Multiple Solvent Crystal Structures: Probing Binding Sites, Plasticity and Hydration

2006 ◽  
Vol 357 (5) ◽  
pp. 1471-1482 ◽  
Author(s):  
Carla Mattos ◽  
Cornelia R. Bellamacina ◽  
Ezra Peisach ◽  
Antonio Pereira ◽  
Dennis Vitkup ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Sites

scholarly journals Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Seiya Watanabe ◽  
Yohsuke Murase ◽  
Yasunori Watanabe ◽  
Yasuhiro Sakurai ◽  
Kunihiko Tajima
Keyword(s):  
Molecular Evolution ◽  
Agrobacterium Tumefaciens ◽  
Crystal Structures ◽  
Epr Spectroscopy ◽  
Binding Sites ◽  
Active Sites ◽  
Type I ◽  
Type Ii ◽  
Thermococcus Kodakarensis ◽  
Evolutionary Scenario

AbstractAconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.

scholarly journals Crystal Structures of Ral-GppNHp and Ral-GDP Reveal Two Binding Sites that Are Also Present in Ras and Rap

Structure ◽  
2004 ◽  
Vol 12 (11) ◽  
pp. 2025-2036 ◽  
Author(s):  
Nathan I. Nicely ◽  
Justin Kosak ◽  
Vesna de Serrano ◽  
Carla Mattos
Keyword(s):  
Crystal Structures ◽  
Binding Sites

Peptide-Binding Sites As Revealed by the Crystal Structures of the Human Hsp40 Hdj1 C-Terminal Domain in Complex with the Octapeptide from Human Hsp70

Biochemistry ◽  
2010 ◽  
Vol 49 (39) ◽  
pp. 8577-8584 ◽  
Author(s):  
Hironori Suzuki ◽  
Shuji Noguchi ◽  
Hiroshi Arakawa ◽  
Tadaaki Tokida ◽  
Mariko Hashimoto ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Sites ◽  
Peptide Binding ◽  
Terminal Domain ◽  
Human Hsp70

Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation 1 1Edited by P. E. Wright

2000 ◽  
Vol 296 (4) ◽  
pp. 1001-1015 ◽  
Author(s):  
Alexander E Aleshin ◽  
Christina Kirby ◽  
Xiaofeng Liu ◽  
Gleb P Bourenkov ◽  
Hans D Bartunik ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Binding Sites ◽  
Allosteric Regulation

scholarly journals Molecular recognition of M1-linked ubiquitin chains by native and phosphorylated UBAN domains

2019 ◽  
Author(s):  
Lina Herhaus ◽  
Henry van den Bedem ◽  
Sean Tang ◽  
Soichi Wakatsuki ◽  
Ivan Dikic ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Sites ◽  
Coiled Coil ◽  
Domain Specificity ◽  
Binding Properties ◽  
Post Translational Modifications ◽  
Binding Characteristics ◽  
Binding Stoichiometry ◽  
Coil Structure ◽  
Concentration Dependency

AbstractAlthough the Ub-binding domain in ABIN proteins and NEMO (UBAN) is highly conserved, UBAN-containing proteins exhibit different Ub-binding properties, resulting in their diverse biological roles. Post-translational modifications further control UBAN domain specificity for poly-Ub chains. However, precisely, how the UBAN domain structurally confers such functional diversity remains poorly understood. Here we report crystal structures of ABIN-1 alone and in complex with one or two M1-linked di-Ub chains. ABIN-1 UBAN forms a homo-dimer that provides two symmetrical Ub-binding sites on either side of the coiled-coil structure. Moreover, crystal structures of ABIN1 UBAN in complex with di-Ub chains reveal a concentration-dependency of UBAN/di-Ub binding stoichiometry. Analysis of UBAN/M1-linked di-Ub binding characteristics indicates that phosphorylated S473 in OPTN and its corresponding phospho-mimetic residue in ABIN-1 (E484) are essential for high affinity interactions with M1-linked Ub chains. Also, a phospho-mimetic mutation of A303 in NEMO, corresponding to S473 of OPTN, increases binding affinity for M1-linked Ub chains. These findings are in line with the diverse physiological roles of UBAN domains, as phosphorylation of OPTN UBAN is required to enhance its binding to Ub during mitophagy.

scholarly journals Molecular dynamics simulations of zfP2X4 receptors

2021 ◽  
Author(s):  
kalyan immadisetty ◽  
Peter Kekenes-Huskey
Keyword(s):  
Molecular Dynamics ◽  
Crystal Structures ◽  
Metal Binding ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Pain Perception ◽  
Gulf Coast ◽  
Md Simulations ◽  
P2x Receptor ◽  
Metal Binding Sites

