scholarly journals Cofactor-Induced Conformational Rearrangements Establish a Catalytically Competent Active Site and a Proton Relay Conduit in FabG

Structure ◽  
2004 ◽  
Vol 12 (3) ◽  
pp. 417-428 ◽  
Author(s):  
Allen C Price ◽  
Yong-Mei Zhang ◽  
Charles O Rock ◽  
Stephen W White
Keyword(s):  
Active Site ◽  
Proton Relay ◽  
Conformational Rearrangements

The catalytic mechanism ofDrosophilaalcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD+ribose OH switch

2003 ◽  
Vol 51 (2) ◽  
pp. 289-298 ◽  
Author(s):  
Assen Koumanov ◽  
Jordi Benach ◽  
Silvia Atrian ◽  
Roser Gonzàlez-Duarte ◽  
Andrey Karshikoff ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Proton Relay

scholarly journals Role of active site conformational changes in photocycle activation of the AppA BLUF photoreceptor

2017 ◽  
Vol 114 (7) ◽  
pp. 1480-1485 ◽  
Author(s):  
Puja Goyal ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Excited State ◽  
Charge Transfer ◽  
Conformational Changes ◽  
Ground State ◽  
Active Site ◽  
Locally Excited ◽  
Proton Relay ◽  
Locally Excited State

Blue light using flavin adenine dinucleotide (BLUF) proteins are essential for the light regulation of a variety of physiologically important processes and serve as a prototype for photoinduced proton-coupled electron transfer (PCET). Free-energy simulations elucidate the active site conformations in the AppA (activation of photopigment and puc expression) BLUF domain before and following photoexcitation. The free-energy profile for interconversion between conformations with either Trp104 or Met106 closer to the flavin, denoted Trpin/Metout and Trpout/Metin, reveals that both conformations are sampled on the ground state, with the former thermodynamically favorable by ∼3 kcal/mol. These results are consistent with the experimental observation of both conformations. To analyze the proton relay from Tyr21 to the flavin via Gln63, the free-energy profiles for Gln63 rotation were calculated on the ground state, the locally excited state of the flavin, and the charge-transfer state associated with electron transfer from Tyr21 to the flavin. For the Trpin/Metout conformation, the hydrogen-bonding pattern conducive to the proton relay is not thermodynamically favorable on the ground state but becomes more favorable, corresponding to approximately half of the configurations sampled, on the locally excited state. The calculated energy gaps between the locally excited and charge-transfer states suggest that electron transfer from Tyr21 to the flavin is more facile for configurations conducive to proton transfer. When the active site conformation is not conducive to PCET from Tyr21, Trp104 can directly compete with Tyr21 for electron transfer to the flavin through a nonproductive pathway, impeding the signaling efficiency.

Fluorescence Spectroscopy of the Tryptophan Microenvironment in Carcinus aestuarii Hemocyanin

2002 ◽  
Vol 57 (11-12) ◽  
pp. 1084-1091 ◽  
Author(s):  
Paolo Di Muroa ◽  
Mariano Beltramini ◽  
Peter Nikolov ◽  
Irina Petkova ◽  
Benedetto Salvato ◽  
...  
Keyword(s):  
Active Site ◽  
Oxygen Binding ◽  
Protein Matrix ◽  
Panulirus Interruptus ◽  
Time Resolved ◽  
Oligomeric Protein ◽  
Close Proximity ◽  
Tryptophan Residues ◽  
Conformational Rearrangements ◽  
Intersubunit Interactions

The steady-state and time-resolved fluorescence properties of the multitryptophan minimal subunit CaeSS2 from Carcinus aestuarii hemocyanin have been studied with the aim of probing the environment of the fluorophores within the protein matrix. Subunit a of Panulirus interruptus hemocyanin, whose X-ray structure is known, has been also studied. The results are compared with those collected with other two monomeric fractions (CaeSS1, CaeSS3) produced by dissociation of the native, oligomeric protein as well as with those of the hexameric aggregate. Three classes of tryptophan residues can be singled out by a combination of fluorescence quenching and lifetime measurements on the holo-Hc (the copper containing, oxygen binding form) and the apo-Hc (the copper-free derivative). One class of tryptophans is exposed to the protein surface. Some of these residues are proposed to be involved in the intersubunit interactions in CaeSS1 and CaeSS3 fractions whereas in CaeSS2 the protein matrix masks them. This suggests the occurrence of conformational rearrangements after detachment of the subunit from the native aggregate, which could explain the inability of CaeSS2 to reassociate. A second class of tryptophan has been correlatively assigned, by comparison with the results obtained with Panulirus interruptus hemocyanin, to residues in close proximity to the active site. The third class includes buried, active site-distant, residues.

