A Dynamic Equilibrium of Three Hydrogen-Bond Conformers Explains the NMR Spectrum of the Active Site of Photoactive Yellow Protein

2016 ◽  
Vol 12 (10) ◽  
pp. 5170-5178 ◽  
Author(s):  
Phillip Johannes Taenzler ◽  
Keyarash Sadeghian ◽  
Christian Ochsenfeld
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Dynamic Equilibrium ◽  
Photoactive Yellow Protein ◽  
Nmr Spectrum

scholarly journals Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein

2018 ◽  
Vol 140 (31) ◽  
pp. 9827-9843 ◽  
Author(s):  
Margaux M. Pinney ◽  
Aditya Natarajan ◽  
Filip Yabukarski ◽  
David M. Sanchez ◽  
Fang Liu ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Photoactive Yellow Protein ◽  
Ketosteroid Isomerase ◽  
Structural Coupling ◽  
Hydrogen Bond Networks

scholarly journals A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase

JACS Au ◽  
2021 ◽  
Author(s):  
Mary Ortmayer ◽  
Florence J. Hardy ◽  
Matthew G. Quesne ◽  
Karl Fisher ◽  
Colin Levy ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Heme Peroxidase

scholarly journals 1P-274 Direct observation of two distinct types of short hydrogen bond in Photoactive Yellow Protein(The 46th Annual Meeting of the Biophysical Society of Japan)

2008 ◽  
Vol 48 (supplement) ◽  
pp. S64
Author(s):  
Shigeo Yamaguchi ◽  
Hironari Kamikubo ◽  
Kazuo Kurihara ◽  
Ryota Kuroki ◽  
Nobuo Niimura ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Annual Meeting ◽  
Direct Observation ◽  
Photoactive Yellow Protein ◽  
Biophysical Society ◽  
Short Hydrogen Bond

scholarly journals Low-barrier hydrogen bond in photoactive yellow protein

2009 ◽  
Vol 106 (2) ◽  
pp. 440-444 ◽  
Author(s):  
S. Yamaguchi ◽  
H. Kamikubo ◽  
K. Kurihara ◽  
R. Kuroki ◽  
N. Niimura ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Photoactive Yellow Protein

The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism

2018 ◽  
Vol 74 (8) ◽  
pp. 748-759
Author(s):  
Robert S. Phillips ◽  
Adriaan A. Buisman ◽  
Sarah Choi ◽  
Anusha Hussaini ◽  
Zachary A. Wood
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Aromatic Ring ◽  
Active Site ◽  
Enzymatic Reaction ◽  
Proteus Vulgaris ◽  
Bacterial Enzyme ◽  
Small Domain ◽  
Out Of Plane ◽  
Reversible Formation

Tryptophan indole-lyase (TIL) is a bacterial enzyme which catalyzes the reversible formation of indole and ammonium pyruvate from L-tryptophan. Oxindolyl-L-alanine (OIA) is an inhibitor of TIL, with a K i value of about 5 µM. The crystal structure of the complex of Proteus vulgaris TIL with OIA has now been determined at 2.1 Å resolution. The ligand forms a closed quinonoid complex with the pyridoxal 5′-phosphate (PLP) cofactor. The small domain rotates about 10° to close the active site, bringing His458 into position to donate a hydrogen bond to Asp133, which also accepts a hydrogen bond from the heterocyclic NH of the inhibitor. This brings Phe37 and Phe459 into van der Waals contact with the aromatic ring of OIA. Mutation of the homologous Phe464 in Escherichia coli TIL to Ala results in a 500-fold decrease in k cat/K m for L-tryptophan, with less effect on the reaction of other nonphysiological β-elimination substrates. Stopped-flow kinetic experiments of F464A TIL show that the mutation has no effect on the formation of quinonoid intermediates. An aminoacrylate intermediate is observed in the reaction of F464A TIL with S-ethyl-L-cysteine and benzimidazole. A model of the L-tryptophan quinonoid complex with PLP in the active site of P. vulgaris TIL shows that there would be a severe clash of Phe459 (∼1.5 Å apart) and Phe37 (∼2 Å apart) with the benzene ring of the substrate. It is proposed that this creates distortion of the substrate aromatic ring out of plane and moves the substrate upwards on the reaction coordinate towards the transition state, thus reducing the activation energy and accelerating the enzymatic reaction.

scholarly journals Short hydrogen bonds in the catalytic mechanism of serine proteases

2008 ◽  
Vol 73 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Vladimir Leskovac ◽  
Svetlana Trivic ◽  
Draginja Pericin ◽  
Mira Popovic ◽  
Julijan Kandrac
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Serine Proteases ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Data Bank ◽  
Ground State Structure ◽  
Low Barrier Hydrogen Bonds ◽  
Short Hydrogen Bonds

The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

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