The ATP activated P2X4 receptor plays a prominent role in pain perception and modulation and thus may constitute an alternative therapeutic target for controlling pain. Given the biomedical relevance of P2X4 receptors, and poor understanding of molecular mechanisms that describe its gating by ATP, a fundamental understanding of the functional mechanism of these channels is warranted. Through classical all-atom molecular dynamics (MD) simulations we investigated the number of ATP molecules required to open (activate) the receptor for it to conduct ions. Since crystal structures of human P2X4 are not yet available, the crystal structures of highly-homologous zebrafish P2X4 (zfP2X4) structures were utilized for this study. It has been identified that at least two ATP molecules are required to prevent the open state receptor from collapsing back to a closed state. Additionally, we have discovered two metal binding sites, one at the intersection of the three monomers in the ectodomain (MBS1) and the second one near the ATP binding site (MBS2), both of which are occupied by the potassium ions. This observation draws its comparison to the gulf coast P2X receptor that it possesses the same two metal binding sites, however, MBS1 and MBS2 in this receptor are occupied by zinc and magnesium, respectively.

Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose

2019 ◽  
Vol 75 (12) ◽  
pp. 1138-1147
Author(s):  
Hsiao-Chuan Huang ◽  
Liu-Hong Qi ◽  
Yo-Chia Chen ◽  
Li-Chu Tsai
Keyword(s):  
Enzymatic Hydrolysis ◽  
Crystal Structures ◽  
Active Site ◽  
Binding Sites ◽  
Glycoside Hydrolase ◽  
Catalytic Domain ◽  
Glycoside Hydrolase Family ◽  
Substrate Binding Sites ◽  
Key Residues ◽  
Hydrolase Family

The catalytic domain (residues 128–449) of the Orpinomyces sp. Y102 CelC7 enzyme (Orp CelC7) exhibits cellobiohydrolase and cellotriohydrolase activities. Crystal structures of Orp CelC7 and its cellobiose-bound complex have been solved at resolutions of 1.80 and 2.78 Å, respectively. Cellobiose occupies subsites +1 and +2 within the active site of Orp CelC7 and forms hydrogen bonds to two key residues: Asp248 and Asp409. Furthermore, its substrate-binding sites have both tunnel-like and open-cleft conformations, suggesting that the glycoside hydrolase family 6 (GH6) Orp CelC7 enzyme may perform enzymatic hydrolysis in the same way as endoglucanases and cellobiohydrolases. LC-MS/MS analysis revealed cellobiose (major) and cellotriose (minor) to be the respective products of endo and exo activity of the GH6 Orp CelC7.

scholarly journals Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

2020 ◽  
Vol 76 (1) ◽  
pp. 122-136 ◽  
Author(s):  
Ivana S. Đorđević ◽  
Marko Popadić ◽  
Mirjana Sarvan ◽  
Marija Petković-Benazzouz ◽  
Goran V. Janjić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Binding Sites ◽  
Quantum Chemical ◽  
Electrostatic Interactions ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Structural Database ◽  
Insight Into ◽  
Influence Of Substituents

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C—H...Se and C—H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C—H...Se (∼−0.8 kcal mol−1) and C—H...S interactions are weaker than the most stable parallel interaction (∼−3.3 kcal mol−1) and electrostatic interactions of σ/π type (∼−2.6 kcal mol−1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O—H...Se (∼−4.4 kcal mol−1) and N—H...Se interactions (∼−2.2 kcal mol−1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography

2020 ◽  
Author(s):  
Florentina Tofoleanu ◽  
Lesley Earl ◽  
Frank Pickard ◽  
Bernard Brooks
Keyword(s):  
Crystal Structures ◽  
Binding Sites ◽  
Md Simulations ◽  
Water Molecules ◽  
Water Residence Time ◽  
Solvent Exposure ◽  
X Ray ◽  
Protein Residues ◽  
X Ray Crystallography ◽  
Beta Galactosidase

<p>We start from the water placement in cryo-EM maps and in X-ray crystal structures of beta-galactosidase. We apply MD simulations to analyze the behavior of the placed water, and how they are bound to the protein residues. We analyze the solvent exposure of binding sites for water, and the water residence time at these locations. Through a statistical analysis, we conclude that water placed by cryo-EM has a similar behavior to conserved water across multiple crystal structures.</p>

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