scholarly journals A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A

2003 ◽  
Vol 185 (14) ◽  
pp. 4074-4080 ◽  
Author(s):  
Tina Izard
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Binding Site ◽  
Active Site ◽  
Binding Sites ◽  
Biosynthetic Pathway ◽  
Coenzyme A ◽  
Asymmetric Unit ◽  
Phosphate Moiety ◽  
Reversible Transfer

ABSTRACT Phosphopantetheine adenylyltransferase (PPAT) regulates the key penultimate step in the essential coenzyme A (CoA) biosynthetic pathway. PPAT catalyzes the reversible transfer of an adenylyl group from Mg2+:ATP to 4′-phosphopantetheine to form 3′-dephospho-CoA (dPCoA) and pyrophosphate. The high-resolution crystal structure of PPAT complexed with CoA has been determined. Remarkably, CoA and the product dPCoA bind to the active site in distinct ways. Although the phosphate moiety within the phosphopantetheine arm overlaps, the pantetheine arm binds to the same pocket in two distinct conformations, and the adenylyl moieties of these two ligands have distinct binding sites. Moreover, the PPAT:CoA crystal structure confirms the asymmetry of binding to the two trimers within the hexameric enzyme. Specifically, the pantetheine arm of CoA bound to one protomer within the asymmetric unit displays the dPCoA-like conformation with the adenylyl moiety disordered, whereas CoA binds the twofold-related protomer in an ordered and unique fashion.

scholarly journals Calixarene-mediated assembly of a small antifungal protein

IUCrJ ◽  
2019 ◽  
Vol 6 (2) ◽  
pp. 238-247 ◽  
Author(s):  
Jimi M. Alex ◽  
Martin L. Rennie ◽  
Sylvain Engilberge ◽  
Gábor Lehoczki ◽  
Hajdu Dorottya ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Antifungal Activity ◽  
High Resolution ◽  
Complex Formation ◽  
Binding Site ◽  
Crystal Structures ◽  
Protein Assembly ◽  
Bidentate Ligand ◽  
Antifungal Protein ◽  
Protein Recognition

Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.

scholarly journals Crystal structure of a pyridoxal 5′-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii

2017 ◽  
Vol 73 (12) ◽  
pp. 651-656 ◽  
Author(s):  
Taichi Mizobuchi ◽  
Risako Nonaka ◽  
Motoki Yoshimura ◽  
Katsumasa Abe ◽  
Shouji Takahashi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Active Site ◽  
Metal Binding ◽  
Bivalve Mollusc ◽  
Active Site Residues ◽  
X Ray ◽  
Aspartate Racemase ◽  
Scapharca Broughtonii

Aspartate racemase (AspR) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 Å resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site. Superposition of the structures of SbAspR and of rat SR bound to the inhibitor malonate reveals that Arg140 recognizes the β-carboxyl group of the substrate aspartate in SbAspR. It is hypothesized that the aromatic proline interaction between the domains, which favours the closed form of SbAspR, influences the arrangement of Arg140 at the active site.

Corrigendum to “Ultra-high Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor TMC114” [J. Mol. Biol. 363 (2006) 161–173]

2007 ◽  
Vol 365 (3) ◽  
pp. 901
Author(s):  
Andrey Y. Kovalevsky ◽  
Fengling Liu ◽  
Sofiya Leshchenko ◽  
Arun K. Ghosh ◽  
John M. Louis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Binding Sites ◽  
Hiv 1

scholarly journals The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA-binding site

2012 ◽  
Vol 21 (11) ◽  
pp. 1754-1767 ◽  
Author(s):  
Andrew B. Min ◽  
Linda Miallau ◽  
Michael R. Sawaya ◽  
Jeff Habel ◽  
Duilio Cascio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Active Site ◽  
Rna Binding

Difference in Conformation of Virginiamycin M1 in Chloroform and Bound Form in the 50S Ribosome or Streptogramin Acetyltransferase

2004 ◽  
Vol 57 (5) ◽  
pp. 415 ◽  
Author(s):  
Jason Dang ◽  
B. Mikael Bergdahl ◽  
Frances Separovic ◽  
Robert T. C. Brownlee ◽  
Robert P. Metzger
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Active Site ◽  
Major Change ◽  
X Ray ◽  
Binding Process ◽  
High Resolution Nmr ◽  
Virginiamycin M1

The conformation of virginiamycin M1 (VM1) in chloroform, determined by high-resolution NMR experiments, differs significantly from that of the X-ray crystal structure of VM1 bound to the 50S ribosome and to the active site of a streptogramin acetyltransferase enzyme. This implies that the binding process to these entities causes a major change in VM1 conformation.

Crystal structure study of selected xanthine derivatives

2010 ◽  
Vol 43 (1) ◽  
pp. 163-167 ◽  
Author(s):  
W. Lasocha ◽  
B. Gaweł ◽  
A. Rafalska-Lasocha ◽  
M. Pawłowski ◽  
P. Talik ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Powder Diffraction ◽  
Structure Study ◽  
Asymmetric Unit ◽  
Pharmaceutical Samples ◽  
X Ray ◽  
Xanthine Derivatives ◽  
Structure Solution ◽  
Theophylline Derivatives

The crystal structures of two compounds belonging to a group of theophylline derivatives have been solved by X-ray powder diffraction methods. Despite the fact that these compounds seemed to be rather simple (23 atoms in an asymmetric unit), the preferred orientation and dominant zone problems created very serious obstacles in the investigations, even for the most modern powder diffraction methods. The crystal structure of the first compound, 8-phenylazoxanthine, C14H14N6O2, was finally solved from laboratory diffractometer data, while in the case of the second compound, 8-(3-bromobenzylidene)xanthine, C15H14N5O2Br, it was not possible to reliably index its diffraction pattern until data had been collected at the high-resolution powder diffractometer ID31 at the ESRF Grenoble. The serious problems encountered during anab initiocrystal structure solution from powder data of these pharmaceutical samples are described and discussed.

