scholarly journals Evidence in Support of Lysine 77 and Histidine 96 as Acid–Base Catalytic Residues in Saccharopine Dehydrogenase from Saccharomyces cerevisiae

Biochemistry ◽  
2012 ◽  
Vol 51 (4) ◽  
pp. 857-866 ◽  
Author(s):  
Vidya Prasanna Kumar ◽  
Leonard M. Thomas ◽  
Kostyantyn D. Bobyk ◽  
Babak Andi ◽  
Paul F. Cook ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Acid Base ◽  
Catalytic Residues ◽  
Saccharopine Dehydrogenase

scholarly journals Identification of Acid-Base Catalytic Residues of High-MrThioredoxin Reductase fromPlasmodium falciparum

2006 ◽  
Vol 281 (44) ◽  
pp. 32967-32977 ◽  
Author(s):  
Paul J. McMillan ◽  
L. David Arscott ◽  
David P. Ballou ◽  
Katja Becker ◽  
Charles H. Williams ◽  
...  
Keyword(s):  
Acid Base ◽  
Catalytic Residues

Structural Studies of the Final Enzyme in the α-Aminoadipate Pathway-Saccharopine Dehydrogenase from Saccharomyces cerevisiae

2007 ◽  
Vol 373 (3) ◽  
pp. 745-754 ◽  
Author(s):  
D.L. Burk ◽  
J. Hwang ◽  
E. Kwok ◽  
L. Marrone ◽  
V. Goodfellow ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Structural Studies ◽  
Saccharopine Dehydrogenase

Overall Kinetic Mechanism of Saccharopine Dehydrogenase (l-Glutamate Forming) from Saccharomyces cerevisiae†

Biochemistry ◽  
2008 ◽  
Vol 47 (19) ◽  
pp. 5417-5423 ◽  
Author(s):  
Ashwani Kumar Vashishtha ◽  
Ann H. West ◽  
Paul F. Cook
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Kinetic Mechanism ◽  
Saccharopine Dehydrogenase

scholarly journals Crystal Structures of Streptomyces Coelicolor Methylmalonyl-CoA Epimerase with Substrate or Transition State Analog Contradicts a Simple General Acid-Base Catalytic Mechanism

2021 ◽  
Author(s):  
Lee M Stunkard ◽  
Aaron B Benjamin ◽  
James Bower ◽  
Tyler Huth ◽  
Jeremy Lohman
Keyword(s):  
Transition State ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Catalytic Mechanism ◽  
Streptomyces Coelicolor ◽  
Base Catalysis ◽  
Acid Base ◽  
Transition State Analog ◽  
Catalytic Residues ◽  
General Acid

Crystal structures of Streptomyces coelicolor methylmalonyl-CoA epimerase in the holo-form, with substrate or the putative transition state analog, 2-nitroproionyl-CoA. The proposed catalytic mechanism is general acid-base catalysis. The proposed catalytic residues are too far from the substrate or analog, unless conformational changes take place or some other mechanism is used. <br>

scholarly journals Functional analysis of mouse Hoxa-7 in Saccharomyces cerevisiae: sequences outside the homeodomain base contact zone influence binding and activation

1994 ◽  
Vol 14 (1) ◽  
pp. 238-254
Author(s):  
M K Gross ◽  
P Gruss
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Contact Zone ◽  
Binding Sites ◽  
Hox Genes ◽  
Three Dimensional ◽  
Acid Base ◽  
Hox Proteins ◽  
Multiple Binding Sites ◽  
Multiple Binding ◽  
Base Contact

The murine developmental control gene product, Hoxa-7, was shown to function as a DNA-binding transactivator in Saccharomyces cerevisiae. The importance of the ATTA core, the preference for antp class flanking nucleotides, the importance of Asn-51 of the homeodomain (HD), and the synergism of multiple binding sites all reflect properties that have previously been described for HOM or Hox proteins in tissue culture systems. A comparison of contact positions among genes of paralog groups and classes of mammalian HDs points to a lack of diversity in positions that make base contact, suggesting that besides the combination of HD amino acid-base pair contacts, another means of recognizing differences between targets must exist if Hox genes select different targets. The HD of antennapedia is identical to the Hoxa-7 HD. The interaction of Hoxa-7 with the exact sequence used in the nuclear magnetic resonance three-dimensional structural analysis on the antennapedia HD was studied. Hoxa-7 binding and transactivation was influenced by sequences outside of the known base contact zone of this site. We conclude that Hoxa-7 protein has a second means to interact with DNA or/and that the sequences flanking the base contact zone influence HD interactions by distorting DNA within the contact zone (base or backbone). This result is discussed in terms of DNA flexure and two modes of transcription used in S. cerevisiae.

scholarly journals His151 and His296 Are the Acid-Base Catalytic Residues of Bacillus cereus Sphingomyelinase in Sphingomyelin Hydrolysis

2003 ◽  
Vol 26 (7) ◽  
pp. 920-926 ◽  
Author(s):  
Takashi Obama ◽  
Shinobu Fujii ◽  
Hiroh Ikezawa ◽  
Kiyoshi Ikeda ◽  
Masayoshi Imagawa ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Acid Base ◽  
Catalytic Residues

scholarly journals Distinct Elements in the Proteasomal β5 Subunit Propeptide Required for Autocatalytic Processing and Proteasome Assembly

2015 ◽  
Vol 291 (4) ◽  
pp. 1991-2003 ◽  
Author(s):  
Xia Li ◽  
Yanjie Li ◽  
Cassandra S. Arendt ◽  
Mark Hochstrasser
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cleavage Site ◽  
20S Proteasome ◽  
Catalytic Residues ◽  
Proteasome Subunit ◽  
Autocatalytic Processing ◽  
Assembly Factor

Eukaryotic 20S proteasome assembly remains poorly understood. The subunits stack into four heteroheptameric rings; three inner-ring subunits (β1, β2, and β5) bear the protease catalytic residues and are synthesized with N-terminal propeptides. These propeptides are removed autocatalytically late in assembly. In Saccharomyces cerevisiae, β5 (Doa3/Pre2) has a 75-residue propeptide, β5pro, that is essential for proteasome assembly and can work in trans. We show that deletion of the poorly conserved N-terminal half of the β5 propeptide nonetheless causes substantial defects in proteasome maturation. Sequences closer to the cleavage site have critical but redundant roles in both assembly and self-cleavage. A conserved histidine two residues upstream of the autocleavage site strongly promotes processing. Surprisingly, although β5pro is functionally linked to the Ump1 assembly factor, trans-expressed β5pro associates only weakly with Ump1-containing precursors. Several genes were identified as dosage suppressors of trans-expressed β5pro mutants; the strongest encoded the β7 proteasome subunit. Previous data suggested that β7 and β5pro have overlapping roles in bringing together two half-proteasomes, but the timing of β7 addition relative to half-mer joining was unclear. Here we report conditions where dimerization lags behind β7 incorporation into the half-mer. Our results suggest that β7 insertion precedes half-mer dimerization, and the β7 tail and β5 propeptide have unequal roles in half-mer joining.

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