Two-Metal Ion Mechanism of Bovine Lens Leucine Aminopeptidase: Active Site Solvent Structure and Binding Mode of L-Leucinal, a gem-Diolate Transition State Analog, by X-ray Crystallography

Biochemistry ◽  
1995 ◽  
Vol 34 (45) ◽  
pp. 14792-14800 ◽  
Author(s):  
Norbert Straeter ◽  
William N. Lipscomb
Keyword(s):  
Transition State ◽  
Active Site ◽  
Metal Ion ◽  
Leucine Aminopeptidase ◽  
Binding Mode ◽  
Solvent Structure ◽  
Transition State Analog ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bovine Lens

Response of a Designed Metalloprotein to Changes in Metal Ion Coordination, Exogenous Ligands, and Active Site Volume Determined by X-ray Crystallography

2005 ◽  
Vol 127 (49) ◽  
pp. 17266-17276 ◽  
Author(s):  
Silvano Geremia ◽  
Luigi Di Costanzo ◽  
Lucio Randaccio ◽  
Donald E. Engel ◽  
Angela Lombardi ◽  
...  
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
X Ray ◽  
X Ray Crystallography ◽  
Exogenous Ligands

An allolactose trapped at the lacZ β-galactosidase active site with its galactosyl moiety in a 4H3 conformation provides insights into the formation, conformation, and stabilization of the transition state

2015 ◽  
Vol 93 (6) ◽  
pp. 531-540 ◽  
Author(s):  
Robert W. Wheatley ◽  
Reuben E. Huber
Keyword(s):  
Transition State ◽  
Active Site ◽  
Axial Position ◽  
Transition State Analog ◽  
X Ray ◽  
Transition State Analogs ◽  
Leaving Group ◽  
Sugar Ring ◽  
Oxocarbenium Ion ◽  
Ring Distortion

When lactose was incubated with G794A-β-galactosidase (a variant with a “closed” active site loop that binds transition state analogs well) an allolactose was trapped with its Gal moiety in a 4H3 conformation, similar to the oxocarbenium ion-like conformation expected of the transition state. The numerous interactions formed between the 4H3 structure and β-galactosidase indicate that this structure is representative of the transition state. This conformation is also very similar to that of d-galactono-1,5-lactone, a good transition state analog. Evidence indicates that substrates take up the 4H3 conformation during migration from the shallow to the deep mode. Steric forces utilizing His418 and other residues are important for positioning the O1 leaving group into a quasi-axial position. An electrostatic interaction between the O5 of the distorted Gal and Tyr503 as well as C–H–π bonds with Trp568 are also significant. Computational studies of the energy of sugar ring distortion show that the β-galactosidase reaction itinerary is driven by energetic considerations in utilization of a 4H3 transition state with a novel 4C1-4H3-4C1 conformation itinerary. To our knowledge, this is the first X-ray crystallographic structural demonstration that the transition state of a natural substrate of a glycosidase has a 4H3 conformation.

scholarly journals Structure ofBacillus subtilisγ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

2014 ◽  
Vol 70 (2) ◽  
pp. 607-614 ◽  
Author(s):  
Tomoyo Ida ◽  
Hideyuki Suzuki ◽  
Keiichi Fukuyama ◽  
Jun Hiratake ◽  
Kei Wada
Keyword(s):  
Escherichia Coli ◽  
Helicobacter Pylori ◽  
Bacillus Subtilis ◽  
Active Site ◽  
Binding Sites ◽  
Binding Mode ◽  
Glutathione Metabolism ◽  
X Ray ◽  
X Ray Crystallography ◽  
Binding Pockets

γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound toBacillus subtilisGGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that inHelicobacter pyloriGGT, but in a different binding mode to that inEscherichia coliGGT. InB. subtilisGGT, acivicin is bound covalently through its C3 atom withsp2hybridization to Thr403 Oγ, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.

scholarly journals Binding of Phosphate and pyrophosphate ions at the active site of human angiogenin as revealed by X-ray crystallography

2001 ◽  
Vol 10 (8) ◽  
pp. 1669-1676 ◽  
Author(s):  
Demetres D. Leonidas ◽  
Gayatri B. Chavali ◽  
Anwar M. Jardine ◽  
Songlin Li ◽  
Robert Shapiro ◽  
...  
Keyword(s):  
Active Site ◽  
X Ray ◽  
X Ray Crystallography

Recent insights into lytic polysaccharide monooxygenases (LPMOs)

2018 ◽  
Vol 46 (6) ◽  
pp. 1431-1447 ◽  
Author(s):  
Tobias Tandrup ◽  
Kristian E. H. Frandsen ◽  
Katja S. Johansen ◽  
Jean-Guy Berrin ◽  
Leila Lo Leggio
Keyword(s):  
Active Site ◽  
Room Temperature ◽  
Experimental Studies ◽  
Binding Mode ◽  
Structural Features ◽  
Oxygen Species ◽  
Animal Kingdom ◽  
X Ray ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases

Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes discovered within the last 10 years. By degrading recalcitrant substrates oxidatively, these enzymes are major contributors to the recycling of carbon in nature and are being used in the biorefinery industry. Recently, two new families of LPMOs have been defined and structurally characterized, AA14 and AA15, sharing many of previously found structural features. However, unlike most LPMOs to date, AA14 degrades xylan in the context of complex substrates, while AA15 is particularly interesting because they expand the presence of LPMOs from the predominantly microbial to the animal kingdom. The first two neutron crystallography structures have been determined, which, together with high-resolution room temperature X-ray structures, have putatively identified oxygen species at or near the active site of LPMOs. Many recent computational and experimental studies have also investigated the mechanism of action and substrate-binding mode of LPMOs. Perhaps, the most significant recent advance is the increasing structural and biochemical evidence, suggesting that LPMOs follow different mechanistic pathways with different substrates, co-substrates and reductants, by behaving as monooxygenases or peroxygenases with molecular oxygen or hydrogen peroxide as a co-substrate, respectively.

scholarly journals Mechanism of IPPase shown by high resolution Neutron and X-ray crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1211-C1211
Author(s):  
Joseph Ng ◽  
Ronny Hughes ◽  
Michelle Morris ◽  
Leighton Coates ◽  
Matthew Blakeley ◽  
...  
Keyword(s):  
High Resolution ◽  
Active Site ◽  
Inorganic Pyrophosphatase ◽  
Inorganic Pyrophosphate ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cellular Processes ◽  
Crystallographic Structures ◽  
Hydrolysis Of ◽  
Low Energy Conformations

Soluble inorganic pyrophosphatase (IPPase) catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to form orthophosphate (Pi). The action of this enzyme shifts the overall equilibrium in favor of synthesis during a number of ATP-dependent cellular processes such as in the polymerization of nucleic acids, production of coenzymes and proteins and sulfate assimilation pathways. Two Neutron crystallographic (2.10-2.50Å) and five high-resolution X-ray (0.99Å-1.92Å) structures of the archaeal IPPase from Thermococcus thioreducens have been determined under both cryo and room temperatures. The structures determined include the recombinant IPPase bound to Mg+2, Ca+2, Br-, SO2-2 or PO4-2 involving those with non-hydrolyzed and hydrolyzed pyrophosphate complexes. All the crystallographic structures provide snapshots of the active site corresponding to different stages of the hydrolysis of inorganic pyrophosphate. As a result, a structure-based model of IPPase catalysis is devised showing the enzyme's low-energy conformations, hydration states, movements and nucleophile generation within the active site.

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