Mechanistic Studies on Class I Polyhydroxybutyrate (PHB) Synthase fromRalstonia eutropha:  Class I and III Synthases Share a Similar Catalytic Mechanism†

Biochemistry ◽  
2001 ◽  
Vol 40 (4) ◽  
pp. 1011-1019 ◽  
Author(s):  
Yong Jia ◽  
Wei Yuan ◽  
Jola Wodzinska ◽  
Chung Park ◽  
Anthony J. Sinskey ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Class I ◽  
Mechanistic Studies ◽  
Phb Synthase

Structure and mechanism of the γ-glutamyl-γ-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa

2021 ◽  
Vol 77 (10) ◽  
pp. 1305-1316
Author(s):  
Yujing Chen ◽  
Haizhu Jia ◽  
Jianyu Zhang ◽  
Yakun Liang ◽  
Ruihua Liu ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Class I ◽  
Polyamine Metabolism ◽  
Binding Assays ◽  
Starting Point ◽  
Family Activity ◽  
Living Organisms

Polyamines are important regulators in all living organisms and are implicated in essential biological processes including cell growth, differentiation and apoptosis. Pseudomonas aeruginosa possesses an spuABCDEFGHI gene cluster that is involved in the metabolism and uptake of two polyamines: spermidine and putrescine. In the proposed γ-glutamylation–putrescine metabolism pathway, SpuA hydrolyzes γ-glutamyl-γ-aminobutyrate (γ-Glu-GABA) to glutamate and γ-aminobutyric acid (GABA). In this study, crystal structures of P. aeruginosa SpuA are reported, confirming it to be a member of the class I glutamine amidotransferase (GAT) family. Activity and substrate-binding assays confirm that SpuA exhibits a preference for γ-Glu-GABA as a substrate. Structures of an inactive H221N mutant were determined with bound glutamate thioester intermediate or glutamate product, thus delineating the active site and substrate-binding pocket and elucidating the catalytic mechanism. The crystal structure of another bacterial member of the class I GAT family from Mycolicibacterium smegmatis (MsGATase) in complex with glutamine was determined for comparison and reveals a binding site for glutamine. Activity assays confirm that MsGATase has activity for glutamine as a substrate but not for γ-Glu-GABA. The work reported here provides a starting point for further investigation of polyamine metabolism in P. aeruginosa.

scholarly journals Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold

2016 ◽  
Vol 113 (35) ◽  
pp. 9804-9809 ◽  
Author(s):  
Patricia R. Feliciano ◽  
Catherine L. Drennan ◽  
M. Cristina Nonato
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Leishmania Major ◽  
Catalytic Mechanism ◽  
Neglected Tropical Diseases ◽  
Fumarate Hydratase ◽  
Class I ◽  
Protein Fold ◽  
Binding Pockets ◽  
Fumarate Hydratases

Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases.

scholarly journals Mechanistic studies of the agmatine deiminase from Listeria monocytogenes

2016 ◽  
Vol 473 (11) ◽  
pp. 1553-1561 ◽  
Author(s):  
Charles A. Soares ◽  
Bryan Knuckley
Keyword(s):  
Listeria Monocytogenes ◽  
Catalytic Mechanism ◽  
Mechanistic Studies ◽  
New Class ◽  
Enzyme Superfamily ◽  
Agmatine Deiminase ◽  
Inhibition Studies

Mechanistic and inhibition studies of the agmatine deiminase found in Listeria monocytogenes reveal a novel catalytic mechanism for the guanidinium-modifying enzyme superfamily. The results of the present study suggest that a new class of mechanism-based inactivators is needed.

Phosphine-catalyzed [3 + 2] annulation of 2-aminoacrylates with allenoates and mechanistic studies

2020 ◽  
Vol 10 (12) ◽  
pp. 3959-3964 ◽  
Author(s):  
Xiao-Yun Wu ◽  
Hou-Ze Gui ◽  
Harish Jangra ◽  
Yin Wei ◽  
Hendrik Zipse ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Kinetic Studies ◽  
Mechanistic Studies ◽  
Stereogenic Center

A phosphine catalyzed formal [3 + 2] annulation was disclosed, affording 3-pyrrolines containing an amino quaternary stereogenic center in good to excellent yields. The catalytic mechanism was investigated by DFT and kinetic studies.

Catalytic addition of amines to carbodiimides by bis(β-diketiminate)lanthanide(ii) complexes and mechanistic studies

2015 ◽  
Vol 44 (46) ◽  
pp. 20075-20086 ◽  
Author(s):  
Mingqiang Xue ◽  
Yu Zheng ◽  
Yubiao Hong ◽  
Yingming Yao ◽  
Fan Xu ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Mechanistic Studies ◽  
Catalytic Addition

Bis(β-diketiminate)lanthanide(ii) complexes L2Ln(THF)n were found to be excellent pre-catalysts for catalytic addition of amines to carbodiimides and a possible catalytic mechanism was proposed on the basis of the isolation of monoguanidinate Eu(ii) and bis(guanidinate) Yb(iii) species.

Electron microscopy analysis of degenerating pancreatic ß cells in transgenic mice expressing the MHC Class I antigen Dd

1990 ◽  
Vol 48 (3) ◽  
pp. 548-549
Author(s):  
T. A. Stewart ◽  
D. Liggitt ◽  
S. Pitts ◽  
L. Martin ◽  
M. Siegel ◽  
...  
Keyword(s):  
Type I Diabetes ◽  
Disease Process ◽  
Class Ii ◽  
Class I ◽  
Type I ◽  
Aberrant Expression ◽  
Mhc Molecules ◽  
Endogenous Insulin ◽  
Class Ii Mhc ◽  
Ifn Γ

Insulin-dependant (Type I) diabetes mellitus (IDDM) is a metabolic disorder resulting from the lack of endogenous insulin secretion. The disease is thought to result from the autoimmune mediated destruction of the insulin producing ß cells within the islets of Langerhans. The disease process is probably triggered by environmental agents, e.g. virus or chemical toxins on a background of genetic susceptibility associated with particular alleles within the major histocompatiblity complex (MHC). The relation between IDDM and the MHC locus has been reinforced by the demonstration of both class I and class II MHC proteins on the surface of ß cells from newly diagnosed patients as well as mounting evidence that IDDM has an autoimmune pathogenesis. In 1984, a series of observations were used to advance a hypothesis, in which it was suggested that aberrant expression of class II MHC molecules, perhaps induced by gamma-interferon (IFN γ) could present self antigens and initiate an autoimmune disease. We have tested some aspects of this model and demonstrated that expression of IFN γ by pancreatic ß cells can initiate an inflammatory destruction of both the islets and pancreas and does lead to IDDM.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

Sign in / Sign up

Export Citation Format

Share Document