scholarly journals Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae

2021 ◽  
Vol 77 (3) ◽  
pp. 61-69
Author(s):  
Xiaofei Wu ◽  
Mengying Zhang ◽  
Zhiling Kuang ◽  
Jian Yue ◽  
Lu Xue ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Crystal Structures ◽  
Substrate Binding ◽  
Binding Mode ◽  
Protein Family ◽  
Future Research ◽  
Type Iii ◽  
Substrate Analogue ◽  
Similar Mode ◽  
Conserved Residue

Anthranilate phosphoribosyltransferase (AnPRT) catalyzes the transfer of the phosphoribosyl group of 5′-phosphoribosyl-1′-pyrophosphate (PRPP) to anthranilate to form phosphoribosyl-anthranilate. Crystal structures of AnPRTs from bacteria and archaea have previously been determined; however, the structure of Saccharomyces cerevisiae AnPRT (ScAnPRT) still remains unsolved. Here, crystal structures of ScAnPRT in the apo form as well as in complex with its substrate PRPP and the substrate analogue 4-fluoroanthranilate (4FA) are presented. These structures demonstrate that ScAnPRT exhibits the conserved structural fold of type III phosphoribosyltransferase enzymes and shares the similar mode of substrate binding found across the AnPRT protein family. In addition, crystal structures of ScAnPRT mutants (ScAnPRTSer121Ala and ScAnPRTGly141Asn) were also determined. These structures suggested that the conserved residue Ser121 is critical for binding PRPP, while Gly141 is dispensable for binding 4FA. In summary, these structures improved the preliminary understanding of the substrate-binding mode of ScAnPRT and laid foundations for future research.

scholarly journals Saccharomyces cerevisiae Hsp70 Mutations Affect [PSI+] Prion Propagation and Cell Growth Differently and Implicate Hsp40 and Tetratricopeptide Repeat Cochaperones in Impairment of [PSI+]

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 495-506 ◽  
Author(s):  
Gary W Jones ◽  
Daniel C Masison
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Growth ◽  
Substrate Binding ◽  
Tetratricopeptide Repeat ◽  
Atpase Domain ◽  
Propagation Effects ◽  
Prion Propagation ◽  
Conserved Residue ◽  
Normal Propagation ◽  
New Mutations

Abstract We previously described an Hsp70 mutant (Ssa1-21p), altered in a conserved residue (L483W), that dominantly impairs yeast [PSI+] prion propagation without affecting growth. We generated new SSA1 mutations that impaired [PSI+] propagation and second-site mutations in SSA1-21 that restored normal propagation. Effects of mutations on growth did not correlate with [PSI+] phenotype, revealing differences in Hsp70 function required for growth and [PSI+] propagation and suggesting that Hsp70 interacts differently with [PSI+] prion aggregates than with other cellular substrates. Complementary suppression of altered activity between forward and suppressing mutations suggests that mutations that impair [PSI+] affect a similar Hsp70 function and that suppressing mutations similarly overcome this effect. All new mutations that impaired [PSI+] propagation were located in the ATPase domain. Locations and homology of several suppressing substitutions suggest that they weaken Hsp70's substrate-trapping conformation, implying that impairment of [PSI+] by forward mutations is due to altered ability of the ATPase domain to regulate substrate binding. Other suppressing mutations are in residues important for interactions with Hsp40 or TPR-containing cochaperones, suggesting that such interactions are necessary for the impairment of [PSI+] propagation caused by mutant Ssa1p.

scholarly journals Manganese toxicity and Saccharomyces cerevisiae Mam3p, a member of the ACDP (ancient conserved domain protein) family

2005 ◽  
Vol 386 (3) ◽  
pp. 479-487 ◽  
Author(s):  
Mei YANG ◽  
Laran T. JENSEN ◽  
Allison J. GARDNER ◽  
Valeria C. CULOTTA
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Integral Membrane Protein ◽  
Manganese Toxicity ◽  
Protein Family ◽  
Neurological Deficits ◽  
Yeast Saccharomyces Cerevisiae ◽  
Conserved Domain ◽  
Genetic Epistasis ◽  
Accumulation Of Metals ◽  
Domain Protein

Manganese is an essential, but potentially toxic, trace metal in biological systems. Overexposure to manganese is known to cause neurological deficits in humans, but the pathways that lead to manganese toxicity are largely unknown. We have employed the bakers' yeast Saccharomyces cerevisiae as a model system to identify genes that contribute to manganese-related damage. In a genetic screen for yeast manganese-resistance mutants, we identified S. cerevisiae MAM3 as a gene which, when deleted, would increase cellular tolerance to toxic levels of manganese and also increased the cell's resistance towards cobalt and zinc. By sequence analysis, Mam3p shares strong similarity with the mammalian ACDP (ancient conserved domain protein) family of polypeptides. Mutations in human ACDP1 have been associated with urofacial (Ochoa) syndrome. However, the functions of eukaryotic ACDPs remain unknown. We show here that S. cerevisiae MAM3 encodes an integral membrane protein of the yeast vacuole whose expression levels directly correlate with the degree of manganese toxicity. Surprisingly, Mam3p contributes to manganese toxicity without any obvious changes in vacuolar accumulation of metals. Furthermore, through genetic epistasis studies, we demonstrate that MAM3 operates independently of the well-established manganese-trafficking pathways in yeast, involving the manganese transporters Pmr1p, Smf2p and Pho84p. This is the first report of a eukaryotic ACDP family protein involved in metal homoeostasis.

