Structural insights into the mechanisms of substrate recognition and catalysis for the N-methyltransferases involved in benzylisoquinoline alkaloid metabolism

Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.

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Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis

Journal of Molecular Biology ◽

10.1016/j.jmb.2019.10.009 ◽

2019 ◽

Vol 431 (24) ◽

pp. 4868-4881 ◽

Cited By ~ 2

Author(s):

Jieyu Tang ◽

Yingchen Ju ◽

Qiong Gu ◽

Jun Xu ◽

Huihao Zhou

Keyword(s):

Substrate Recognition ◽

Activity Regulation ◽

Structural Insights

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Structural Insights Into Substrate Recognition by theNeurosporaVarkud Satellite Ribozyme: Importance of U-Turns at the Kissing-Loop Junction

Biochemistry ◽

10.1021/bi401491g ◽

2013 ◽

Vol 53 (1) ◽

pp. 258-269 ◽

Cited By ~ 16

Author(s):

Patricia Bouchard ◽

Pascale Legault

Keyword(s):

Substrate Recognition ◽

Structural Insights ◽

Kissing Loop

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Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri

Biochimie ◽

10.1016/j.biochi.2017.03.015 ◽

2017 ◽

Vol 137 ◽

pp. 165-173 ◽

Cited By ~ 7

Author(s):

Rida Awad ◽

Pierre Gans ◽

Jean-Baptiste Reiser

Keyword(s):

Substrate Recognition ◽

Type I ◽

Lactobacillus Buchneri ◽

Fold Type ◽

Reaction Specificity ◽

Structural Insights

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Structural Insights into Substrate Recognition by Clostridium difficile Sortase

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2016.00160 ◽

2016 ◽

Vol 6 ◽

Cited By ~ 4

Author(s):

Jui-Chieh Yin ◽

Chun-Hsien Fei ◽

Yen-Chen Lo ◽

Yu-Yuan Hsiao ◽

Jyun-Cyuan Chang ◽

...

Keyword(s):

Clostridium Difficile ◽

Substrate Recognition ◽

Structural Insights

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Structural Insights into the Multispecific Recognition of Dipeptides of Deep-Sea Gram-Negative Bacterium Pseudoalteromonas sp. Strain SM9913

Journal of Bacteriology ◽

10.1128/jb.02600-14 ◽

2015 ◽

Vol 197 (6) ◽

pp. 1125-1134 ◽

Cited By ~ 5

Author(s):

Chun-Yang Li ◽

Xiu-Lan Chen ◽

Qi-Long Qin ◽

Peng Wang ◽

Wei-Xin Zhang ◽

...

Keyword(s):

Nitrogen Cycling ◽

Marine Bacteria ◽

Deep Sea ◽

Substrate Binding ◽

Substrate Recognition ◽

Recognition Mechanism ◽

Gram Negative ◽

Content Type ◽

Peptide Uptake ◽

Structural Insights

ABSTRACTPeptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-seaPseudoalteromonassp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements.PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism ofPsDppA, we solved the crystal structures of unligandedPsDppA and ofPsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr).PsDppA alternates between an “open” and a “closed” form during substrate binding. Structural analyses of the 4PsDppA-substrate complexes combined with mutational assays indicate thatPsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones andPsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism ofPsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake.IMPORTANCEPeptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria recognize and absorb peptides is still unclear. This study analyzed the substrate binding specificity of deep-seaPseudoalteromonassp. strain SM9913 DppA (PsDppA; the dipeptide-binding protein of dipeptide permease) and solved the crystal structures of unligandedPsDppA andPsDppA in complex with 4 different types of dipeptides. The multispecific recognition mechanism ofPsDppA for dipeptides is explained based on structural and mutational analyses. We also find that the substrate-binding mechanism ofPsDppA may be common in Gram-negative bacteria. This study sheds light on marine Gram-negative bacterial peptide uptake and marine nitrogen cycling.

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