scholarly journals Interplay of nucleophilic catalysis with proton transfer in the nitrile reductase QueF from Escherichia coli

2019 ◽  
Vol 9 (3) ◽  
pp. 842-853 ◽  
Author(s):  
Jihye Jung ◽  
Jan Braun ◽  
Tibor Czabany ◽  
Bernd Nidetzky
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Active Site ◽  
Nucleophilic Catalysis ◽  
Proton Relay ◽  
Network Of Hydrogen Bonds ◽  
Site Network ◽  
Nitrile Reduction ◽  
Enzyme Intermediate

Proton relay through an active-site network of hydrogen bonds promotes enzymatic nitrile reduction to amine via a covalent thioimidate enzyme intermediate.

scholarly journals Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Christina M Zimanyi ◽  
Percival Yang-Ting Chen ◽  
Gyunghoon Kang ◽  
Michael A Funk ◽  
Catherine L Drennan
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Bonds ◽  
Substrate Specificity ◽  
Ribonucleotide Reductase ◽  
Active Site ◽  
Molecular Basis ◽  
Allosteric Site ◽  
Dna Biosynthesis ◽  
Conformational Rearrangements ◽  
Proper Balance

Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR ‘reads’ the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.

scholarly journals Alternative catalytic residues in the active site of Esco acetyltransferases

2019 ◽  
Author(s):  
Tahereh Ajam ◽  
Inessa De ◽  
Nikolai Petkau ◽  
Gabriela Whelan ◽  
Vladimir Pena ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Mouse Embryonic Fibroblast ◽  
Enzymatic Assays ◽  
Sister Chromatids ◽  
Proton Relay ◽  
Active Site Cleft ◽  
Embryonic Fibroblast

AbstractCohesin is a protein complex encircles the DNA and regulates the separation of sister chromatids during cell division. Following a catalytic mechanism that is insufficiently understood, Esco1 and Esco2 acetyltransferases acetylate Smc3 subunit of cohesin, thereby inducing a stabilization of cohesin on DNA. As a prerequisite for structure-guided investigation of enzymatic activity, we determine here the crystal structure of the mouse Esco2/CoA complex at 1.8 Å resolution. We reconstitute the entire cohesin as a tetrameric assembly and use it as a physiologically-relevant substrate for enzymatic assays in vitro. Furthermore, we employ cell-based complementation studies in mouse embryonic fibroblast deficient for Esco1 and Esco2, as a means to identify catalytically-important residues in vivo. These analyses demonstrate that D567/S566 and E491/S527, located on opposite sides of the MmEsco2 active site cleft, are critical for catalysis. Our experiments supports a catalytic mechanism of acetylation where residues D567 and E491 are general bases that deprotonate the ε-amino group of lysine substrate, via two nearby serine residues - S566 and S527-that possess a proton relay function.

Locating Al in the DABCO catalyst before and after Al extraction

1990 ◽  
Vol 48 (4) ◽  
pp. 265-267
Author(s):  
Kathleen B. Reuter
Keyword(s):  
Active Site ◽  
Inverse Relationship ◽  
Transverse Direction ◽  
Reaction Rate ◽  
Acid Phosphate ◽  
Fracture Surfaces ◽  
Al Content ◽  
Before And After ◽  
Relationship Of

The reaction rate and efficiency of piperazine to 1,4-diazabicyclo-octane (DABCO) depends on the Si/Al ratio of the MFI topology catalysts. The Al was shown to be the active site, however, in the Si/Al range of 30-200 the reaction rate increases as the Si/Al ratio increases. The objective of this work was to determine the location and concentration of Al to explain this inverse relationship of Al content with reaction rate.Two silicalite catalysts in the form of 1/16 inch SiO2/Al2O3 bonded extrudates were examined: catalyst A with a Si/Al of 83; and catalyst B, the acid/phosphate Al extracted form of catalyst A, with a Si/Al of 175. Five extrudates from each catalyst were fractured in the transverse direction and particles were obtained from the fracture surfaces near the center of the extrudate diameter. Particles were also obtained from the outside surfaces of five extrudates.

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