Structural Basis for Substrate Specificity in Group I Nucleoside Hydrolases†,‡

Biochemistry ◽  
2008 ◽  
Vol 47 (15) ◽  
pp. 4418-4426 ◽  
Author(s):  
Elena Iovane ◽  
Barbara Giabbai ◽  
Laura Muzzolini ◽  
Vittoria Matafora ◽  
Arianna Fornili ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Structural Basis ◽  
Group I ◽  
Nucleoside Hydrolases

scholarly journals Structural basis of the substrate specificity of the FPOD/FAOD family revealed by fructosyl peptide oxidase fromEupenicillium terrenum

2015 ◽  
Vol 71 (4) ◽  
pp. 381-387 ◽  
Author(s):  
Weiqiong Gan ◽  
Feng Gao ◽  
Keke Xing ◽  
Minze Jia ◽  
Haiping Liu ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Enzyme Engineering ◽  
Structural Basis ◽  
Substrate Selection ◽  
Structure Comparison ◽  
Glucose Levels ◽  
Blood Glucose Levels ◽  
Group I ◽  
Structural Details ◽  
Fructosyl Peptide Oxidase

The FAOD/FPOD family of proteins has the potential to be useful for the longterm detection of blood glucose levels in diabetes patients. A bottleneck for this application is to find or engineer a FAOD/FPOD family enzyme that is specifically active towards α-fructosyl peptides but is inactive towards other types of glycated peptides. Here, the crystal structure of fructosyl peptide oxidase fromEupenicillium terrenum(EtFPOX) is reported at 1.9 Å resolution. In contrast to the previously reported structure of amadoriase II, EtFPOX has an open substrate entrance to accommodate the large peptide substrate. The functions of residues critical for substrate selection are discussed based on structure comparison and sequence alignment. This study reveals the first structural details of group I FPODs that prefer α-fructosyl substrates and could provide significant useful information for uncovering the mechanism of substrate specificity of FAOD/FPODs and guidance towards future enzyme engineering for diagnostic purposes.

scholarly journals Correction: Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study

2017 ◽  
Vol 13 (12) ◽  
pp. 2729-2730
Author(s):  
M. Tomin ◽  
S. Tomić
Keyword(s):  
Substrate Specificity ◽  
Computational Study ◽  
Dynamic Properties ◽  
Dipeptidyl Peptidase ◽  
Structural Basis ◽  
Bacteroides Thetaiotaomicron

Correction for ‘Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study’ by M. Tomin et al., Mol. BioSyst., 2017, 13, 2407–2417.

Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

2017 ◽  
Vol 474 (20) ◽  
pp. 3373-3389 ◽  
Author(s):  
Dong-Dong Meng ◽  
Xi Liu ◽  
Sheng Dong ◽  
Ye-Fei Wang ◽  
Xiao-Qing Ma ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Glycoside Hydrolase ◽  
Complex Structure ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Substrate Selectivity ◽  
Glucose Residue ◽  
Structural Insights

Glycoside hydrolase (GH) family 5 is one of the largest GH families with various GH activities including lichenase, but the structural basis of the GH5 lichenase activity is still unknown. A novel thermostable lichenase F32EG5 belonging to GH5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor sp. F32. F32EG5 is a bi-functional cellulose and a lichenan-degrading enzyme, and exhibited a high activity on β-1,3-1,4-glucan but side activity on cellulose. Thin-layer chromatography and NMR analyses indicated that F32EG5 cleaved the β-1,4 linkage or the β-1,3 linkage while a 4-O-substitued glucose residue linked to a glucose residue through a β-1,3 linkage, which is completely different from extensively studied GH16 lichenase that catalyses strict endo-hydrolysis of the β-1,4-glycosidic linkage adjacent to a 3-O-substitued glucose residue in the mixed-linked β-glucans. The crystal structure of F32EG5 was determined to 2.8 Å resolution, and the crystal structure of the complex of F32EG5 E193Q mutant and cellotetraose was determined to 1.7 Å resolution, which revealed that the exit subsites of substrate-binding sites contribute to both thermostability and substrate specificity of F32EG5. The sugar chain showed a sharp bend in the complex structure, suggesting that a substrate cleft fitting to the bent sugar chains in lichenan is a common feature of GH5 lichenases. The mechanism of thermostability and substrate selectivity of F32EG5 was further demonstrated by molecular dynamics simulation and site-directed mutagenesis. These results provide biochemical and structural insights into thermostability and substrate selectivity of GH5 lichenases, which have potential in industrial processes.

scholarly journals Structural Basis for Substrate Specificity ofEscherichia coliPurine Nucleoside Phosphorylase

2003 ◽  
Vol 278 (47) ◽  
pp. 47110-47118 ◽  
Author(s):  
Eric M. Bennett ◽  
Chenglong Li ◽  
Paula W. Allan ◽  
William B. Parker ◽  
Steven E. Ealick
Keyword(s):  
Substrate Specificity ◽  
Structural Basis ◽  
Nucleoside Phosphorylase

scholarly journals Structural basis for catalysis and substrate specificity of human ACAT1

Nature ◽  
2020 ◽  
Vol 581 (7808) ◽  
pp. 333-338 ◽  
Author(s):  
Hongwu Qian ◽  
Xin Zhao ◽  
Renhong Yan ◽  
Xia Yao ◽  
Shuai Gao ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Structural Basis

Structural Basis of Substrate Specificity of Plant 12-Oxophytodienoate Reductases

2009 ◽  
Vol 392 (5) ◽  
pp. 1266-1277 ◽  
Author(s):  
Constanze Breithaupt ◽  
Robert Kurzbauer ◽  
Florian Schaller ◽  
Annick Stintzi ◽  
Andreas Schaller ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Structural Basis

Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D β-Lactamase

2019 ◽  
Vol 6 (2) ◽  
pp. 261-271 ◽  
Author(s):  
Afroza Akhtar ◽  
Orville A. Pemberton ◽  
Yu Chen
Keyword(s):  
Substrate Specificity ◽  
Structural Basis ◽  
Class D

scholarly journals Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria

2020 ◽  
Vol 117 (28) ◽  
pp. 16324-16332
Author(s):  
Xiaobo Chen ◽  
Jiayue Chen ◽  
Bing Yan ◽  
Wei Zhang ◽  
Luke W. Guddat ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Mycobacterium Smegmatis ◽  
Hydrophobic Interactions ◽  
Carbon Chain ◽  
Structural Basis ◽  
Broad Substrate Specificity ◽  
Carbon Chains ◽  
Binding Cavity ◽  
Π Stacking Interaction ◽  
Acyl Coa Dehydrogenases

FadE, an acyl-CoA dehydrogenase, introduces unsaturation to carbon chains in lipid metabolism pathways. Here, we report that FadE5 fromMycobacterium tuberculosis(MtbFadE5) andMycobacterium smegmatis(MsFadE5) play roles in drug resistance and exhibit broad specificity for linear acyl-CoA substrates but have a preference for those with long carbon chains. Here, the structures ofMsFadE5 andMtbFadE5, in the presence and absence of substrates, have been determined. These reveal the molecular basis for the broad substrate specificity of these enzymes. FadE5 interacts with the CoA region of the substrate through a large number of hydrogen bonds and an unusual π–π stacking interaction, allowing these enzymes to accept both short- and long-chain substrates. Residues in the substrate binding cavity reorient their side chains to accommodate substrates of various lengths. Longer carbon-chain substrates make more numerous hydrophobic interactions with the enzyme compared with the shorter-chain substrates, resulting in a preference for this type of substrate.

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