scholarly journals Influence of Substrate Binding Residues on the Substrate Scope and Regioselectivity of a Plant O ‐Methyltransferase against Flavonoids

ChemCatChem ◽  
2020 ◽  
Vol 12 (14) ◽  
pp. 3721-3727
Author(s):  
Qingyun Tang ◽  
Yoanes M. Vianney ◽  
Klaus Weisz ◽  
Christoph W. Grathwol ◽  
Andreas Link ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Residues ◽  
Influence Of Substrate

scholarly journals Small Heat Shock Protein IbpB Acts as a Robust Chaperone in Living Cells by Hierarchically Activating Its Multi-type Substrate-binding Residues

2013 ◽  
Vol 288 (17) ◽  
pp. 11897-11906 ◽  
Author(s):  
Xinmiao Fu ◽  
Xiaodong Shi ◽  
Linxiang Yin ◽  
Jiafeng Liu ◽  
Keehyoung Joo ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Substrate Binding ◽  
Small Heat Shock Protein ◽  
Living Cells ◽  
Binding Residues

Catalytic Roles of Substrate-Binding Residues in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase

Biochemistry ◽  
2014 ◽  
Vol 53 (16) ◽  
pp. 2661-2671 ◽  
Author(s):  
Koichi Mori ◽  
Toshihiro Oiwa ◽  
Satoshi Kawaguchi ◽  
Kyosuke Kondo ◽  
Yusuke Takahashi ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Coenzyme B12 ◽  
Binding Residues

scholarly journals Structure of the Cdc48 segregase in the act of unfolding an authentic substrate

Science ◽  
2019 ◽  
Vol 365 (6452) ◽  
pp. 502-505 ◽  
Author(s):  
Ian Cooney ◽  
Han Han ◽  
Michael G. Stewart ◽  
Richard H. Carson ◽  
Daniel T. Hansen ◽  
...  
Keyword(s):  
Protein Translocation ◽  
Substrate Binding ◽  
Adaptor Protein ◽  
Biological Pathways ◽  
Protein Substrates ◽  
Adenosine Triphosphatases ◽  
Binding Residues ◽  
Aaa Atpases ◽  
Helical Configuration ◽  
Resolution Structure

The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom–resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases.

scholarly journals Crystal Structures of Yeast β-Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements

2007 ◽  
Vol 282 (49) ◽  
pp. 36037-36047 ◽  
Author(s):  
Stina Lundgren ◽  
Birgit Andersen ◽  
Jure Piškur ◽  
Doreen Dobritzsch
Keyword(s):  
Crystal Structures ◽  
Large Scale ◽  
Catalytic Domain ◽  
Substrate Binding ◽  
Salt Bridge ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
Dimerization Domain ◽  
Binding Residues ◽  
Present Site

β-Alanine synthase is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of uracil and thymine in higher organisms. The fold of the homodimeric enzyme from the yeast Saccharomyces kluyveri identifies it as a member of the AcyI/M20 family of metallopeptidases. Its subunit consists of a catalytic domain harboring a di-zinc center and a smaller dimerization domain. The present site-directed mutagenesis studies identify Glu159 and Arg322 as crucial for catalysis and His262 and His397 as functionally important but not essential. We determined the crystal structures of wild-type β-alanine synthase in complex with the reaction product β-alanine, and of the mutant E159A with the substrate N-carbamyl-β-alanine, revealing the closed state of a dimeric AcyI/M20 metallopeptidase-like enzyme. Subunit closure is achieved by a ∼30° rigid body domain rotation, which completes the active site by integration of substrate binding residues that belong to the dimerization domain of the same or the partner subunit. Substrate binding is achieved via a salt bridge, a number of hydrogen bonds, and coordination to one of the zinc ions of the di-metal center.

Glycosidic bond specificity of glucansucrases: on the role of acceptor substrate binding residues

2012 ◽  
Vol 30 (3) ◽  
pp. 366-376 ◽  
Author(s):  
Hans Leemhuis ◽  
Tjaard Pijning ◽  
Justyna M. Dobruchowska ◽  
Bauke W. Dijkstra ◽  
Lubbert Dijkhuizen
Keyword(s):  
Substrate Binding ◽  
Glycosidic Bond ◽  
Acceptor Substrate ◽  
Binding Residues

scholarly journals Mutagenesis of the NS3 Protease of Dengue Virus Type 2

1998 ◽  
Vol 72 (1) ◽  
pp. 624-632 ◽  
Author(s):  
Rosaura P. C. Valle ◽  
Barry Falgout
Keyword(s):  
Amino Acid ◽  
Dengue Virus ◽  
Virus Type ◽  
Protease Activity ◽  
Substrate Binding ◽  
Amino Terminal ◽  
Binding Residues ◽  
Ns3 Protease ◽  
Dengue Virus Type 2

ABSTRACT The flavivirus protease is composed of two viral proteins, NS2B and NS3. The amino-terminal portion of NS3 contains sequence and structural motifs characteristic of bacterial and cellular trypsin-like proteases. We have undertaken a mutational analysis of the region of NS3 which contains the catalytic serine, five putative substrate binding residues, and several residues that are highly conserved among flavivirus proteases and among all serine proteases. In all, 46 single-amino-acid substitutions were created in a cloned NS2B-NS3 cDNA fragment of dengue virus type 2, and the effect of each mutation on the extent of self-cleavage of the NS2B-NS3 precursor at the NS2B-NS3 junction was assayed in vivo. Twelve mutations almost completely or completely inhibited protease activity, 9 significantly reduced it, 14 decreased cleavage, and 11 yielded wild-type levels of activity. Substitution of alanine at ultraconserved residues abolished NS3 protease activity. Cleavage was also inhibited by substituting some residues that are conserved among flavivirus NS3 proteins. Two (Y150 and G153) of the five putative substrate binding residues could not be replaced by alanine, and only Y150 and N152 could be replaced by a conservative change. The two other putative substrate binding residues, D129 and F130, were more freely substitutable. By analogy with the trypsin model, it was proposed that D129 is located at the bottom of the substrate binding pocket so as to directly interact with the basic amino acid at the substrate cleavage site. Interestingly, we found that significant cleavage activity was displayed by mutants in which D129 was replaced by E, S, or A and that low but detectable protease activity was exhibited by mutants in which D129 was replaced by K, R, or L. Contrary to the proposed model, these results indicate that D129 is not a major determinant of substrate binding and that its interaction with the substrate, if it occurs at all, is not essential. This mutagenesis study provided us with an array of mutations that alter the cleavage efficiency of the dengue virus protease. Mutations that decrease protease activity without abolishing it are candidates for introduction into the dengue virus infectious full-length cDNA clone with the aim of creating potentially attenuated virus stocks.

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