Genomes and Genes
Summary: Enzymes of the isomerase class that catalyze the transfer of acyl-, phospho-, amino- or other groups from one position within a molecule to another. EC 5.4.
- Sorensen J, Stetefeld J. Kinemage of action - proposed reaction mechanism of glutamate-1-semialdehyde aminomutase at an atomic level. Biochem Biophys Res Commun. 2011;413:572-6 pubmed publisher..In a MD simulation approach, using snapshots provided by X-ray crystallography and protein crystal absorption spectrometry data, the individual catalytic steps in this unique intramolecular transamination have been elucidated. ..
- Lamarre C, Beau R, Balloy V, Fontaine T, Wong Sak Hoi J, Guadagnini S, et al. Galactofuranose attenuates cellular adhesion of Aspergillus fumigatus. Cell Microbiol. 2009;11:1612-23 pubmed publisher..Removal of the mannan layer from the mutant surface by a mannosidase treatment abolishes mycelial adhesion to surfaces. ..
- Görl J, Timm M, Seibel J. Mechanism-oriented redesign of an isomaltulose synthase to an isomelezitose synthase by site-directed mutagenesis. Chembiochem. 2012;13:149-56 pubmed publisher..The variants F297A, F297P, R333K, F321A_F319A and E428D catalyze the formation of isomelezitose in up to 70 % yield. ..
- Kiss T, Fayet Lebaron E, Jady B. Box H/ACA small ribonucleoproteins. Mol Cell. 2010;37:597-606 pubmed publisher..Recently, great progress has been made toward understanding of the biogenesis, intracellular trafficking, structure, and function of H/ACA RNPs...
- Strawn M, Marr S, Inoue K, Inada N, Zubieta C, Wildermuth M. Arabidopsis isochorismate synthase functional in pathogen-induced salicylate biosynthesis exhibits properties consistent with a role in diverse stress responses. J Biol Chem. 2007;282:5919-33 pubmed
- El Ganiny A, Sanders D, Kaminskyj S. Aspergillus nidulans UDP-galactopyranose mutase, encoded by ugmA plays key roles in colony growth, hyphal morphogenesis, and conidiation. Fungal Genet Biol. 2008;45:1533-42 pubmed publisher..These effects were partially remediated by growth on high osmolarity medium, or on medium containing 10 microg/mL Calcofluor, consistent with Galf being important in cell wall structure and/or function. ..
- Xu J, Xu Y, Zhong J. Production of individual ganoderic acids and expression of biosynthetic genes in liquid static and shaking cultures of Ganoderma lucidum. Appl Microbiol Biotechnol. 2010;85:941-8 pubmed publisher..The work is helpful to the production of individual GAs and provided an insight into why the liquid static culture was superior to the shaking culture in view of biosynthetic gene expression...
- Chad J, Sarathy K, Gruber T, Addala E, Kiessling L, Sanders D. Site-directed mutagenesis of UDP-galactopyranose mutase reveals a critical role for the active-site, conserved arginine residues. Biochemistry. 2007;46:6723-32 pubmed..These results provide strong evidence that the mobile loop, noted in all the reported crystal structures, must move in order for UGM to bind its UDP-galactose substrate. ..
- Oppenheimer M, Poulin M, Lowary T, Helm R, Sobrado P. Characterization of recombinant UDP-galactopyranose mutase from Aspergillus fumigatus. Arch Biochem Biophys. 2010;502:31-8 pubmed publisher..Functional and structural differences between the bacterial and eukaryotic UGMs are discussed. ..
- Carlson E, May J, Kiessling L. Chemical probes of UDP-galactopyranose mutase. Chem Biol. 2006;13:825-37 pubmed..Our studies offer a blueprint for identifying inhibitors of the growing family of UGM homologs and provide insight into UGM inhibition. ..
- Shang C, Shi L, Ren A, Qin L, Zhao M. Molecular cloning, characterization, and differential expression of a lanosterol synthase gene from Ganoderma lucidum. Biosci Biotechnol Biochem. 2010;74:974-8 pubmed..lucidum during development. Up-regulation of expression of the Gl-LS gene by methyl jasmonate (MeJA) in the mycelia was also demonstrated by real-time RT-PCR. Up-regulation of the Gl-LS promoter activity by MeJA was also investigated...
