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Purification and Properties of Lactate Racemase from Lactobacillus Sake
The Journal of Biochemistry, Vol . 64, No. I, 1968 Purification and Properties of Lactate Racemase from Lactobacillus sake By TETSUG HIYAMA, SAKUzo FUKUI and KAKUO KITAHARA* (From the Institute of Applied Microbiology,University of Tokyo, Bunkyo-ku, Tokyo) (Received for publication, February 12, 1968) A lactate racemase [EC 5.1.2.1] was isolated and purified about 190 fold in specific activity from the sonic extract of Lactobacillus sake. The purified preparation was almost homogeneous by ultracentrifugal and electrophoretical analyses. Characteristic properties of the enzyme were as follows : (a) absorption spectrum showed a single peak at 274 my, (b) molecular weight was 25,000, (c) the enzyme did not require any additional cofactors and showed no activity of lactate dehydrogenase, (d) K, values were 1.7 •~ 10-2 M and 8.0 •~ 10-2 M for D and L-lactate, respectively, (e) optimal pH was 5.8-6.2, (f) an equilibrium point was at a molar ratio of 1/1 (L-isomer/D-isomer), (g) the enzyme activity was inhibited by atebrin, adenosine monosulfate, oxamate and some of Fe chelating agents, (h) pyruvate and acrylate were not incorporated into lactate during the reaction, and (i) exchange reaction of hydrogen between lactate and water did not occur during the reaction. Since the first observation on the enzy the addition of both NAD and pyridoxamine matic racemization of optical active lactate phosphate. In this paper we deal with the by lactic acid bacteria had been reported by purification and properties of the lactate KATAGIRI and KITAHARA in 1936 (1), racemases racemizing enzyme from the cells of L. -
Dr. Martin St. Maurice's Publications
Dr. Martin St. Maurice’s Publications 2013 Lin, Y., and St. Maurice, M. 2013. The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family. Biochemistry. 52: 690-700. 2012 Waldrop, G.L., Holden, H.M., and St. Maurice, M. 2012. The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms. Protein Science 21(11):1597-1619. Adina-Zada, A., Sereeruk, C., Jitrapakdee, S., Zeczycki, T.N., St. Maurice, M., Cleland, W.W., Wallace, J.C., and Attwood, P.V. 2012. Roles of Arg427 and Arg472 in the binding and allosteric effects of acetyl CoA in pyruvate carboxylase. Biochemistry 51(41): 1597-1619. 2011 Adina-Zada, A., Hazra, R., Sereeruk, C., Jitrapakdee, S., Zeczycki, T.N., St. Maurice, M., Cleland, W.W., Wallace, J.C., and Attwood, P.V. 2011. Probing the allosteric activation of pyruvate carboxylase using 2′,3′-O-(2,4,6-trinitrophenyl) adenosine 5′-triphosphate as a fluorescent mimic of the allosteric activator acetyl CoA. Arch. Biochem. Biophys. 117-126. Zeczycki, T.N., Menefee, A.L., Jitrapakdee, S., Wallace, J.C., Attwood, P.V., St. Maurice, M. and Cleland, W.W. 2011. Activation and inhibition of pyruvate carboxylase from Rhizobium etli. Biochemistry. 9694-9707. Lietzan, A.D., Menefee, A.L., Zeczycki, T.N., Kumar, S., Attwood, P.V., Wallace, J.C., Cleland, W.W. and St. Maurice, M. 2011. Interaction between the biotin carrier domain and the biotin carboxylase domain in the structure of Rhizobium etli pyruvate carboxylase. Biochemistry. 9708-9723. Zeczycki, T.N., Menefee, A.L., Adina-Zada, A., Surinya, K.H., Wallace, J.C., Attwood, P.V., St. -
Articles Catalytic Cycling in Β-Phosphoglucomutase: a Kinetic
9404 Biochemistry 2005, 44, 9404-9416 Articles Catalytic Cycling in â-Phosphoglucomutase: A Kinetic and Structural Analysis†,‡ Guofeng Zhang, Jianying Dai, Liangbing Wang, and Debra Dunaway-Mariano* Department of Chemistry, UniVersity of New Mexico, Albuquerque, New Mexico 87131-0001 Lee W. Tremblay and Karen N. Allen* Department of Physiology and Biophysics, Boston UniVersity School of Medicine, Boston, Massachusetts 02118-2394 ReceiVed March 26, 2005; ReVised Manuscript ReceiVed May 18, 2005 ABSTRACT: Lactococcus lactis â-phosphoglucomutase (â-PGM) catalyzes the interconversion of â-D-glucose 1-phosphate (â-G1P) and â-D-glucose 6-phosphate (G6P), forming â-D-glucose 1,6-(bis)phosphate (â- G16P) as an intermediate. â-PGM conserves the core domain catalytic scaffold of the phosphatase