Mechanism of Thioredoxin-Catalyzed Disulfide Reduction. Activation of the Buried Thiol and Role of the Variable Active-Site Residues

2008 ◽  
Vol 112 (8) ◽  
pp. 2511-2523 ◽  
Author(s):  
Alexandra T. P. Carvalho ◽  
Marcel Swart ◽  
Joost N. P. van Stralen ◽  
Pedro A. Fernandes ◽  
Maria J. Ramos ◽  
...  
Keyword(s):  
Active Site ◽  
Active Site Residues ◽  
Disulfide Reduction

scholarly journals The mechanistic role of active site residues in non-stereo haloacid dehalogenase E (DehE)

2019 ◽  
Vol 90 ◽  
pp. 219-225 ◽  
Author(s):  
Muhammad Hasanuddin Zainal Abidin ◽  
Khairul Bariyyah Abd Halim ◽  
Fahrul Huyop ◽  
Tengku Haziyamin Tengku Abdul Hamid ◽  
Roswanira Abdul Wahab ◽  
...  
Keyword(s):  
Active Site ◽  
Active Site Residues ◽  
Haloacid Dehalogenase

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

2001 ◽  
Vol 353 (3) ◽  
pp. 645-653 ◽  
Author(s):  
Istvan J. ENYEDY ◽  
Ildiko M. KOVACH ◽  
Akos BENCSURA
Keyword(s):  
Molecular Dynamics ◽  
Glutamic Acid ◽  
Active Site ◽  
Indole Ring ◽  
Active Site Residues ◽  
Parallel Simulations ◽  
Electrostatic Stabilization ◽  
Carbenium Ion ◽  
Dynamics Simulations

The role of active-site residues in the dealkylation reaction in the PSCS diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californicaacetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: > 400ps equilibration was followed by 150–200ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Oγ of AChE and acetylcholine. We found that the NεH in histidine H+-440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NεH in histidine H+-440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H+-440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment of the inhibitor enforce methyl migration from Cβ to Cα concerted with C—O bond breaking in soman-inhibited AChE. Tryptophan-84, phenyalanine-331 and glutamic acid-199 are within 3.7–3.9 Å (1 Å=10-10 m) from a methyl group in Cβ, 4.5–5.1 Å from Cβ and 4.8–5.8 Å from Cα, and can better stabilize the developing carbenium ion on Cβ than on Cα. The Trp84Ala mutation eliminates interactions between the incipient carbenium ion and the indole ring, but also reduces its interactions with phenylalanine-331 and aspartic acid-72. Tyrosine-130 promotes dealkylation by interacting with the indole ring of tryptophan-84. Glutamic acid-443 can influence the orientation of active-site residues through tyrosine-421, tyrosine-442 and histidine-440 in soman-inhibited AChE, and thus facilitate dealkylation.

Topological role of cytochrome P450 2D6 active site residues

2006 ◽  
Vol 447 (1) ◽  
pp. 53-58 ◽  
Author(s):  
Robert A.B. van Waterschoot ◽  
Peter H.J. Keizers ◽  
Chris de Graaf ◽  
Nico P.E. Vermeulen ◽  
Richard A. Tschirret-Guth
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Cytochrome P450 2D6 ◽  
Active Site Residues ◽  
P450 2D6

scholarly journals Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties

2012 ◽  
Vol 446 (1) ◽  
pp. 149-157 ◽  
Author(s):  
Marianne Schimpl ◽  
Christina L. Rush ◽  
Marie Betou ◽  
Ian M. Eggleston ◽  
Anneliese D. Recklies ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Active Site ◽  
Elevated Serum ◽  
Serum Levels ◽  
Chitinase Activity ◽  
Active Site Residues ◽  
Binding Properties ◽  
Binding Partners ◽  
Tryptophan Residues

The chitinase-like proteins YKL-39 (chitinase 3-like-2) and YKL-40 (chitinase 3-like-1) are highly expressed in a number of human cells independent of their origin (mesenchymal, epithelial or haemapoietic). Elevated serum levels of YKL-40 have been associated with a negative outcome in a number of diseases ranging from cancer to inflammation and asthma. YKL-39 expression has been associated with osteoarthritis. However, despite the reported association with disease, the physiological or pathological role of these proteins is still very poorly understood. Although YKL-39 is homologous to the two family 18 chitinases in the human genome, it has been reported to lack any chitinase activity. In the present study, we show that human YKL-39 possesses a chitinase-like fold, but lacks key active-site residues required for catalysis. A glycan screen identified oligomers of N-acetylglucosamine as preferred binding partners. YKL-39 binds chitooligosaccharides and a newly synthesized derivative of the bisdionin chitinase-inhibitor class with micromolar affinity, through a number of conserved tryptophan residues. Strikingly, the chitinase activity of YKL-39 was recovered by reverting two non-conservative substitutions in the active site to those found in the active enzymes, suggesting that YKL-39 is a pseudo-chitinase with retention of chitinase-like ligand-binding properties.

scholarly journals Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

2006 ◽  
Vol 401 (2) ◽  
pp. 421-428 ◽  
Author(s):  
Paul A. O'Farrell ◽  
Leemor Joshua-Tor
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Bound Water ◽  
Active Site Residues ◽  
Site Structure ◽  
Active Site Cysteine ◽  
C Terminus ◽  
Bleomycin Hydrolase ◽  
Active Site Mutants

Bleomycin hydrolase (BH) is a hexameric papain family cysteine protease which is involved in preparing peptides for antigen presentation and has been implicated in tumour cell resistance to bleomycin chemotherapy. Structures of active-site mutants of yeast BH yielded unexpected results. Replacement of the active-site asparagine with alanine, valine or leucine results in the destabilization of the histidine side chain, demonstrating unambiguously the role of the asparagine residue in correctly positioning the histidine for catalysis. Replacement of the histidine with alanine or leucine destabilizes the asparagine position, indicating a delicate arrangement of the active-site residues. In all of the mutants, the C-terminus of the protein, which lies in the active site, protrudes further into the active site. All mutants were compromised in their catalytic activity. The structures also revealed the importance of a tightly bound water molecule which stabilizes a loop near the active site and which is conserved throughout the papain family. It is displaced in a number of the mutants, causing destabilization of this loop and a nearby loop, resulting in a large movement of the active-site cysteine. The results imply that this water molecule plays a key structural role in this family of enzymes.

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