scholarly journals Allosteric Regulation of the Photosynthetic C4 Isoenzyme of Phosphoenolpyruvate Carboxylase: A Comparative Study Between Enzymes from Monocot and Dicot Plants

2017 ◽  
Vol 56 (1) ◽  
Author(s):  
Rodrigo Güémez-Toro ◽  
Carlos Mújica-Jiménez ◽  
Rosario A. Muñoz-Clares
Keyword(s):  
Phosphoenolpyruvate Carboxylase ◽  
Allosteric Regulation ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Velocity Data ◽  
Structural Determinants ◽  
Multiple Alignments ◽  
High Flexibility ◽  
Loop Conformation ◽  
Conserved Residue

In the present study, we have investigated the complex allosteric regulation of the non-phosphorylated forms of the photosynthetic phosphoenolpyruvate carboxylase isoenzymes (PEPC-C4) from amaranth (AhPEPC-C4) and maize (ZmPEPC-C4) leaves. Previous studies showed that glycine (Gly) only activates PEPC-C4 from monocot plants, as maize, but not from dicot plants, as amaranth. Our initial velocity data confirm this, in spite that AhPEPC-C4 binds Gly with much higher affinity than ZmPEPC-C4. In AhPEPC-C4, the lack of Gly activation is overcome mainly by its higher affinity for the substrate phosphoenolpyruvate and its lower affinity for the inhibitor malate compared with ZmPEPC-C4. We have also explored the structural determinants of the differences in Gly activation by performing multiple alignments between the known monocot and dicot PEPC-C4 sequences and by modeling, in both the AhPEPC-C4 and ZmPEPC-C4 isoenzymes, the three-dimensional structure of the loop proposed as the Gly binding site, which was not observed in the crystal structure of the maize enzyme due to its high flexibility. The models suggest that conserved lysyl and aspartyl residues are important for binding to the activator molecule, and that a nearby non-conserved residue may be responsible for differences between the amaranth and maize enzymes in the loop conformation, which would account for the poorer affinity for Gly of the maize enzyme as well as for its higher degree of activation.

scholarly journals Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum

2013 ◽  
Vol 288 (23) ◽  
pp. 16460-16475 ◽  
Author(s):  
Linda J. Olson ◽  
Ramiro Orsi ◽  
Solana G. Alculumbre ◽  
Francis C. Peterson ◽  
Ivan D. Stigliano ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Mannose Residue ◽  
Glucosidase Ii ◽  
Mannose 6 Phosphate ◽  
First Time ◽  
Conserved Residue

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.

scholarly journals The structural determinants of intra-protein compensatory substitutions

2021 ◽  
Author(s):  
Shilpi Chaurasia ◽  
Julien Y Dutheil
Keyword(s):  
Fitness Landscape ◽  
General Scheme ◽  
Protein Structures ◽  
Three Dimensional ◽  
Charge Compensation ◽  
Dimensional Structure ◽  
Solvent Exposure ◽  
Structural Determinants ◽  
Sequence Alignments ◽  
Compensatory Mutations

Compensating substitutions happen when one mutation is advantageously selected because it restores the loss of fitness induced by a previous deleterious mutation. How frequent such mutations occur in evolution and what is the structural and functional context permitting their emergence remain open questions. We built an atlas of intra-protein compensatory substitutions using a phylogenetic approach and a dataset of 1,630 bacterial protein families for which high-quality sequence alignments and experimentally derived protein structures were available. We identified more than 51,000 positions coevolving by the mean of predicted compensatory mutations. Using the evolutionary and structural properties of the analyzed positions, we demonstrate that compensatory mutations are scarce (typically only a few in the protein history) but widespread (the majority of proteins experienced at least one). Typical coevolving residues are evolving slowly, are located in the protein core outside secondary structure motifs, and are more often in contact than expected by chance, even after accounting for their evolutionary rate and solvent exposure. An exception to this general scheme are residues coevolving for charge compensation, which are evolving faster than non-coevolving sites, in contradiction with predictions from simple coevolutionary models, but similar to stem pairs in RNA. While sites with a significant pattern of coevolution by compensatory mutations are rare, the comparative analysis of hundreds of structures ultimately permits a better understanding of the link between the three-dimensional structure of a protein and its fitness landscape.

