scholarly journals A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study

Metallomics ◽  
2014 ◽  
Vol 6 (11) ◽  
pp. 2090-2099 ◽  
Author(s):  
Anikó Czene ◽  
Eszter Tóth ◽  
Eszter Németh ◽  
Harm Otten ◽  
Jens-Christian N. Poulsen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Cleavage ◽  
Catalytic Mechanism ◽  
Computational Study ◽  
Colicin E7 ◽  
Insight Into

The crystal structure of a colicin E7 metallonuclease mutant complemented by QM/MM calculations suggests an alternative catalytic mechanism of Zn2+-containing HNH nucleases.

The Crystal Structure of the H48Q Active Site Mutant of Human Group IIA Secreted Phospholipase A2at 1.5 Å Resolution Provides an Insight into the Catalytic Mechanism†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (52) ◽  
pp. 15468-15476 ◽  
Author(s):  
Suzanne H. Edwards ◽  
Darren Thompson ◽  
Sharon F. Baker ◽  
Stephen P. Wood ◽  
David C. Wilton
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Human Group ◽  
Insight Into

scholarly journals Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate

2013 ◽  
Vol 42 (1) ◽  
pp. 509-525 ◽  
Author(s):  
Zhenhua Shao ◽  
Wei Yan ◽  
Junhui Peng ◽  
Xiaobing Zuo ◽  
Yang Zou ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Trna Substrate ◽  
Insight Into

scholarly journals Crystal Structure ofN-Succinylarginine Dihydrolase AstB, Bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway ofEscherichia coli

2005 ◽  
Vol 280 (16) ◽  
pp. 15800-15808 ◽  
Author(s):  
Ante Tocilj ◽  
Joseph D. Schrag ◽  
Yunge Li ◽  
Barbara L. Schneider ◽  
Larry Reitzer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Catabolic Pathway ◽  
Major Pathway ◽  
Product Release ◽  
Flexible Loop ◽  
Ammonia Release ◽  
Arginine Catabolism ◽  
Insight Into

The ammonia-producing arginine succinyltransferase pathway is the major pathway inEscherichia coliand related bacteria for arginine catabolism as a sole nitrogen source. This pathway consists of five steps, each catalyzed by a distinct enzyme. Here we report the crystal structure ofN-succinylarginine dihydrolase AstB, the second enzyme of the arginine succinyltransferase pathway, providing the first structural insight into enzymes from this pathway. The enzyme exhibits a pseudo 5-fold symmetric α/β propeller fold of circularly arranged ββαβ modules enclosing the active site. The crystal structure indicates clearly that this enzyme belongs to the amidinotransferase (AT) superfamily and that the active site contains a Cys–His-Glu triad characteristic of the AT superfamily. Structures of the complexes of AstB with the reaction product and a C365S mutant with bound theN-succinylarginine substrate suggest a catalytic mechanism that consists of two cycles of hydrolysis and ammonia release, with each cycle utilizing a mechanism similar to that proposed for arginine deiminases. Like other members of the AT superfamily of enzymes, AstB possesses a flexible loop that is disordered in the absence of substrate and assumes an ordered conformation upon substrate binding, shielding the ligand from the bulk solvent, thereby controlling substrate access and product release.

scholarly journals Allosteric activation of CwlD amidase activity by the GerS lipoprotein during Clostridioides difficile spore formation

2021 ◽  
Author(s):  
Carolina Alves Feliciano ◽  
Brian E Eckenroth ◽  
Oscar R Diaz ◽  
Syvlie Doublie ◽  
Aimee Shen
Keyword(s):  
Crystal Structure ◽  
Spore Germination ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Allosteric Activation ◽  
Amidase Activity ◽  
Clostridioides Difficile ◽  
Binding Partners ◽  
Insight Into ◽  
Peptidoglycan Layer

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. Spore germination depends on the degradation of the protective spore peptidoglycan layer known as the spore cortex. Cortex degradation is mediated by enzymes that recognize the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL). In C. difficile, MAL synthesis depends on the activity of the CwlD amidase and the GerS lipoprotein, which directly binds CwlD. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind zinc stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to zinc, which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of zinc co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

Crystal Structure of α-Amino-β-carboxymuconate-ε-semialdehyde Decarboxylase: Insight into the Active Site and Catalytic Mechanism of a Novel Decarboxylation Reaction†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (35) ◽  
pp. 10412-10421 ◽  
Author(s):  
Dariusz Martynowski ◽  
Yvonne Eyobo ◽  
Tingfeng Li ◽  
Kun Yang ◽  
Aimin Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Decarboxylation Reaction ◽  
Insight Into

scholarly journals A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009791
Author(s):  
Carolina Alves Feliciano ◽  
Brian E. Eckenroth ◽  
Oscar R. Diaz ◽  
Sylvie Doublié ◽  
Aimee Shen
Keyword(s):  
Crystal Structure ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Protective Layer ◽  
Lytic Enzymes ◽  
Amidase Activity ◽  
Binding Partner ◽  
Clostridioides Difficile ◽  
Binding Partners ◽  
Insight Into

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. In C. difficile, MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn2+ stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn2+, which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn2+ co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

scholarly journals Favipiravir: insight into the crystal structure, Hirshfeld surface analysis and computational study

2021 ◽  
Author(s):  
Maria G. Babashkina ◽  
Antonio Frontera ◽  
Alexander V. Kertman ◽  
Yasemin Saygideger ◽  
Swaminathan Murugavel ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Computational Study ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Insight Into
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