scholarly journals Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine-coordinated manganese in substrate recognition

2009 ◽  
Vol 11 (9) ◽  
pp. 2138-2147 ◽  
Author(s):  
Subhra Chakraborty ◽  
Niranjan Chakraborty ◽  
Deepti Jain ◽  
Dinakar M. Salunke ◽  
Asis Datta
Keyword(s):  
Active Site ◽  
Substrate Recognition ◽  
Flammulina Velutipes ◽  
Oxalate Decarboxylase

Role of active site arginine residues in substrate recognition by PPM1A

2021 ◽  
Author(s):  
Itsumi Tani ◽  
Shogo Ito ◽  
Yukiko Shirahata ◽  
Yutaka Matsuyama ◽  
James G. Omichinski ◽  
...  
Keyword(s):  
Active Site ◽  
Substrate Recognition ◽  
Arginine Residues

scholarly journals New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Louise Lassalle ◽  
Sylvain Engilberge ◽  
Dominique Madern ◽  
Pierre Vauclare ◽  
Bruno Franzetti ◽  
...  
Keyword(s):  
Renal Failure ◽  
Active Site ◽  
Ternary Complex ◽  
Substrate Recognition ◽  
Binding Mode ◽  
X Ray ◽  
Hyperoxaluria Type

Abstract Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 Å resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 Å resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action.

Role of Two Residues Proximal to the Active Site of Ubc9 in Substrate Recognition by the Ubc9·SUMO-1 Thiolester Complex†

Biochemistry ◽  
2003 ◽  
Vol 42 (11) ◽  
pp. 3168-3179 ◽  
Author(s):  
Michael H. Tatham ◽  
Yuan Chen ◽  
Ronald T. Hay
Keyword(s):  
Active Site ◽  
Substrate Recognition

scholarly journals Shaping Substrate Selectivity in a Broad-Spectrum Metallo-β-Lactamase

2018 ◽  
Vol 62 (4) ◽  
Author(s):  
Lisandro J. González ◽  
Cintia Stival ◽  
Juan L. Puzzolo ◽  
Diego M. Moreno ◽  
Alejandro J. Vila
Keyword(s):  
Broad Spectrum ◽  
Active Site ◽  
Substrate Recognition ◽  
Chimeric Protein ◽  
Major Group ◽  
Substrate Selectivity ◽  
Incomplete Knowledge ◽  
Naturally Occurring ◽  
The One

ABSTRACTMetallo-β-lactamases (MBLs) are the major group of carbapenemases produced by bacterial pathogens. The design of MBL inhibitors has been limited by, among other issues, incomplete knowledge about how these enzymes modulate substrate recognition. While most MBLs are broad-spectrum enzymes, B2 MBLs are exclusive carbapenemases. This narrower substrate profile has been attributed to a sequence insertion present in B2 enzymes that limits accessibility to the active site. In this work, we evaluate the role of sequence insertions naturally occurring in the B2 enzyme Sfh-I and in the broad-spectrum B1 enzyme SPM-1. We engineered a chimeric protein in which the sequence insertion of SPM-1 was replaced by the one present in Sfh-I. The chimeric variant is a selective cephalosporinase, revealing that the substrate profile of MBLs can be further tuned depending on the protein context. These results also show that the stable scaffold of MBLs allows a modular engineering much richer than the one observed in nature.

scholarly journals Role of Arginine 117 in Substrate Recognition by Human Cytochrome P450 2J2

2018 ◽  
Vol 19 (7) ◽  
pp. 2066 ◽  
Author(s):  
Pierre Lafite ◽  
François André ◽  
Joan Graves ◽  
Darryl Zeldin ◽  
Patrick Dansette ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Substrate Recognition ◽  
Salt Bridge ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
Human Cytochrome ◽  
Dynamic Docking ◽  
Homology Models

The influence of Arginine 117 of human cytochrome P450 2J2 in the recognition of ebastine and a series of terfenadone derivatives was studied by site-directed mutagenesis. R117K, R117E, and R117L mutants were produced, and the behavior of these mutants in the hydroxylation of ebastine and terfenadone derivatives was compared to that of wild-type CYP2J2. The data clearly showed the importance of the formation of a hydrogen bond between R117 and the keto group of these substrates. The data were interpreted on the basis of 3D homology models of the mutants and of dynamic docking of the substrates in their active site. These modeling studies also suggested the existence of a R117-E222 salt bridge between helices B’ and F that would be important for maintaining the overall folding of CYP2J2.

Heparan sulphate N-sulphotransferase activity: reaction mechanism and substrate recognition

2003 ◽  
Vol 31 (2) ◽  
pp. 331-334 ◽  
Author(s):  
Y. Kakuta ◽  
L. Li ◽  
L.C. Pedersen ◽  
L.G. Pedersen ◽  
M. Negishi
Keyword(s):  
Active Site ◽  
Transfer Reaction ◽  
Substrate Recognition ◽  
Heparan Sulphate ◽  
Critical Role ◽  
Random Coil ◽  
Group Transfer ◽  
Α Helix ◽  
Model Chain

Human heparan sulphate N-deacetylase/N-sulphotransferase 1 sulphates the NH3+ group of the glucosamine moiety of the heparan chain in heparan sulphate/heparin biosynthesis. An open cleft that runs perpendicular to the sulphate donor 3´-phosphoadenosine 5´-phosphosulphate may constitute the acceptor substrate-binding site of the sulphotransferase domain (hNST1) [Kakuta, Sueyoshi, Negishi and Pedersen (1999) J. Biol. Chem. 274, 10673–10676]. When a hexasaccharide model chain is docked into the active site, only a trisaccharide (-IdoA-GlcN-IdoA-) portion interacts directly with the cleft residues: Trp-713, His-716 and His-720 from α helix 6, and Phe-640, Glu-641, Glu-642, Gln-644 and Asn-647 from random coil (residues 640–647). Mutation of these residues either abolishes or greatly reduces hNST1 activity. Glu-642 may play the critical role of catalytic base in the sulphuryl group transfer reaction, as indicated by its hydrogen-bonding distance to the NH3+ group of the glucosamine moiety in the model and by mutational data.

Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13C Labeling and ENDOR Spectroscopy

2021 ◽  
Author(s):  
Ana Pérez-González ◽  
Zhi-Yong Yang ◽  
Dmitriy A. Lukoyanov ◽  
Dennis R. Dean ◽  
Lance C. Seefeldt ◽  
...  
Keyword(s):  
Active Site ◽  
13C Labeling ◽  
Endor Spectroscopy ◽  
Femo Cofactor
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