Crystal Structure and Biochemical Properties of the Human Mitochondrial Ferritin and its Mutant Ser144Ala

2004 ◽  
Author(s):  
B LANGLOISDESTAINTOT
Keyword(s):  
Crystal Structure ◽  
Biochemical Properties

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.

scholarly journals Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

2014 ◽  
Vol 70 (3) ◽  
pp. 877-888 ◽  
Author(s):  
Makoto Nakabayashi ◽  
Misumi Kataoka ◽  
Yumiko Mishima ◽  
Yuka Maeno ◽  
Kazuhiko Ishikawa
Keyword(s):  
Crystal Structure ◽  
Pyrococcus Furiosus ◽  
Structural Data ◽  
Biochemical Properties ◽  
Intrinsic Activity ◽  
Oligomeric Structure ◽  
Tetrameric Structure ◽  
Crystal Structural Data ◽  
Dimeric Form

β-Glucosidase fromPyrococcus furiosus(BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed.

Crystal Structure and Biochemical Properties of a Novel Thermostable Esterase Containing an Immunoglobulin-Like Domain

2009 ◽  
Vol 385 (3) ◽  
pp. 949-962 ◽  
Author(s):  
Mark Levisson ◽  
Lei Sun ◽  
Sjon Hendriks ◽  
Peter Swinkels ◽  
Twan Akveld ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Properties

Crystal Structure and Biochemical Properties of the d-Arabinose Dehydrogenase from Sulfolobus solfataricus

2007 ◽  
Vol 371 (5) ◽  
pp. 1249-1260 ◽  
Author(s):  
Stan J.J. Brouns ◽  
Andrew P. Turnbull ◽  
Hanneke L.D.M. Willemen ◽  
Jasper Akerboom ◽  
John van der Oost
Keyword(s):  
Crystal Structure ◽  
Sulfolobus Solfataricus ◽  
Biochemical Properties

Synthesis, Molecular and Crystal Structure of 3′-N-Alkylamino-3′-deoxythymidines and Some Biochemical Properties of Their Phosphorous Esters

1995 ◽  
Vol 14 (1-2) ◽  
pp. 23-37 ◽  
Author(s):  
Maxim V. Jasko ◽  
lvati I. Fedorov ◽  
Alexey M. Atrazhev ◽  
Diriiitry Yu. Mozzherin ◽  
Nicolay A. Novicov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Properties ◽  
Molecular And Crystal Structure

scholarly journals Biochemical Properties and Crystal Structure of a β-Phenylalanine Aminotransferase from Variovorax paradoxus

2012 ◽  
Vol 79 (1) ◽  
pp. 185-195 ◽  
Author(s):  
Ciprian G. Crismaru ◽  
Gjalt G. Wybenga ◽  
Wiktor Szymanski ◽  
Hein J. Wijma ◽  
Bian Wu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Kinetic Resolution ◽  
Specific Activity ◽  
Enantiomeric Excess ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Sequence Motif ◽  
Content Type ◽  
Variovorax Paradoxus

ABSTRACTBy selective enrichment, we isolated a bacterium that can use β-phenylalanine as a sole nitrogen source. It was identified by 16S rRNA gene sequencing as a strain ofVariovorax paradoxus. Enzyme assays revealed an aminotransferase activity. Partial genome sequencing and screening of a cosmid DNA library resulted in the identification of a 1,302-bp aminotransferase gene, which encodes a 46,416-Da protein. The gene was cloned and overexpressed inEscherichia coli. The recombinant enzyme was purified and showed a specific activity of 17.5 U mg−1for (S)-β-phenylalanine at 30°C and 33 U mg−1at the optimum temperature of 55°C. The β-specific aminotransferase exhibits a broad substrate range, acceptingortho-,meta-, andpara-substituted β-phenylalanine derivatives as amino donors and 2-oxoglutarate and pyruvate as amino acceptors. The enzyme is highly enantioselective toward (S)-β-phenylalanine (enantioselectivity [E], >100) and derivatives thereof with different substituents on the phenyl ring, allowing the kinetic resolution of various racemic β-amino acids to yield (R)-β-amino acids with >95% enantiomeric excess (ee). The crystal structures of the holoenzyme and of the enzyme in complex with the inhibitor 2-aminooxyacetate revealed structural similarity to the β-phenylalanine aminotransferase fromMesorhizobiumsp. strain LUK. The crystal structure was used to rationalize the stereo- and regioselectivity ofV. paradoxusaminotransferase and to define a sequence motif with which new aromatic β-amino acid-converting aminotransferases may be identified.

Crystal Structure and Biochemical Properties of the Human Mitochondrial Ferritin and its Mutant Ser144Ala

2004 ◽  
Vol 340 (2) ◽  
pp. 277-293 ◽  
Author(s):  
Béatrice Langlois d'Estaintot ◽  
Paolo Santambrogio ◽  
Thierry Granier ◽  
Bernard Gallois ◽  
Jean Marc Chevalier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Properties
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