scholarly journals Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase

2020 ◽  
Vol 56 (68) ◽  
pp. 9850-9853
Author(s):  
Ahmed Djeghader ◽  
Melanie Rossotti ◽  
Saleh Abdulkarim ◽  
Frédéric Biaso ◽  
Guillaume Gerbaud ◽  
...  
Keyword(s):  
Active Site ◽  
Spectroscopic Evidence ◽  
Reaction Intermediate

We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.

Examination of a reaction intermediate in the active site of riboflavin synthase

2003 ◽  
Vol 31 (4) ◽  
pp. 278-287 ◽  
Author(s):  
Ya-Jun Zheng ◽  
Douglas B. Jordan ◽  
Der-Ing Liao
Keyword(s):  
Active Site ◽  
Reaction Intermediate

Kinetic and Spectroscopic Evidence for Active Site Inhibition of Human Aldose Reductase†,‡

Biochemistry ◽  
1996 ◽  
Vol 35 (34) ◽  
pp. 11196-11202 ◽  
Author(s):  
Takayuki Nakano ◽  
J. Mark Petrash
Keyword(s):  
Aldose Reductase ◽  
Active Site ◽  
Spectroscopic Evidence

Spectroscopic Evidence of Reversible Disassembly of the [FeFe] Hydrogenase Active Site

2017 ◽  
Vol 8 (16) ◽  
pp. 3834-3839 ◽  
Author(s):  
Patricia Rodríguez-Maciá ◽  
Edward Reijerse ◽  
Wolfgang Lubitz ◽  
James A. Birrell ◽  
Olaf Rüdiger
Keyword(s):  
Active Site ◽  
Spectroscopic Evidence

scholarly journals Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

2020 ◽  
Vol 25 (6) ◽  
pp. 847-861
Author(s):  
Lili Cao ◽  
Octav Caldararu ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Bound State ◽  
Real Space ◽  
Quantum Mechanical ◽  
Storage Site ◽  
Quantum Mechanical Calculations ◽  
Reaction Intermediate ◽  
Sulphide Ions ◽  
Vanadium Nitrogenase

Abstract Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH−-bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract

scholarly journals Structures of a human blood group glycosyltransferase in complex with a photo-activatable UDP-Gal derivative reveal two different binding conformations

2014 ◽  
Vol 70 (8) ◽  
pp. 1015-1021 ◽  
Author(s):  
René Jørgensen ◽  
Gaëlle Batot ◽  
Karin Mannerstedt ◽  
Anne Imberty ◽  
Christelle Breton ◽  
...  
Keyword(s):  
Low Temperature ◽  
Blood Group ◽  
Human Blood ◽  
Active Site ◽  
Biological Processes ◽  
Dynamic Nature ◽  
Reaction Intermediate ◽  
Dual Specificity ◽  
Intermediate States ◽  
Sequential Addition

Glycosyltransferases (GTs) catalyse the sequential addition of monosaccharides to specific acceptor molecules and play major roles in key biological processes. GTs are classified into two main families depending on the inverted or retained stereochemistry of the glycosidic bond formed during the reaction. While the mechanism of inverting enzymes is well characterized, the precise nature of retaining GTs is still a matter of much debate. In an attempt to clarify this issue, studies were initiated to identify reaction-intermediate states by using a crystallographic approach based on caged substrates. In this paper, two distinct structures of AA(Gly)B, a dual-specificity blood group synthase, are described in complex with a UDP-galactose derivative in which the O6′′ atom is protected by a 2-nitrobenzyl group. The distinct conformations of the caged substrate in both structures of the enzyme illustrate the highly dynamic nature of its active site. An attempt was also made to photolyse the caged compound at low temperature, which unfortunately is not possible without damaging the uracil group as well. These results pave the way for kinetic crystallography experiments aiming at trapping and characterizing reaction-intermediate states in the mechanism of enzymatic glycosyl transfer.

Crystallographic and FTIR Spectroscopic Evidence of Changes in Fe Coordination Upon Reduction of the Active Site of the Fe-Only Hydrogenase fromDesulfovibriodesulfuricans

2001 ◽  
Vol 123 (8) ◽  
pp. 1596-1601 ◽  
Author(s):  
Yvain Nicolet ◽  
Antonio L. de Lacey ◽  
Xavier Vernède ◽  
Victor M. Fernandez ◽  
E. Claude Hatchikian ◽  
...  
Keyword(s):  
Active Site ◽  
Spectroscopic Evidence

The Active-Site Arginine ofS-Adenosylmethionine Synthetase Orients the Reaction Intermediate†

Biochemistry ◽  
1998 ◽  
Vol 37 (39) ◽  
pp. 13499-13506 ◽  
Author(s):  
Robert S. Reczkowski ◽  
John C. Taylor ◽  
George D. Markham
Keyword(s):  
Active Site ◽  
Reaction Intermediate ◽  
Adenosylmethionine Synthetase
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