- Eppe G, Peltier P, Daniellou R, Nugier Chauvin C, Ferrieres V, Vincent S. Probing UDP-galactopyranose mutase binding pocket: a dramatic effect on substitution of the 6-position of UDP-galactofuranose. Bioorg Med Chem Lett. 2009;19:814-6 pubmed publisher..This result demonstrated that key interactions occur at the vicinity of the 6-position of UDP-galactose in the Michaelis complex. ..
- Partha S, Van Straaten K, Sanders D. Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP. J Mol Biol. 2009;394:864-77 pubmed publisher..These structures provide valuable insights into substrate recognition and a basis for understanding the mechanism. These complex structures may serve as a platform for structure-guided design of inhibitors of UGM. ..
- Hur S, Stroud R, Finer Moore J. Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective. J Biol Chem. 2006;281:38969-73 pubmed
- Li S, Duan J, Li D, Yang B, Dong M, Ye K. Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase. Genes Dev. 2011;25:2409-21 pubmed publisher..Our results reveal significant novel features of eukaryotic H/ACA RNPs. ..
- Duan J, Li L, Lu J, Wang W, Ye K. Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. Mol Cell. 2009;34:427-39 pubmed publisher..Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5. ..
- Oppenheimer M, Valenciano A, Sobrado P. Isolation and characterization of functional Leishmania major virulence factor UDP-galactopyranose mutase. Biochem Biophys Res Commun. 2011;407:552-6 pubmed publisher..A k(cat) value of 5 ± 0.2s(-1) and a K(M) value of 87 ± 11 ?M were determined with UDP-galactofuranose as the substrate. Different from the dimeric bacterial and tetrameric fungal UGMs, this parasitic enzyme functions as a monomer. ..
- You B, Lee H, Chung K, Lee M, Huang M, Tien N, et al. Enhanced production of ganoderic acids and cytotoxicity of Ganoderma lucidum using solid-medium culture. Biosci Biotechnol Biochem. 2012;76:1529-34 pubmed..This indicates that it may be possible to enhance the production of GAs by implementing mycelium culture on solid medium. ..
- Oppenheimer M, Valenciano A, Kizjakina K, Qi J, Sobrado P. Chemical mechanism of UDP-galactopyranose mutase from Trypanosoma cruzi: a potential drug target against Chagas' disease. PLoS ONE. 2012;7:e32918 pubmed publisher..In support of this role, a flavin-galactose adduct was isolated and characterized. A detailed kinetic and chemical mechanism for the unique non-redox reaction of UGM is presented. ..
- Gurha P, Joardar A, Chaurasia P, Gupta R. Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation. RNA Biol. 2007;4:101-9 pubmed..Conserved A58 in tRNA normally forms a tertiary reverse Hoogstein base pair with an equally conserved U54. This base pair is recognized by TruB. Apparently aCbf5 does not require this base pair to recognize U55 for conversion to Psi55. ..
- Dhatwalia R, Singh H, Oppenheimer M, Karr D, Nix J, Sobrado P, et al. Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus. J Biol Chem. 2012;287:9041-51 pubmed publisher..The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design...
- Gruber T, Westler W, Kiessling L, Forest K. X-ray crystallography reveals a reduced substrate complex of UDP-galactopyranose mutase poised for covalent catalysis by flavin. Biochemistry. 2009;48:9171-3 pubmed publisher..In the latter, C1 of the substrate is 3.6 A from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin. ..
- Richards M, Lowary T. Chemistry and biology of galactofuranose-containing polysaccharides. Chembiochem. 2009;10:1920-38 pubmed publisher..Recent advances both in the understanding of the mechanism of UGM and in the synthesis of galactofuranose and its derivatives are highlighted in this review. ..
- McDonald M, Miracco E, Chen J, Xie Y, Mueller E. The handling of the mechanistic probe 5-fluorouridine by the pseudouridine synthase TruA and its consistency with the handling of the same probe by the pseudouridine synthases TruB and RluA. Biochemistry. 2011;50:426-36 pubmed..The discovery that digestion products are dinucleotides accounts for the previously puzzling differences in the isolated products obtained following the action of the pseudouridine synthases TruB and RluA on F(5)U in RNA. ..
- Blaby I, Majumder M, Chatterjee K, Jana S, Grosjean H, De Crecy Lagard V, et al. Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. RNA. 2011;17:1367-80 pubmed publisher..coli, respectively. Finally, we demonstrate that HVO_1852, the TruA/Pus3 homolog, is responsible for the pseudouridylation of position 39 in H. volcanii tRNAs and that the corresponding gene is not essential...