scholarly journals Structure–Function Relationships of the Repeat Domains of RTX Toxins

Toxins ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 657 ◽  
Author(s):  
Ulrich Baumann
Keyword(s):  
Calcium Binding ◽  
Tandem Repeats ◽  
Three Dimensional ◽  
Large Family ◽  
Variable Number ◽  
General Purpose ◽  
Dimensional Structure ◽  
Type I ◽  
Structural Determinants ◽  
Extracellular Medium

RTX proteins are a large family of polypeptides of mainly Gram-negative origin that are secreted into the extracellular medium by a type I secretion system featuring a non-cleavable C-terminal secretion signal, which is preceded by a variable number of nine-residue tandem repeats. The three-dimensional structure forms a parallel β-roll, where β-strands of two parallel sheets are connected by calcium-binding linkers in such a way that a right-handed spiral is built. The Ca2+ ions are an integral part of the structure, which cannot form without them. The structural determinants of this unique architecture will be reviewed with its conservations and variations together with the implication for secretion and folding of these proteins. The general purpose of the RTX domains appears to act as an internal chaperone that keeps the polypeptide unfolded in the calcium-deprived cytosol and triggers folding in the calcium-rich extracellular medium. A rather recent addition to the structural biology of the RTX toxin is a variant occurring in a large RTX adhesin, where this non-canonical β-roll binds to ice and diatoms.

scholarly journals Structural model of a putrescine-cadaverine permease from Trypanosoma cruzi predicts residues vital for transport and ligand binding

2013 ◽  
Vol 452 (3) ◽  
pp. 423-432 ◽  
Author(s):  
Radika Soysa ◽  
Hanka Venselaar ◽  
Jacqueline Poston ◽  
Buddy Ullman ◽  
Marie-Pierre Hasne
Keyword(s):  
Trypanosoma Cruzi ◽  
Structural Model ◽  
Three Dimensional ◽  
Salt Bridge ◽  
Homology Model ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Helical Structures ◽  
Structural Determinants ◽  
Key Residues

The TcPOT1.1 gene from Trypanosoma cruzi encodes a high affinity putrescine-cadaverine transporter belonging to the APC (amino acid/polyamine/organocation) transporter superfamily. No experimental three-dimensional structure exists for any eukaryotic member of the APC family, and thus the structural determinants critical for function of these permeases are unknown. To elucidate the key residues involved in putrescine translocation and recognition by this APC family member, a homology model of TcPOT1.1 was constructed on the basis of the atomic co-ordinates of the Escherichia coli AdiC arginine/agmatine antiporter crystal structure. The TcPOT1.1 homology model consisted of 12 transmembrane helices with the first ten helices organized in two V-shaped antiparallel domains with discontinuities in the helical structures of transmembrane spans 1 and 6. The model suggests that Trp241 and a Glu247–Arg403 salt bridge participate in a gating system and that Asn245, Tyr148 and Tyr400 contribute to the putrescine-binding pocket. To test the validity of the model, 26 site-directed mutants were created and tested for their ability to transport putrescine and to localize to the parasite cell surface. These results support the robustness of the TcPOT1.1 homology model and reveal the importance of specific aromatic residues in the TcPOT1.1 putrescine-binding pocket.

scholarly journals Allosteric Modulation of Ligand Gated Ion Channels by Ivermectin

2014 ◽  
pp. S215-S224 ◽  
Author(s):  
H. ZEMKOVA ◽  
V. TVRDONOVA ◽  
A. BHATTACHARYA ◽  
M. JINDRICHOVA
Keyword(s):  
Ion Channels ◽  
Binding Site ◽  
Glycine Receptor ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Determinants ◽  
P2x4 Receptor ◽  
Electrophysiological Recordings ◽  
Gated Ion Channels ◽  
Ligand Gated Ion Channels

