34. Berto GL, Velasco J, Tasso Cabos Ribeiro C, Zanphorlin LM, Noronha Domingues M, Tyago Murakami M, Polikarpov I, de Oliveira LC, Ferraz A, and Segato F. (2019). Functional characterization and comparative analysis of two heterologous endoglucanases from diverging subfamilies of glycosyl hydrolase family 45. Enzyme Microb Technol. 2019;120:23-35. DOI:10.1016/j.enzmictec.2018.09.005 |
35. Souza TA, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, and Murakami MT. (2011). Structure of a novel thermostable GH51 α-L-arabinofuranosidase from Thermotoga petrophila RKU-1. Protein Sci. 2011;20(9):1632-7. DOI:10.1002/pro.693 |
36. Dos Santos CR, de Giuseppe PO, de Souza FHM, Zanphorlin LM, Domingues MN, Pirolla RAS, Honorato RV, Tonoli CCC, de Morais MAB, de Matos Martins VP, Fonseca LM, Büchli F, de Oliveira PSL, Gozzo FC, and Murakami MT. (2018). The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. Biotechnol Biofuels. 2018;11:223. DOI:10.1186/s13068-018-1212-y |
37. Gonçalves TA, Damásio AR, Segato F, Alvarez TM, Bragatto J, Brenelli LB, Citadini AP, Murakami MT, Ruller R, Paes Leme AF, Prade RA, and Squina FM. (2012). Functional characterization and synergic action of fungal xylanase and arabinofuranosidase for production of xylooligosaccharides. Bioresour Technol. 2012;119:293-9. DOI:10.1016/j.biortech.2012.05.062 |
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 |
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 |
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