- Wang L, Tsuda K, Sato M, Cohen J, Katagiri F, Glazebrook J. Arabidopsis CaM binding protein CBP60g contributes to MAMP-induced SA accumulation and is involved in disease resistance against Pseudomonas syringae. PLoS Pathog. 2009;5:e1000301 pubmed publisher..These studies show that CBP60g constitutes a Ca(2+) link between MAMP recognition and SA accumulation that is important for resistance to P. syringae. ..
- Tsuda K, Sato M, Glazebrook J, Cohen J, Katagiri F. Interplay between MAMP-triggered and SA-mediated defense responses. Plant J. 2008;53:763-75 pubmed..These results indicate that the SA increase triggered by MAMPs is a major component of the MAMP-triggered signaling mechanism, explaining the overlapping spectra of MAMP-triggered and SA-mediated responses. ..
- Wright J, Keffer Wilkes L, Dobing S, Kothe U. Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis. RNA. 2011;17:2074-84 pubmed publisher..7 and 0.35 sec(-1), respectively. Hence, uniformly slow catalysis might be a general feature of pseudouridine synthases that share a conserved catalytic domain and supposedly use the same catalytic mechanism. ..
- Garcion C, Lohmann A, Lamodière E, Catinot J, Buchala A, Doermann P, et al. Characterization and biological function of the ISOCHORISMATE SYNTHASE2 gene of Arabidopsis. Plant Physiol. 2008;147:1279-87 pubmed publisher..Furthermore, detection of SA in the double ics1 ics2 double mutant that is completely devoid of phylloquinone provides genetic evidence of the existence of an ICS-independent SA biosynthetic pathway in Arabidopsis. ..
- Dykhuizen E, May J, Tongpenyai A, Kiessling L. Inhibitors of UDP-galactopyranose mutase thwart mycobacterial growth. J Am Chem Soc. 2008;130:6706-7 pubmed publisher..From a focused library of synthetic aminothiazoles, several compounds that block the UGM from Klebsiella pneumoniae or Mycobacterium tuberculosis were identified. These inhibitors block the growth of M. smegmatis. ..
- Liang B, Zhou J, Kahen E, Terns R, Terns M, Li H. Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. Nat Struct Mol Biol. 2009;16:740-6 pubmed publisher..Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity. ..
- Rohwerder T, Breuer U, Benndorf D, Lechner U, Müller R. The alkyl tert-butyl ether intermediate 2-hydroxyisobutyrate is degraded via a novel cobalamin-dependent mutase pathway. Appl Environ Microbiol. 2006;72:4128-35 pubmed..The physiological and evolutionary aspects of this novel pathway involved in MTBE and ETBE metabolism are discussed...
- Hunter L, Westwood J, Heath G, Macaulay K, Smith A, MacFarlane S, et al. Regulation of RNA-dependent RNA polymerase 1 and isochorismate synthase gene expression in Arabidopsis. PLoS ONE. 2013;8:e66530 pubmed publisher..RDR1 is regulated by a much broader range of phytohormones than previously thought, indicating that it plays roles beyond those already suggested in virus resistance and plant-insect interactions. SA positively regulates ICS1. ..
- Behshad E, Ruzicka F, Mansoorabadi S, Chen D, Reed G, Frey P. Enantiomeric free radicals and enzymatic control of stereochemistry in a radical mechanism: the case of lysine 2,3-aminomutases. Biochemistry. 2006;45:12639-46 pubmed..coli LAM is determined by the conformation of the lysine side chain in the active site. Stereochemical models for the actions of LAM from C. subterminale and E. coli are presented. ..
- Collin V, Eymery F, Genty B, Rey P, Havaux M. Vitamin E is essential for the tolerance of Arabidopsis thaliana to metal-induced oxidative stress. Plant Cell Environ. 2008;31:244-57 pubmed..Taken together, these results demonstrate that vitamin E plays a crucial role in the tolerance of Arabidopsis to oxidative stress induced by heavy metals such as Cu and Cd. ..
- Yuan Y, Chung J, Fu X, Johnson V, Ranjan P, Booth S, et al. Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis. Proc Natl Acad Sci U S A. 2009;106:22020-5 pubmed publisher..AtICS1 represents a divergent isoform for inducible SA synthesis during defense. Populus ICS primarily functions in phylloquinone biosynthesis, a process that can be sustained at low ICS transcript levels. ..
