scholarly journals Crystal Structure of the Active Site Mutant Form of Soluble Fumarate Reductase, Osm1

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 504 ◽  
Author(s):  
Kim ◽  
Kwon ◽  
Jung ◽  
Chun ◽  
Ha ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Flavin Adenine Dinucleotide ◽  
Structural Information ◽  
Redox Balance ◽  
Underlying Mechanism ◽  
Fumarate Reductase ◽  
Mutant Form ◽  
Characteristic Features ◽  
Fad Binding

Soluble fumarate reductase is essential for survival under anaerobic conditions. This enzyme can maintain the redox balance in the cell by catalyzing the reduction of fumarate to succinate. Although the overall reaction mechanism of soluble fumarate reductase in yeast, Osm1, has been proposed by a previous structural study, the details of the underlying mechanism are not completely elucidated. The present study provides the structural information regarding the active site mutant form of Osm1 (R326A), thus, revealing that R326A mutation does not affect the substrate binding. Structural alterations of the residues surrounding the active site, and the missing 2nd flavin adenine dinucleotide (FAD) in the previously defined 2nd FAD binding site, were observed as characteristic features of the Osm1 R326A crystal structure. Based on these findings, we provided a clue that can explain the loss of activity of Osm1 R326A.

scholarly journals Crystal Structure of Complete Rhinovirus RNA Polymerase Suggests Front Loading of Protein Primer

2005 ◽  
Vol 79 (1) ◽  
pp. 277-288 ◽  
Author(s):  
Todd C. Appleby ◽  
Hartmut Luecke ◽  
Jae Hoon Shim ◽  
Jim Z. Wu ◽  
I. Wayne Cheney ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rna Polymerase ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Structural Features ◽  
Replication Initiation ◽  
Front Face ◽  
Large Cleft ◽  
Active Site Cavity

ABSTRACT Picornaviruses utilize virally encoded RNA polymerase and a uridylylated protein primer to ensure replication of the entire viral genome. The molecular details of this mechanism are not well understood due to the lack of structural information. We report the crystal structure of human rhinovirus 16 3D RNA-dependent RNA polymerase (HRV16 3Dpol) at a 2.4-Å resolution, representing the first complete polymerase structure from the Picornaviridae family. HRV16 3Dpol shares the canonical features of other known polymerase structures and contains an N-terminal region that tethers the fingers and thumb subdomains, forming a completely encircled active site cavity which is accessible through a small tunnel on the backside of the molecule. The small thumb subdomain contributes to the formation of a large cleft on the front face of the polymerase which also leads to the active site. The cleft appears large enough to accommodate a template:primer duplex during RNA elongation or a protein primer during the uridylylation stage of replication initiation. Based on the structural features of HRV16 3Dpo1 and the catalytic mechanism known for all polymerases, a front-loading model for uridylylation is proposed.

scholarly journals Structural basis for regiospecific midazolam oxidation by human cytochrome P450 3A4

2016 ◽  
Vol 114 (3) ◽  
pp. 486-491 ◽  
Author(s):  
Irina F. Sevrioukova ◽  
Thomas L. Poulos
Keyword(s):  
Crystal Structure ◽  
Cytochrome P450 ◽  
Active Site ◽  
Structural Information ◽  
Binding Mode ◽  
Structural Basis ◽  
Cytochrome P450 3A4 ◽  
Human Cytochrome ◽  
Cyp3a4 Substrate

Human cytochrome P450 3A4 (CYP3A4) is a major hepatic and intestinal enzyme that oxidizes more than 60% of administered therapeutics. Knowledge of how CYP3A4 adjusts and reshapes the active site to regioselectively oxidize chemically diverse compounds is critical for better understanding structure–function relations in this important enzyme, improving the outcomes for drug metabolism predictions, and developing pharmaceuticals that have a decreased ability to undergo metabolism and cause detrimental drug–drug interactions. However, there is very limited structural information on CYP3A4–substrate interactions available to date. Despite the vast variety of drugs undergoing metabolism, only the sedative midazolam (MDZ) serves as a marker substrate for the in vivo activity assessment because it is preferentially and regioselectively oxidized by CYP3A4. We solved the 2.7 Å crystal structure of the CYP3A4–MDZ complex, where the drug is well defined and oriented suitably for hydroxylation of the C1 atom, the major site of metabolism. This binding mode requires H-bonding to Ser119 and a dramatic conformational switch in the F–G fragment, which transmits to the adjacent D, E, H, and I helices, resulting in a collapse of the active site cavity and MDZ immobilization. In addition to providing insights on the substrate-triggered active site reshaping (an induced fit), the crystal structure explains the accumulated experimental results, identifies possible effector binding sites, and suggests why MDZ is predominantly metabolized by the CYP3A enzyme subfamily.

