Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

1998 ◽  
Vol 46 (4) ◽  
pp. 488-493 ◽  
Author(s):  
Paul J. Gane ◽  
Jim M. Dunwell ◽  
Jim Warwickr
Keyword(s):  
Active Site ◽  
Oxalate Oxidase

scholarly journals Barley (Hordeum vulgare) oxalate oxidase is a manganese-containing enzyme

1999 ◽  
Vol 343 (1) ◽  
pp. 185-190 ◽  
Author(s):  
Laura REQUENA ◽  
Stephen BORNEMANN
Keyword(s):  
Hordeum Vulgare ◽  
Epr Spectroscopy ◽  
Active Site ◽  
Homology Model ◽  
Direct Conversion ◽  
Oxalate Oxidase ◽  
Metal Analysis ◽  
Seedling Root

Oxalate oxidase (EC 1.2.3.4) catalyses the conversion of oxalate and dioxygen into CO2 and H2O2. The barley (Hordeum vulgare) seedling root enzyme was purified to homogeneity and shown by metal analysis and EPR spectroscopy to contain Mn(II) at up to 0.80 atom per subunit. The involvement of Mn and neither flavin, Cu nor Fe in the direct conversion of dioxygen to H2O2 makes oxalate oxidase unique. A model of the active site of the holoenzyme based on a homology model of the apoenzyme is proposed.

scholarly journals The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

2007 ◽  
Vol 407 (3) ◽  
pp. 397-406 ◽  
Author(s):  
Victoria J. Just ◽  
Matthew R. Burrell ◽  
Laura Bowater ◽  
Iain McRobbie ◽  
Clare E. M. Stevenson ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Structural Information ◽  
Side Reaction ◽  
Oxalate Oxidase ◽  
Decarboxylase Activity ◽  
Oxalate Decarboxylase ◽  
Catalytically Active ◽  
The Stability ◽  
Kinetics Of

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural.

Oxalate Decarboxylase and Oxalate Oxidase Activities Can Be Interchanged with a Specificity Switch of up to 282 000 by Mutating an Active Site Lid†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (43) ◽  
pp. 12327-12336 ◽  
Author(s):  
Matthew R. Burrell ◽  
Victoria J. Just ◽  
Laura Bowater ◽  
Shirley A. Fairhurst ◽  
Laura Requena ◽  
...  
Keyword(s):  
Active Site ◽  
Oxalate Oxidase ◽  
Oxalate Decarboxylase

scholarly journals Kinetic and Spectroscopic Studies of Bicupin Oxalate Oxidase and Putative Active Site Mutants

2013 ◽  
Vol 27 (S1) ◽  
Author(s):  
Ellen W Moomaw ◽  
Eric Hoffer ◽  
Patricia Moussatche ◽  
John Salerno ◽  
Morgan Grant ◽  
...  
Keyword(s):  
Active Site ◽  
Spectroscopic Studies ◽  
Oxalate Oxidase ◽  
Putative Active Site ◽  
Active Site Mutants

scholarly journals Kinetic and Spectroscopic Studies of Bicupin Oxalate Oxidase and Putative Active Site Mutants

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e57933 ◽  
Author(s):  
Ellen W. Moomaw ◽  
Eric Hoffer ◽  
Patricia Moussatche ◽  
John C. Salerno ◽  
Morgan Grant ◽  
...  
Keyword(s):  
Active Site ◽  
Spectroscopic Studies ◽  
Oxalate Oxidase ◽  
Putative Active Site ◽  
Active Site Mutants

scholarly journals Burst Kinetics and Redox Transformations of the Active Site Manganese Ion in Oxalate Oxidase

2007 ◽  
Vol 282 (10) ◽  
pp. 7011-7023 ◽  
Author(s):  
Mei M. Whittaker ◽  
Heng-Yen Pan ◽  
Erik T. Yukl ◽  
James W. Whittaker
Keyword(s):  
Active Site ◽  
Oxalate Oxidase ◽  
Redox Transformations ◽  
Manganese Ion ◽  
Burst Kinetics

Locating Al in the DABCO catalyst before and after Al extraction

1990 ◽  
Vol 48 (4) ◽  
pp. 265-267
Author(s):  
Kathleen B. Reuter
Keyword(s):  
Active Site ◽  
Inverse Relationship ◽  
Transverse Direction ◽  
Reaction Rate ◽  
Acid Phosphate ◽  
Fracture Surfaces ◽  
Al Content ◽  
Before And After ◽  
Relationship Of

The reaction rate and efficiency of piperazine to 1,4-diazabicyclo-octane (DABCO) depends on the Si/Al ratio of the MFI topology catalysts. The Al was shown to be the active site, however, in the Si/Al range of 30-200 the reaction rate increases as the Si/Al ratio increases. The objective of this work was to determine the location and concentration of Al to explain this inverse relationship of Al content with reaction rate.Two silicalite catalysts in the form of 1/16 inch SiO2/Al2O3 bonded extrudates were examined: catalyst A with a Si/Al of 83; and catalyst B, the acid/phosphate Al extracted form of catalyst A, with a Si/Al of 175. Five extrudates from each catalyst were fractured in the transverse direction and particles were obtained from the fracture surfaces near the center of the extrudate diameter. Particles were also obtained from the outside surfaces of five extrudates.

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.

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