Crystal Structures of Paenibacillus polymyxa β-Glucosidase B Complexes Reveal the Molecular Basis of Substrate Specificity and Give New Insights into the Catalytic Machinery of Family I Glycosidases

Isorna, P.; Polaina, Julio; Latorre-García, Lorena; Cañada, F. Javier; González, Beatriz; Sanz‐Aparicio, Julia

doi:10.1016/j.jmb.2007.05.082

Cited by 115 publications

(113 citation statements)

References 57 publications

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“…Whilst, Tyr298 which is hydrogen bonded to Glu356 involved in recognition of the inhibitor. In agreement with P. Isorna et al (2007), it is observed that Glu167, Glu356, Glu409 and Tyr298 play an important role in catalytic function for both BglB-cellobiose and BglB-laminaribiose complexes. …”

Section: B Protein Ligand Interaction C Active Residue Analysissupporting

confidence: 79%

“…It has been reported that the residues Glu167 acts as a protonated agent of interglycosidic oxygen atom in hydrolysis mechanism, Glu356 acts as nucleophilic in stabilizing the transition state and Glu409 as catalytic residue [8]. Whilst, Tyr298 which is hydrogen bonded to Glu356 involved in recognition of the inhibitor.…”

Section: B Protein Ligand Interaction C Active Residue Analysismentioning

confidence: 99%

“…The x-ray crystal structures of β-glucosidase B (BglB) was obtained from the RCSB Protein Data Bank (http://www.rscb.org) with accession code 209T [8] respectively as show in Fig. 2.…”

Section: Introductionmentioning

confidence: 99%

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Binding Mode Study of β-glucosidase B from P. Polymyxca with Cellobiose and Laminaribiose

Mazlan¹,

Khairudin²

2013

IJCEA

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Abstract-Beta-glucosidase (3.2.1.21) plays an essential role in the removal of non-reducing terminal glucosyl residues from sacharides and glycosides. Recently, beta-glucosidase has been of interest for biomass conversion that acts in synergy with two other enzymes, endo-glucanase and exo-glucanase. However, there is not much information regarding the molecular interactions of beta-glucosidase with cellobiose. Thus, this study reports on the binding modes between beta-glucosidase from glycoside hydrolase family 1 namely BglB with cellobiose and laminaribiose via molecular docking method. Further analysis on the hydrophobic interactions revealed the key residues involved in forming hydrogen bonds (h-bond) with the substrates. The important residues were reported to be Gln22, Glu167, Tyr298, Glu356, Glu402, and Trp410. These findings may provide valuable insigths in designing beta-glucosidase with higher cellulose-hydrolyzing efficiency.

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Section: B Protein Ligand Interaction C Active Residue Analysissupporting

confidence: 79%

Section: B Protein Ligand Interaction C Active Residue Analysismentioning

confidence: 99%

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Binding Mode Study of β-glucosidase B from P. Polymyxca with Cellobiose and Laminaribiose

Mazlan¹,

Khairudin²

2013

IJCEA

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“…A structural overlay of the template sequences created using the DALI server (20) was used to verify that template regions identified as similar to SFR2 loops were loop structures in the template. The highest scoring template candidates included the following: S. solfataricus PDB entry 1UWT (17) and R. serpentina PDB entry 4A3Y (18), and also included Thermosphaera aggregans PDB entry 1QVB, a hyperthermophilic ␤-glycosidase (21); Paenibacillus polymyxa PDB entry 2JIE, a ␤-glucosidase B in complex with 2-fluoroglucose (22); and Triticum aestivum PDB entry 2DGA, a ␤-D-glucosidase in complex with glucose (23).…”

Section: Alignment and Selection Of Crystal Structure Templates Formentioning

confidence: 99%

Structural Determinants Allowing Transferase Activity in SENSITIVE TO FREEZING 2, Classified as a Family I Glycosyl Hydrolase

Roston

Wang

Kuhn

et al. 2014

Journal of Biological Chemistry

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Background: SENSITIVE TO FREEZING 2 (SFR2) is classified as a glycosyl hydrolase, and by using glycosyltransferase activity, it modifies membrane lipids to promote freeze tolerance. Results: Although the active site of SFR2 is identical to hydrolases, adjacent loop regions contribute to its transferase activity. Conclusion: Transferase activity evolved by modifications external to the core catalytic site. Significance: Defined structure-function relationships will inform engineering of transferases and freeze tolerance.

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“…LPH domains III and IV share a comparable, quite high degree of sequence identity (around 40%) with highly conserved family 1 glycoside hydrolases of known three-dimensional structure from humans (25), plants (26), fungi (27), and bacteria (28,29). Structure-based sequence alignments with the aforesaid homologous proteins generated by GenTHREADER (30) were used to dissect the LPH domains.…”

Section: Methodsmentioning

confidence: 99%

Structural Hierarchy of Regulatory Elements in the Folding and Transport of an Intestinal Multidomain Protein

Behrendt¹,

Polaina

Naim³

2010

Journal of Biological Chemistry

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Crystal Structures of Paenibacillus polymyxa β-Glucosidase B Complexes Reveal the Molecular Basis of Substrate Specificity and Give New Insights into the Catalytic Machinery of Family I Glycosidases

Cited by 115 publications

References 57 publications

Binding Mode Study of β-glucosidase B from P. Polymyxca with Cellobiose and Laminaribiose

Binding Mode Study of β-glucosidase B from P. Polymyxca with Cellobiose and Laminaribiose

Structural Determinants Allowing Transferase Activity in SENSITIVE TO FREEZING 2, Classified as a Family I Glycosyl Hydrolase

Structural Hierarchy of Regulatory Elements in the Folding and Transport of an Intestinal Multidomain Protein

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