Selectivity of the surface binding site (SBS) on barley starch synthase I

Biologia ◽  
2014 ◽  
Vol 69 (9) ◽  
Author(s):  
Casper Wilkens ◽  
Jose Cuesta-Seijo ◽  
Monica Palcic ◽  
Birte Svensson
Keyword(s):  
Crystal Structure ◽  
Surface Plasmon Resonance ◽  
Binding Site ◽  
Active Site ◽  
Mutational Analysis ◽  
Starch Synthase ◽  
Surface Binding ◽  
Binding Studies ◽  
A Chain ◽  
Surface Binding Site

AbstractStarch synthase I (SSI) from various sources has been shown to preferentially elongate branch chains of degree of polymerisation (DP) from 6–7 to produce chains of DP 8–12. In the recently determined crystal structure of barley starch synthase I (HvSSI) a so-called surface binding site (SBS) was seen, which was found by mutational analysis to be essential for the activity of HvSSI on glycogen. We now show in binding studies using surface plasmon resonance that HvSSI has no detectable affinity for malto-triose and -tetraose, but clearly binds maltopentaose, -hexaose, -heptaose (M7) and β-cyclodextrin (β-CD) albeit with a measurable K D for only β-CD and M7. Moreover, an HvSSI SBS mutant F538A lost the ability to bind β-CD and maltooligosaccharides. This behaviour suggests that a chain in the α-glucan molecule (amylopectin) that is undergoing extension attaches itself at the SBS and that the active site itself, likely working on a different end chain, has low affinity for both substrate and product.

scholarly journals Self-association configures the NAD+-binding site of plant NLR TIR domains

2021 ◽  
Author(s):  
Hayden Burdett ◽  
Xiahao Hu ◽  
Maxwell X Rank ◽  
Natsumi Maruta ◽  
Bostjan Kobe
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Active Site ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Structural Features ◽  
Active Conformation ◽  
Effector Triggered Immunity ◽  
Self Association ◽  
Tir Domains

TIR domains are signalling domains present in plant nucleotide-binding leucine-rich repeat receptors (NLRs), with key roles in plant innate immunity. They are required for the induction of a hypersensitive response (HR) in effector-triggered immunity, but the mechanism by which this occurs is not yet fully understood. It has been recently shown that the TIR domains from several plant NLRs possess NADase activity. The oligomeric structure of TIR-containing NLRs ROQ1 and RPP1 reveals how the TIR domains arrange into an active conformation, but low resolution around the NAD+ binding sites leaves questions unanswered about the molecular mechanisms linking self-association and NADase activity. In this study, a number of crystal structures of the TIR domain from the grapevine NLR RUN1 reveal how self-association and enzymatic activity may be linked. Structural features previously proposed to play roles involve the ″AE interface″ (mediated by helices A and E), the ″BB-loop″ (connecting β-strand B and helix B in the structure), and the ″BE interface″ (mediated by the BB-loop from one TIR and the ″DE surface″ of another). We demonstrate that self-association through the AE interface induces conformational changes in the NAD+-binding site, shifting the BB-loop away from the catalytic site and allowing NAD+ to access the active site. We propose that an intact ″DE surface″ is necessary for production of the signalling product (variant cyclic ADPR), as it constitutes part of the active site. Addition of NAD+ or NADP+ is not sufficient to induce self-association, suggesting that NAD+ binding occurs after TIR self-association. Our study identifies a mechanistic link between TIR self-association and NADase activity.

Molecular Modeling and Virtual Screening of Molecular Inhibitors for Leptospiral Collagenase

2021 ◽  
Author(s):  
Vikram Kumar ◽  
Nagesh Srikaku ◽  
Veeranarayanan Surya Aathmanathan ◽  
Padikara K Satheeshkumar ◽  
Madanan Gopalakrishnan Madathiparambil ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Modeling ◽  
Active Site ◽  
Binding Sites ◽  
Catalytic Site ◽  
Simulation Studies ◽  
C Terminus ◽  
Ligand Binding Sites ◽  
N Terminus ◽  
The Stability

Abstract Collagenase is a virulence factor which facilitates the invasion of pathogenic Leptospira into the host. In the present study, the model of Leptopsiral collagenase was constructed by employing threading method with the crystal structure of collagenase G. Three ligand binding sites at N- terminus, catalytic site and C-terminus were predicted by Metapocket server. Among sixty seven inhibitors from the ChEBI and Zinc databases, Protohypericin is predicted as the best inhibitor since it binds at the catalytic site of Leptopsiral collagenase. Molecular dynamic simulation studies validated the stability of interaction between the active site of Leptospiral collagenase and Protohypericin. The docking and molecular simulation studies corroborated the potential of the ligand to curb leptospiral infection.

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