- Damveld R, Franken A, Arentshorst M, Punt P, Klis F, van den Hondel C, et al. A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis. Genetics. 2008;178:873-81 pubmed publisher..Our results indicate that galactofuranose formation is important for fungal cell wall biosynthesis and represents an attractive target for the development of antifungals. ..
- Miracco E, Mueller E. The products of 5-fluorouridine by the action of the pseudouridine synthase TruB disfavor one mechanism and suggest another. J Am Chem Soc. 2011;133:11826-9 pubmed publisher..The arabino product strongly disfavors a mechanism involving a Michael addition to the pyrimidine ring. ..
- Wang L, Mitra R, Hasselmann K, Sato M, Lenarz Wyatt L, Cohen J, et al. The genetic network controlling the Arabidopsis transcriptional response to Pseudomonas syringae pv. maculicola: roles of major regulators and the phytotoxin coronatine. Mol Plant Microbe Interact. 2008;21:1408-20 pubmed publisher
- Gruber T, Borrok M, Westler W, Forest K, Kiessling L. Ligand binding and substrate discrimination by UDP-galactopyranose mutase. J Mol Biol. 2009;391:327-40 pubmed publisher..To understand the consequences of these differences, we derived a model for the productive UGM-substrate complex that highlights interactions that can contribute to catalysis and substrate discrimination. ..
- Konishi T, Miyazaki Y, Yamakawa S, Iwai H, Satoh S, Ishii T. Purification and biochemical characterization of recombinant rice UDP-arabinopyranose mutase generated in insect cells. Biosci Biotechnol Biochem. 2010;74:191-4 pubmed..Recombinant UAMs might serve as useful tools for the biosynthesis of UDP-Araf and might be better than chemical synthesis. ..
- Erb T, Retey J, Fuchs G, Alber B. Ethylmalonyl-CoA mutase from Rhodobacter sphaeroides defines a new subclade of coenzyme B12-dependent acyl-CoA mutases. J Biol Chem. 2008;283:32283-93 pubmed publisher..In combination with molecular modeling, two signature sequences were identified that presumably contribute to the substrate specificity of these enzymes. ..
- Oliaro Bosso S, Taramino S, Viola F, Tagliapietra S, Ermondi G, Cravotto G, et al. Umbelliferone aminoalkyl derivatives as inhibitors of human oxidosqualene-lanosterol cyclase. J Enzyme Inhib Med Chem. 2009;24:589-98 pubmed..Molecular docking analyses, carried out to clarify details of inhibitors/enzyme interactions, proved useful to explain the observed differences in inhibitory activities. ..
- Kleczka B, Lamerz A, van Zandbergen G, Wenzel A, Gerardy Schahn R, Wiese M, et al. Targeted gene deletion of Leishmania major UDP-galactopyranose mutase leads to attenuated virulence. J Biol Chem. 2007;282:10498-505 pubmed..These structural changes do not influence the in vitro growth of the parasite but lead to an attenuation of virulence comparable with that observed with a mutant exclusively deficient in LPG. ..
- Borrelli S, Zandberg W, Mohan S, Ko M, Martinez Gutierrez F, Partha S, et al. Antimycobacterial activity of UDP-galactopyranose mutase inhibitors. Int J Antimicrob Agents. 2010;36:364-8 pubmed publisher..bovis BCG or M. tuberculosis as well as demonstrating higher cellular toxicity. These data validate the choice of UGM as a target for active antimycobacterial therapy and confirm the pyrazole compound as a viable lead candidate. ..
- Stetefeld J, Jenny M, Burkhard P. Intersubunit signaling in glutamate-1-semialdehyde-aminomutase. Proc Natl Acad Sci U S A. 2006;103:13688-93 pubmed..Together, they form a molecular switch in which the cofactor acts as a central signal transmitter linking the subunit interface with the gating loop. ..
- Xiang T, Shibuya M, Katsube Y, Tsutsumi T, Otsuka M, Zhang H, et al. A new triterpene synthase from Arabidopsis thaliana produces a tricyclic triterpene with two hydroxyl groups. Org Lett. 2006;8:2835-8 pubmed..This is the first example of a triterpene synthase that yields a tricyclic triterpene with two hydroxyl groups. ..
- Shibuya M, Katsube Y, Otsuka M, Zhang H, Tansakul P, Xiang T, et al. Identification of a product specific beta-amyrin synthase from Arabidopsis thaliana. Plant Physiol Biochem. 2009;47:26-30 pubmed publisher..cerevisiae strain. LC-MS and NMR analyses of the accumulated product in the host cells showed that the product of At1g78950 is beta-amyrin, indicating that At1g78950 encodes a beta-amyrin synthase (EC 5.4.99.-). ..
