(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Archaea: NE > Euryarchaeota: NE > Thermococci: NE > Thermococcales: NE > Thermococcaceae: NE > Pyrococcus: NE > Pyrococcus furiosus: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Pyrococcus furiosus COM1: N, E.
Molecular evidence
Database
No mutation 4 structures(e.g. : 5G59, 5G5C, 5G5M... more)(less) 5G59: Structure of the Pyrococcus Furiosus Esterase Pf2001 with space group P3121, 5G5C: Structure of the Pyrococcus Furiosus Esterase Pf2001 with space group C2221, 5G5M: Structure of the Pyrococcus Furiosus Esterase Pf2001 with space group P21, 5LCN: Structure of the Pyrococcus Furiosus Esterase Pf2001 with space group P212121 No kinetic
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MIIEILVAALVLFLVFTAFVGYKMVNPPRVVGNWTPKDLSFEYKDVEITT EDNVKLSGWWIDNGSDKTVIPLHGYTSSRWAEHYMRPVIEFLLKEGYNVL AFDFRAHGKSGGKYTTVGDKEILDLKAGVKWLKDNYPEKSKRIGVIGFSM GALVAIRGLSEVKEICCGVADSPPIYLDKTGARGMKYFAKLPEWLYSFVK PFSELFSGGRPINVLNYTNSIKKPLFLIIGRRDTLVKVEEVQEFYERNKH VNPNVELWVTDAPHVRTIQVFPEEWKSRVGEFLKRWMG
References
Title: Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics Zhang X, Li L, Zheng Q Ref: J Chem Inf Model, :, 2023 : PubMed
Pf2001 esterase (Pf2001) from Pyrococcus furiosus has hyperthermophilic properties and exerts a biocatalytic function in a dimeric state. Crystal structures revealed that the structural rearrangement of the cap domain is responsible for the Pf2001 dimer formation. However, the details of the cap domain remodeling and the effects of temperature on the dimerization process remain elusive at the molecular level, taking into account that experimental methods are difficult to capture the dynamic process of dimerization to some extent. Herein, four dimer models based on the monomeric crystal structure (PDB ID: 5G59) were constructed to investigate the conformational transition details and temperature effects in the dimerization by conventional molecular dynamics and accelerated molecular dynamics simulations. Our simulation results indicate that the monomer undergoes a conformational change into a "preparatory state" at high temperatures, which is more favorable for its transformation into a stable dimer. The subsequent free energy landscape analysis further identifies four intermediate states (from separated state to dimeric state) and discloses that a more accessible alpha-helix driven by stronger hydrophobic interactions induces a rearrangement of the cap domain, displaying a "tic-tac-toe" activation feature that is important for stabilizing the dimer interface and facilitating the formation of hydrophobic pockets. In addition, the electrostatic potential surface analysis illustrates that the weaker electrostatic repulsion (Lys and Arg) in the dimer interface at high temperatures is also a key factor for dimer stabilization. Altogether, our results can provide molecular-level insight into the dimer formation process of hyperthermophilic esterase and would be useful to understand the enzymatic specificity of alpha/beta-hydrolase.
Lipases and esterases constitute a group of enzymes that catalyze the hydrolysis or synthesis of ester bonds. A major biotechnological interest corresponds to thermophilic esterases, due to their intrinsic stability at high temperatures. The Pf2001 esterase from Pyrococcus furiosus reaches its optimal activity between 70 degrees C and 80 degrees C. The crystal structure of the Pf2001 esterase shows two different conformations: monomer and dimer. The structures reveal important rearrangements in the "cap" subdomain between monomer and dimer, by the formation of an extensive intertwined helical interface. Moreover, the dimer interface is essential for the formation of the hydrophobic channel for substrate selectivity, as confirmed by mutagenesis and kinetic analysis. We also provide evidence for dimer formation at high temperatures, a process that correlates with its enzymatic activation. Thus, we propose a temperature-dependent activation mechanism of the Pf2001 esterase via dimerization that is necessary for the substrate channel formation in the active-site cleft.