Evolution of Enzymatic Activities in the Orotidine 5‘-Monophosphate Decarboxylase Suprafamily:  Mechanistic Evidence for a Proton Relay System in the Active Site of 3-Keto-l-gulonate 6-Phosphate Decarboxylase†

Biochemistry ◽  
2004 ◽  
Vol 43 (21) ◽  
pp. 6427-6437 ◽  
Author(s):  
Wen Shan Yew ◽  
Eric L. Wise ◽  
Ivan Rayment ◽  
John A. Gerlt
Keyword(s):  
Active Site ◽  
Enzymatic Activities ◽  
Relay System ◽  
Proton Relay ◽  
Monophosphate Decarboxylase

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 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

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.

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