Ivermectin acts as a positive allosteric regulator of several ligand-gated channels including the glutamate-gated chloride channel (GluCl),  aminobutyric acid type-A receptor, glycine receptor, neuronal α7-nicotinic receptor and purinergic P2X4 receptor. In most of the ivermectin-sensitive channels, the effects of ivermectin include the potentiation of agonist-induced currents at low concentrations and channel opening at higher concentrations. Based on mutagenesis, electrophysiological recordings and functional analysis of chimeras between ivermectin-sensitive and ivermectin-insensitive receptors, it has been concluded that ivermectin acts by insertion between transmembrane helices. The three-dimensional structure of C. elegans GluCl complexed with ivermectin has revealed the details of the ivermectin-binding site, however, no generic motif of amino acids could accurately predict ivermectin binding site for other ligand gated channels. Here, we will review what is currently known about ivermectin binding and modulation of Cys-loop receptor family of ligand-gated ion channels and what are the critical structural determinants underlying potentiation of the P2X4 receptor channel.

Identification of a region of strong discrimination in the pore of CFTR

2001 ◽  
Vol 281 (4) ◽  
pp. L852-L867 ◽  
Author(s):  
Nael A. McCarty ◽  
Zhi-Ren Zhang
Keyword(s):  
Cystic Fibrosis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Transmembrane Conductance Regulator ◽  
Transmembrane Conductance ◽  
Structural Determinants ◽  
Anion Selectivity ◽  
Relative Conductance ◽  
Pore Domain ◽  
Cystic Fibrosis Transmembrane

The variety of methods used to identify the structural determinants of anion selectivity in the cystic fibrosis transmembrane conductance regulator Cl− channel has made it difficult to assemble the data into a coherent framework that describes the three-dimensional structure of the pore. Here, we compare the relative importance of sites previously studied and identify new sites that contribute strongly to anion selectivity. We studied Cl−and substitute anions in oocytes expressing wild-type cystic fibrosis transmembrane conductance regulator or 12-pore-domain mutants to determine relative permeability and relative conductance for 9 monovalent anions and 1 divalent anion. The data indicate that the region of strong discrimination resides between T338 and S341 in transmembrane 6, where mutations affected selectivity between Cl− and both large and small anions. Mutations further toward the extracellular end of the pore only strongly affected selectivity between Cl− and larger anions. Only mutations at S341 affected selectivity between monovalent and divalent anions. The data are consistent with a narrowing of the pore between the extracellular end and a constriction near the middle of the pore.

scholarly journals Structural determinants defining common stereoselectivity of lipases toward secondary alcohols

1995 ◽  
Vol 41 (13) ◽  
pp. 289-296 ◽  
Author(s):  
Miroslaw Cygler ◽  
Pawel Grochulski ◽  
Joseph D. Schrag
Keyword(s):  
Molecular Basis ◽  
Candida Rugosa ◽  
Three Dimensional ◽  
Geotrichum Candidum ◽  
Fatty Acyl ◽  
Dimensional Structure ◽  
Secondary Alcohols ◽  
Structural Determinants ◽  
Conformational Rearrangement ◽  
Hydrolysis Of

In this review we summarize some aspects of the enantiopreference of the lipase from Candida rugosa following structural analysis of complexes of this lipase with two enantiomers of an analog of a tetrahedral intermediate in the hydrolysis of simple esters. The analysis of the molecular basis of the enantiomeric differentiation suggests that these results can be generalized to a large class of lipases and esterases. We also summarize our experiments on identification of the key regions in the lipases from Geotrichum candidum lipase responsible for differentiation between fatty acyl chains.Key words: lipases, stereoselectivity, three-dimensional structure, conformational rearrangement.

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