scholarly journals Carbohydrate Kinases: A Conserved Mechanism Across Differing Folds

Catalysts ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 29 ◽  
Author(s):  
Sumita Roy ◽  
Mirella Vivoli Vega ◽  
Nicholas J. Harmer
Keyword(s):  
Hydrogen Bonds ◽  
Divalent Cation ◽  
Side Chain ◽  
Control Points ◽  
Critical Control Points ◽  
Wide Range ◽  
Common Strategy ◽  
Network Of Hydrogen Bonds ◽  
Main Protein ◽  
Positively Charged

Carbohydrate kinases activate a wide variety of monosaccharides by adding a phosphate group, usually from ATP. This modification is fundamental to saccharide utilization, and it is likely a very ancient reaction. Modern organisms contain carbohydrate kinases from at least five main protein families. These range from the highly specialized inositol kinases, to the ribokinases and galactokinases, which belong to families that phosphorylate a wide range of substrates. The carbohydrate kinases utilize a common strategy to drive the reaction between the sugar hydroxyl and the donor phosphate. Each sugar is held in position by a network of hydrogen bonds to the non-reactive hydroxyls (and other functional groups). The reactive hydroxyl is deprotonated, usually by an aspartic acid side chain acting as a catalytic base. The deprotonated hydroxyl then attacks the donor phosphate. The resulting pentacoordinate transition state is stabilized by an adjacent divalent cation, and sometimes by a positively charged protein side chain or the presence of an anion hole. Many carbohydrate kinases are allosterically regulated using a wide variety of strategies, due to their roles at critical control points in carbohydrate metabolism. The evolution of a similar mechanism in several folds highlights the elegance and simplicity of the catalytic scheme.

scholarly journals The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Han Han ◽  
Nicole Monroe ◽  
Wesley I Sundquist ◽  
Peter S Shen ◽  
Christopher P Hill
Keyword(s):  
Hydrogen Bonds ◽  
Main Chain ◽  
Substrate Binding ◽  
Conveyor Belt ◽  
Side Chain ◽  
Peptide Substrate ◽  
Aaa Atpase ◽  
Membrane Fission ◽  
Wide Range ◽  
Binding Pockets

The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (<xref ref-type="bibr" rid="bib29">Monroe et al., 2017</xref>), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a ‘conveyor belt’ model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end.

(R)-1-Hydroxybutan-2-ammonium (2R,3R)-tartrate monohydrate

2006 ◽  
Vol 62 (4) ◽  
pp. o1511-o1512 ◽  
Author(s):  
Yue-Cheng Zhang ◽  
Guo-Yi Bai ◽  
Tao Zeng ◽  
Jiang-Sheng Li ◽  
Xi-Long Yan
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Amino Group ◽  
Acid Molecule ◽  
Cationic Form ◽  
Compound C ◽  
Dimensional Network ◽  
Network Of Hydrogen Bonds ◽  
Tartrate Anion ◽  
Positively Charged

In the formation of the title compound, C4H12NO+·C4H5O6 −·H2O, the (R)-2-amino-1-butanol molecule is converted to a cationic form containing a positively charged amino group, and the tartaric acid molecule to a mono- or half-ionized tartrate anion. The structure is stabilized by a three-dimensional network of hydrogen bonds.

On-farm udder health monitoring

2011 ◽  
Vol 39 (02) ◽  
pp. 95-100
Author(s):  
J. C. van Veersen ◽  
O. Sampimon ◽  
R. G. Olde Riekerink ◽  
T. J. G. Lam
Keyword(s):  
Management Practices ◽  
Health Management ◽  
Action Plan ◽  
Real Life ◽  
Health Data ◽  
Control Points ◽  
Udder Health ◽  
Critical Control Points ◽  
On Farm ◽  
Clinical Problems

SummaryIn this article an on-farm monitoring approach on udder health is presented. Monitoring of udder health consists of regular collection and analysis of data and of the regular evaluation of management practices. The ultimate goal is to manage critical control points in udder health management, such as hygiene, body condition, teat ends and treatments, in such a way that results (udder health parameters) are always optimal. Mastitis, however, is a multifactorial disease, and in real life it is not possible to fully prevent all mastitis problems. Therefore udder health data are also monitored with the goal to pick up deviations before they lead to (clinical) problems. By quantifying udder health data and management, a farm is approached as a business, with much attention for efficiency, thought over processes, clear agreements and goals, and including evaluation of processes and results. The whole approach starts with setting SMART (Specific, Measurable, Acceptable, Realistic, Time-bound) goals, followed by an action plan to realize these goals.

Critical Control Points in DPR: Quantifying the Multi-Barrier Approach to Treatment

2015 ◽  
Vol 2015 (14) ◽  
pp. 5477-5488
Author(s):  
Ben Stanford ◽  
Troy Walker ◽  
Stuart Khan ◽  
Shane Snyder ◽  
Cedric Robillot
Keyword(s):  
Control Points ◽  
Critical Control Points

scholarly journals Structural Basis for Inhibition of Protein-tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics

2006 ◽  
Vol 281 (43) ◽  
pp. 32784-32795 ◽  
Author(s):  
Paul J. Ala ◽  
Lucie Gonneville ◽  
Milton C. Hillman ◽  
Mary Becker-Pasha ◽  
Min Wei ◽  
...  
Keyword(s):  
Protein Tyrosine Phosphatase ◽  
Tyrosine Phosphatase ◽  
Structural Basis ◽  
Side Chain ◽  
Protein Tyrosine Phosphatase 1B ◽  
Phosphate Binding ◽  
Protein Tyrosine ◽  
Starting Point ◽  
Network Of Hydrogen Bonds ◽  
Orthogonal Orientation

Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe182 of the flap, and the side chain of Arg221. When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors.

Critical control points for foods prepared in households whose members had either alleged typhoid fever or diarrhea

1988 ◽  
Vol 7 (2) ◽  
pp. 123-134 ◽  
Author(s):  
Silvia Michanie ◽  
Frank L. Bryan ◽  
Persia Alvarez ◽  
Auria Barros Olivo ◽  
Aurelio Paniagua
Keyword(s):  
Typhoid Fever ◽  
Control Points ◽  
Critical Control Points
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