Iron superoxide dismutases: structure and function of an archaic enzyme

2003 ◽  
Vol 31 (6) ◽  
pp. 1330-1334 ◽  
Author(s):  
G. Schäfer ◽  
S. Kardinahl
Keyword(s):  
Three Dimensional ◽  
In Silico Analysis ◽  
Dimensional Structure ◽  
Superoxide Dismutases ◽  
X Ray ◽  
Manganese Superoxide ◽  
Manganese Superoxide Dismutases ◽  
And Function ◽  
Silico Analysis ◽  
Iron And Manganese

Iron and manganese superoxide dismutases are phylogenetically closely related. They are compared by in silico analysis with regard to their metal specificity and their three-dimensional structure. Special attention is given to the structure and properties of superoxide dismutases from archaeal prokaryotes. The mechanism and the extreme thermostability of superoxide dismutase from Sulfolobus acidocaldarius are discussed on the basis of its high-resolution X-ray structure. An alternating-site mechanism and an evolutionary origin of superoxide dismutases under the environmental conditions on the early Earth are proposed.

In silico analysis of Nattokinase from Bacillus subtilis sp natto

2017 ◽  
Vol 9 (04) ◽  
Author(s):  
Cambyz Irajie ◽  
Milad Mohkam ◽  
Navid Nezafat ◽  
Fatemeh Mohammadi ◽  
Younes Ghasemi
Keyword(s):  
Bacillus Subtilis ◽  
Serine Protease ◽  
In Silico ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Dimensional Structure ◽  
Cardiovascular Therapy ◽  
And Function ◽  
Outlier Region ◽  
Silico Analysis

Nattokinase or subtilisin NAT (EC 3.4.21.62) is one of the most remarkable enzymes produced by Bacillus subtilis sp. Natto, which posses direct fibrinolytic activity. The aim of this study is in silico analysis of Nattokinase structure and function. The three-dimensional structure of serine protease Nattokinase from Bacillus subtilis sp. natto was determined using homology modeling performed by Geno3D2 Web Server and refined by ModRefiner. The obtained models were validated via programs such as RAMPAGE, ERRAT, 3D Match and verify 3D for consistency; moreover, functional analysis performed by PFP from Kihara Bioinformatics laboratory. RAMPAGE analysis showed that 96.7% of the residues are located in the favored region, 3.0% in allowed region and 0.4% in outlier region of the Ramachandran plot. The verify 3D value of 0.73 indicates that the environmental sketch of the model is fine. SOPMA and PSIPRED were exploited for computation of the secondary structural properties of serine protease Nattokinase. Active site determination via AADS suggested that this enzyme can be applied as a potent enzyme for cardiovascular therapy. However, these results should be more confirmed by wet lab researches for designing the more active enzyme for better functions on its fibrinolysis activity.

Structure-Function Relationships in Iron and Manganese Superoxide Dismutases

1991 ◽  
Vol 12 (1) ◽  
pp. 259-268 ◽  
Author(s):  
William C. Stallings ◽  
Anita L. Metzger ◽  
Katherine A. Paitridge ◽  
James A. Fee ◽  
Martha L. Ludwig
Keyword(s):  
Structure Function ◽  
Superoxide Dismutases ◽  
Manganese Superoxide ◽  
Manganese Superoxide Dismutases ◽  
Iron And Manganese

scholarly journals Iron and manganese superoxide dismutases

1983 ◽  
Vol 79 ◽  
pp. 34-35
Author(s):  
J.A. Fee ◽  
C. Bull ◽  
W. Stallings ◽  
M.L. Ludwig
Keyword(s):  
Superoxide Dismutases ◽  
Manganese Superoxide ◽  
Manganese Superoxide Dismutases ◽  
Iron And Manganese

scholarly journals Molecular modeling of the Plasmodium falciparum pre-mRNA splicing and nuclear export factor PfU52

2013 ◽  
Author(s):  
Alain Narcisse Newo Soufo
Keyword(s):  
Plasmodium Falciparum ◽  
Nuclear Export ◽  
Drug Targets ◽  
De Novo ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Mrna Splicing ◽  
Dimensional Structure ◽  
Metazoan Parasites ◽  
And Function

UAP56/SUB2 is a DExD/H-box RNA helicase that is critically involved in pre-mRNA splicing and mRNA nuclear export. This helicase is broadly conserved and essential in many eukaryotic lineages, including protozoan and metazoan parasites. Previous research suggests that helicases from parasites could be promising drug targets for treating parasitic diseases. Accordingly, characterizing the structure and function of these proteins is of interest for structure-based, de novo design of new lead compounds. Here, we used homology modeling to construct a three-dimensional structure of PfU52 (PMDB ID: PM0079288), the Plasmodium falciparum ortholog of UAP56/SUB2. Comparative in silico analysis revealed that although PfU52 shared many physicochemical, structural and dynamic similarities with its human homolog, it also displayed some unique features that could be exploited for drug design.

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