Expression, characterization and crystal structure of thioredoxin from Schistosoma japonicum

Parasitology ◽  
2015 ◽  
Vol 142 (8) ◽  
pp. 1044-1052 ◽  
Author(s):  
YONGDONG LI ◽  
PAN LI ◽  
YUN PENG ◽  
QUNFENG WU ◽  
FUYAN HUANG ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Schistosoma Japonicum ◽  
Structural Information ◽  
Redox Homeostasis ◽  
Critical Role ◽  
Redox Balance ◽  
Functional Assay ◽  
Disulphide Bonds ◽  
Expression Characterization ◽  
Thioredoxin Glutathione Reductase

SUMMARYSchistosoma japonicum, a human blood fluke, causes a parasitic disease affecting millions of people in Asia. Thioredoxin–glutathione system of S. japonicum plays a critical role in maintaining the redox balance in parasite, which is a potential target for development of novel antischistosomal agents. Here we cloned the gene of S. japonicum thioredoxin (SjTrx), expressed and purified the recombinant SjTrx in Escherichia coli. Functional assay shows that SjTrx catalyses the dithiothreitol (DTT) reduction of insulin disulphide bonds. The coupling assay of SjTrx with its endogenous reductase, thioredoxin glutathione reductase from S. japonicum (SjTGR), supports its biological function to maintain the redox homeostasis in the cell. Furthermore, the crystal structure of SjTrx in the oxidized state was determined at 2·0 Å resolution, revealing a typical architecture of thioredoxin fold. The structural information of SjTrx provides us important clues for understanding the maintenance function of redox homeostasis in S. japonicum and pathogenesis of this chronic disease.

scholarly journals Crystal structure of Rv1220c, a SAM-dependentO-methyltransferase fromMycobacterium tuberculosis

2017 ◽  
Vol 73 (6) ◽  
pp. 315-320 ◽  
Author(s):  
Qiaoling Yan ◽  
Neil Shaw ◽  
Lanfang Qian ◽  
Dunquan Jiang
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Mycobacterium Tuberculosis ◽  
Electron Density ◽  
Active Site ◽  
Metal Binding ◽  
Structural Information

Rv1220c fromMycobacterium tuberculosisis annotated as anO-methyltransferase (MtbOMT). Currently, no structural information is available for this protein. Here, the crystal structure ofMtbOMT refined to 2.0 Å resolution is described. The structure reveals the presence of a methyltransferase fold and shows clear electron density for one molecule ofS-adenosylmethionine (SAM), which was apparently bound by the protein during its production inEscherichia coli. Although the overall structure ofMtbOMT resembles the structures ofO-methyltransferases fromCornybacterium glutamicum,Coxiella burnettiandAlfa alfa, differences are observed in the residues that make up the active site. Notably, substitution of Asp by His164 seems to abrogate metal binding byMtbOMT. A putative catalytic His–Asp pair located in the vicinity of SAM is absolutely conserved inMtbOMT homologues from all species ofMycobacterium, suggesting a conserved function for this protein.

scholarly journals Crystal Structure, Exogenous Ligand Binding, and Redox Properties of an Engineered Diiron Active Site in a Bacterial Hemerythrin

2013 ◽  
Vol 52 (22) ◽  
pp. 13014-13020 ◽  
Author(s):  
Yasunori Okamoto ◽  
Akira Onoda ◽  
Hiroshi Sugimoto ◽  
Yu Takano ◽  
Shun Hirota ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ligand Binding ◽  
Active Site ◽  
Redox Properties ◽  
Exogenous Ligand

scholarly journals Crystal Structure of the Dithiol Oxidase DsbA Enzyme fromProteus MirabilisBound Non-covalently to an Active Site Peptide Ligand

2014 ◽  
Vol 289 (28) ◽  
pp. 19810-19822 ◽  
Author(s):  
Fabian Kurth ◽  
Wilko Duprez ◽  
Lakshmanane Premkumar ◽  
Mark A. Schembri ◽  
David P. Fairlie ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Peptide Ligand
Sign in / Sign up

Export Citation Format

Share Document