Stereochemistry of Nucleic Acids and Their Constituents. VIII. Metal Binding Studies. Crystal Structure of a Guanine-Copper Chloride Complex, a Trigonal-Bipyramidally Coordinated Copper

1970 ◽  
Vol 92 (2) ◽  
pp. 369-371 ◽  
Author(s):  
J A. Carrabine ◽  
M. Sundaralingam
Keyword(s):  
Crystal Structure ◽  
Nucleic Acids ◽  
Metal Binding ◽  
Copper Chloride ◽  
Chloride Complex ◽  
Binding Studies

scholarly journals Crystal Structure of Exotoxin A from Aeromonas Pathogenic Species

Toxins ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 397 ◽  
Author(s):  
Geoffrey Masuyer
Keyword(s):  
Crystal Structure ◽  
Metal Binding ◽  
Elongation Factor ◽  
Pathogenic Species ◽  
Exotoxin A ◽  
Pseudomonas Exotoxin A ◽  
Eukaryotic Elongation Factor 2 ◽  
Eukaryotic Elongation Factor ◽  
Bacterial Virulence Factor ◽  
Interdomain Interactions

Aeromonas exotoxin A (AE) is a bacterial virulence factor recently discovered in a clinical case of necrotising fasciitis caused by the flesh-eating Aeromonas hydrophila. Here, database mining shows that AE is present in the genome of several emerging Aeromonas pathogenic species. The X-ray crystal structure of AE was solved at 2.3 Å and presents all the hallmarks common to diphthamide-specific mono-ADP-ribosylating toxins, suggesting AE is a fourth member of this family alongside the diphtheria toxin, Pseudomonas exotoxin A and cholix. Structural homology indicates AE may use a similar mechanism of cytotoxicity that targets eukaryotic elongation factor 2 and thus inhibition of protein synthesis. The structure of AE also highlights unique features including a metal binding site, and a negatively charged cleft that could play a role in interdomain interactions and may affect toxicity. This study raises new opportunities to engineer alternative toxin-based molecules with pharmaceutical potential.

Chemical Modification and Metal Binding Studies ofDatura innoxia

1996 ◽  
Vol 30 (1) ◽  
pp. 110-114 ◽  
Author(s):  
Lawrence R. Drake ◽  
Shan Lin ◽  
Gary D. Rayson ◽  
Paul J. Jackson
Keyword(s):  
Chemical Modification ◽  
Metal Binding ◽  
Binding Studies

Crystal Structure of Diphenyl Pyraline Hydrochloride-Cobalt Chloride Complex

1994 ◽  
Vol 250 (1) ◽  
pp. 285-291
Author(s):  
M. A. Sridhar ◽  
A. Indira ◽  
S. B. Bellad ◽  
A. M. Babu ◽  
M. M. M. Abdoh ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cobalt Chloride ◽  
Chloride Complex

Vibrational spectra and crystal structure of ethyl methyl sulfide-mercury(II) chloride complex

1980 ◽  
Vol 69 ◽  
pp. 53-58 ◽  
Author(s):  
Masaaki Sakakibara ◽  
Yoko Yonemura ◽  
Zenzo Tanaka ◽  
Satoshi Matsumoto ◽  
Keiichi Fukuyama ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Vibrational Spectra ◽  
Chloride Complex ◽  
Methyl Sulfide ◽  
Ethyl Methyl

scholarly journals The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids

2014 ◽  
Vol 42 (7) ◽  
pp. 4712-4722 ◽  
Author(s):  
P.-H. Kuo ◽  
C.-H. Chiang ◽  
Y.-T. Wang ◽  
L. G. Doudeva ◽  
H. S. Yuan
Keyword(s):  
Crystal Structure ◽  
Nucleic Acids ◽  
Specific Recognition ◽  
Dna Complex

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.

Helicase mechanisms and the coupling of helicases within macromolecular machines Part I: Structures and properties of isolated helicases

2002 ◽  
Vol 35 (4) ◽  
pp. 431-478 ◽  
Author(s):  
Emmanuelle Delagoutte ◽  
Peter H. von Hippel
Keyword(s):  
Crystal Structure ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Site ◽  
Crystal Structures ◽  
Base Pair ◽  
Biochemical Properties ◽  
Functional Coupling ◽  
Hexameric Helicases ◽  
Base Pair Opening

1. Mechanisms of nucleic acid (NA) unwinding by helicases 4322. Helicases may take advantage of ‘breathing’ fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs 4342.2 dsNAs ‘breathe’ in isolation 4352.3 Thermodynamics of terminal base pairs of dsNA 4382.4 Thermal fluctuations may be responsible for sequential base-pair opening at replication forks 4392.5 Helicases may capture single base-pair opening events sequentially 4403. Biochemical properties of helicases 4433.1 Binding of NAs 4433.2 Binding and hydrolysis of NTP 4453.3 Coordination between NA binding and NTP binding and hydrolysis activities 4464. Helicase structures and mechanistic consequences 4474.1 Amino-acid sequence analysis reveals conserved motifs that constitute the NTP-binding pocket and a portion of the NA-binding site 4474.2 Organization of hepatitis virus C NS3 RNA helicase 4494.2.1 Biochemical properties of HCV NS3 4494.2.2 Crystal structures of HCV NS3 helicase 4504.2.2.1 The apoprotein 4504.2.2.2 The protein–dU8 complex 4504.2.3 A possible unwinding mechanism 4524.2.4 What is the functional oligomeric state of HCV NS3? 4524.3 Organization of the PcrA helicase 4534.3.1 The apoenzyme and ADP–PcrA complex 4544.3.2 The protein–DNA–sulfate complex 4564.3.3 The PcrA–DNA–ADPNP complex 4564.3.4 A closer look at the NTP-binding site in the crystal structure of PcrA–ADPNP–DNA 4574.3.5 Communication between domains A and B 4574.3.6 How might ssDNA stimulate the ATPase activity of PcrA? 4574.3.7 A possible helicase translocation mechanism 4584.3.8 A possible unwinding mechanism 4584.4 Organization of the Rep helicase 4594.4.1 Biochemical properties 4594.4.2 Crystal structure of Rep bound to ssDNA 4624.5 Organization of the RecG helicase 4624.6 Hexameric helicases 4664.6.1 Insights from crystal structures of hexameric helicases 4674.6.2 Possible translocation and unwinding mechanisms 4685. Conclusions 4696. Acknowledgments 4727. References 472Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven ‘breathing’ of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.

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