- Phillips D, Rasbery J, Bartel B, Matsuda S. Biosynthetic diversity in plant triterpene cyclization. Curr Opin Plant Biol. 2006;9:305-14 pubmed..By contrast, the phylogenetic relationships of cyclases that generate nonsteroidal triterpene alcohols do not consistently reflect their catalytic properties and might indicate recent and rapid catalytic evolution. ..
- Schmalhorst P, Krappmann S, Vervecken W, Rohde M, Muller M, Braus G, et al. Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryot Cell. 2008;7:1268-77 pubmed publisher..fumigatus. Its absence from mammalian cells indeed offers a considerable advantage to achieve therapeutic selectivity. ..
- Muller S, Fourmann J, Loegler C, Charpentier B, Branlant C. Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Psi55-synthase and RNA-guided RNA:Psi-synthase activities. Nucleic Acids Res. 2007;35:5610-24 pubmed..This negative effect can also be compensated by the presence of aNOP10...
- Hoang C, Chen J, Vizthum C, Kandel J, Hamilton C, Mueller E, et al. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol Cell. 2006;24:535-45 pubmed..Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping. ..
- Konishi T, Takeda T, Miyazaki Y, Ohnishi Kameyama M, Hayashi T, O Neill M, et al. A plant mutase that interconverts UDP-arabinofuranose and UDP-arabinopyranose. Glycobiology. 2007;17:345-54 pubmed
- Ichimura K, Casais C, Peck S, Shinozaki K, Shirasu K. MEKK1 is required for MPK4 activation and regulates tissue-specific and temperature-dependent cell death in Arabidopsis. J Biol Chem. 2006;281:36969-76 pubmed
- Zhou J, Liang B, Li H. Functional and structural impact of target uridine substitutions on the H/ACA ribonucleoprotein particle pseudouridine synthase. Biochemistry. 2010;49:6276-81 pubmed publisher..Our results suggest a potential role of these elements and the subunit that contacts them in substrate binding and product release. ..
- Chan C, Huang R. Enzymatic characterization and mutational studies of TruD--the fifth family of pseudouridine synthases. Arch Biochem Biophys. 2009;489:15-9 pubmed publisher..Our studies indicate that a Glu, strictly conserved in only TruD family is likely to be the general base in TruD. We also proposed a possible distinct mechanism of TruD-catalyzed Psi formation compared to the first four families. ..
- Yuan Y, Bleile D, Wen X, Sanders D, Itoh K, Liu H, et al. Investigation of binding of UDP-Galf and UDP-[3-F]Galf to UDP-galactopyranose mutase by STD-NMR spectroscopy, molecular dynamics, and CORCEMA-ST calculations. J Am Chem Soc. 2008;130:3157-68 pubmed publisher..Taken together, these results are used to rationalize the different rates of catalytic turnover of UDP-Galf and UDP-[3-F]Galf and shed light on the mechanism of action of UGM. ..
- Lodeiro S, Xiong Q, Wilson W, Kolesnikova M, Onak C, Matsuda S. An oxidosqualene cyclase makes numerous products by diverse mechanisms: a challenge to prevailing concepts of triterpene biosynthesis. J Am Chem Soc. 2007;129:11213-22 pubmed..Our findings suggest that mechanistic diversity is the default for triterpene biosynthesis and that product accuracy results from exclusion of alternative pathways. ..
- Ravaud S, Robert X, Watzlawick H, Haser R, Mattes R, Aghajari N. Structural determinants of product specificity of sucrose isomerases. FEBS Lett. 2009;583:1964-8 pubmed publisher..The results provide a rationale for the specific design of optimized enzymes. ..
- Abe I. Enzymatic synthesis of cyclic triterpenes. Nat Prod Rep. 2007;24:1311-31 pubmed..126 References are cited. ..
- Sun H, Ruszczycky M, Chang W, Thibodeaux C, Liu H. Nucleophilic participation of reduced flavin coenzyme in mechanism of UDP-galactopyranose mutase. J Biol Chem. 2012;287:4602-8 pubmed publisher..4 ± 0.4. Together, these findings are most consistent with a chemical mechanism for UGM involving an S(N)2-type displacement of UDP from UDP-Galf/p by N5 of FAD(red). ..