A structural and functional analysis of type III periplasmic and substrate binding proteins: their role in bacterial siderophore and heme transport

2011 ◽  
Vol 392 (1-2) ◽  
Author(s):  
Byron C.H. Chu ◽  
Hans J. Vogel
Keyword(s):  
Binding Proteins ◽  
Substrate Binding ◽  
Transport Systems ◽  
Complex Structures ◽  
Type Iii ◽  
Heme Transport ◽  
Periplasmic Binding Proteins ◽  
Outer Membrane Transporter ◽  
Α Helix ◽  
Carboxy Terminal

AbstractInEscherichia colithe Fhu, Fep and Fec transport systems are involved in the uptake of chelated ferric iron-siderophore complexes, whereas in pathogenic strains heme can also be used as an iron source. An essential step in these pathways is the movement of the ferric-siderophore complex or heme from the outer membrane transporter across the periplasm to the cognate cytoplasmic membrane ATP-dependent transporter. This is accomplished in each case by a dedicated periplasmic binding protein (PBP). Ferric-siderophore binding PBPs belong to the PBP protein superfamily and adopt a bilobal type III structural fold in which the two independently folded amino and carboxy terminal domains are linked together by a single long α-helix of approximately 20 amino acids. Recent structural studies reveal how the PBPs of the Fhu, Fep, Fec and Chu systems are able to bind their corresponding ligands. These complex structures will be discussed and placed in the context of our current understanding of the entire type III family of Gram-negative periplasmic binding proteins and related Gram-positive substrate binding proteins.

scholarly journals A best-fit probability distribution for the estimation of rainfall in northern regions of Pakistan

2016 ◽  
Vol 11 (1) ◽  
pp. 432-440 ◽  
Author(s):  
M. T. Amin ◽  
M. Rizwan ◽  
A. A. Alazba
Keyword(s):  
Probability Distribution ◽  
Goodness Of Fit ◽  
Probability Distributions ◽  
Future Research ◽  
Maximum Rainfall ◽  
Type Iii ◽  
Goodness Of Fit Tests ◽  
Pearson Type ◽  
Northern Regions ◽  
Best Fit

AbstractThis study was designed to find the best-fit probability distribution of annual maximum rainfall based on a twenty-four-hour sample in the northern regions of Pakistan using four probability distributions: normal, log-normal, log-Pearson type-III and Gumbel max. Based on the scores of goodness of fit tests, the normal distribution was found to be the best-fit probability distribution at the Mardan rainfall gauging station. The log-Pearson type-III distribution was found to be the best-fit probability distribution at the rest of the rainfall gauging stations. The maximum values of expected rainfall were calculated using the best-fit probability distributions and can be used by design engineers in future research.

scholarly journals Capped mRNA Degradation Intermediates Accumulate in the Yeast spb8-2 Mutant

1998 ◽  
Vol 18 (9) ◽  
pp. 5062-5072 ◽  
Author(s):  
Ronald Boeck ◽  
Bruno Lapeyre ◽  
Christine E. Brown ◽  
Alan B. Sachs
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Family Member ◽  
Gene Deletion ◽  
Binding Protein ◽  
Mrna Degradation ◽  
Protein Family ◽  
Suppressor Mutation ◽  
Mrna Decapping ◽  
Mrna Species ◽  
Degradation Intermediates

ABSTRACT mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8(YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that thespb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3′ end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3′-5′ mRNA degradation intermediates in yeast.

scholarly journals Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome

2016 ◽  
Author(s):  
Zheng Zhao ◽  
Lei Xie ◽  
Philip E. Bourne
Keyword(s):  
Molecular Dynamics ◽  
Binding Site ◽  
Protein Kinases ◽  
Drug Targets ◽  
Kinase Inhibitors ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Allosteric Inhibitors ◽  
Type Iii ◽  
Human Kinome

AbstractProtein kinases are critical drug targets for treating a large variety of human diseases. Type-I and type-II kinase inhibitors frequently exhibit off-target toxicity or lead to mutation acquired resistance. Two highly specific allosteric type-III MEK-targeted drugs, Trametinib and Cobimetinib, offer a new approach. Thus, understanding the binding mechanism of existing type-III kinase inhibitors will provide insights for designing new type-III kinase inhibitors. In this work we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors. We propose that the helix-folding activation loop is a hallmark allosteric binding site for type-III inhibitors. Subsequently we screened and predicted allosteric binding sites across the human kinome, suggesting other kinases as potential targets suitable for type-III inhibitors. Our findings will provide new insights into the design of potent and selective kinases inhibitors.Author SummaryHuman protein kinases represent a large protein family relevant to many diseases, especially cancers, and have become important drug targets. However, developing the desired selective kinase-targeted inhibitors remain challenging. Kinase allosteric inhibitors provide that opportunity, but, to date, few have been designed other than MEK inhibitors. To more efficiently develop kinase allosteric inhibitors, we systematically studied the binding mode of the MEK type-III allosteric kinase inhibitors using structural system pharmacology and molecular dynamics approaches. New insights into the binding mode and mechanism of type-III inhibitors were revealed that may facilitate the design of new prospective type-III kinase inhibitors.

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