branch of the HAD (haloalkanoic acid dehalogenase) enzyme superfamily, yet it has evolved to function as a mutase rather than as a phosphatase. This work was carried out to identify the structural basis underlying this diversification of function. In this paper, we examine â-PGM activation by the Mg2+ cofactor, â-PGM activation by Asp8 phosphorylation, and the role of cap domain closure in substrate discrimination. First, the 1.90 Å resolution X-ray crystal structure of the Mg2+-â-PGM complex is examined in the context of + + previously reported structures of the Mg2 -R-D-galactose-1-phosphate-â-PGM, Mg2 -phospho-â-PGM, and Mg2+-â-glucose-6-phosphate-1-phosphorane-â-PGM complexes to identify conformational changes that occur during catalytic turnover. The essential role of Asp8 in nucleophilic catalysis was confirmed by demonstrating that the D8A and D8E mutants are devoid of catalytic activity. -
Transcriptomic Characterization of Bradyrhizobium Diazoefficiens
International Journal of Molecular Sciences Article Transcriptomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules Sooyoung Franck 1, Kent N. Strodtman 1 , Jing Qiu 2 and David W. Emerich 1,* 1 Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; [email protected] (S.F.); [email protected] (K.N.S.) 2 Applied Economics and Statistics, University of Delaware, Newark, DE 19716, USA; [email protected] * Correspondence: [email protected]; Tel: +1-573-882-4252 Received: 8 October 2018; Accepted: 28 November 2018; Published: 7 December 2018 Abstract: The transcriptional activity of Bradyrhizobium diazoefficens isolated from soybean nodules was monitored over the period from symbiosis to late plant nodule senescence. The bacteria retained a near constant level of RNA throughout this period, and the variation in genes demonstrating increased, decreased, and/or patterned transcriptional activity indicates that the bacteria are responding to the changing environment within the nodule as the plant cells progress from an organized cellular structure to an unorganized state of internal decay. The transcriptional variation and persistence of the bacteria suggest that the bacteria are adapting to their environment and acting similar to hemibiotrophs, which survive both as saprophytes on live plant tissues and then as necrophytes on decaying plant tissues. The host plant restrictions of symbiosis make B. diazoefficiens a highly specialized, restricted hemibiotroph. Keywords: bradyrhizobium diazoefficiens; soybean; Glycine max; nitrogen fixation; senescence; transcriptomics; hemibiotroph 1. Introduction Soybean nodules are symbiotic organs that are formed on roots by the complex interaction between soybean plants and rhizobia, nitrogen-fixing bacteria, under nitrogen-limiting conditions. -
(12) United States Patent (10) Patent No.: US 8,530,724 B2 Whitelaw Et Al
US008530724B2 (12) United States Patent (10) Patent No.: US 8,530,724 B2 Whitelaw et al. (45) Date of Patent: Sep. 10, 2013 (54) ALTERING THE FATTY ACID COMPOSITION 2011/0054198 A1 3/2011 Singh et al. OF RICE 2011/O190521 A1 8/2011 Damcevski et al. 2011/02O1065 A1 8/2011 Singh et al. 2011/02233.11 A1 9, 2011 Liu et al. (75) Inventors: Ella Whitelaw, Albury (AU); Sadequr 2011/0229623 A1 9, 2011 Liu et al. Rahman, Nicholls (AU); Zhongyi Li, 2012/0041218 A1 2/2012 Singh et al. Kaleen (AU); Qing Liu, Girralang (AU); Surinder Pal Singh, Downer (AU): FOREIGN PATENT DOCUMENTS WO WO99,049050 9, 1999 Robert Charles de Feyter, Monash WO WOO3,080802 10, 2003 (AU) WO WO 2003/080802 A2 10/2003 WO WO 2004/001001 12/2003 (73) Assignee: Commonwealth Scientific and WO WO 2004/001001 A2 12/2003 Industrial Research Organisation, WO WO 2008/O25068 6, 2008 Campbell (AU) WO WO 2009/12958 10/2009 WO WO 2010/009:500 1, 2010 (*) Notice: Subject to any disclaimer, the term of this WO WO 2010/057246 5, 2010 patent is extended or adjusted under 35 OTHER PUBLICATIONS U.S.C. 154(b) by 772 days. Supplementary European Search Report issued Feb. 23, 2010 in connection with corresponding European Patent Application No. (21) Appl. No.: 12/309.276 0776.37759. Taira et al. (1989) “Fatty Acid Composition of Indica-Types and (22) PCT Filed: Jul. 13, 2007 Japonica-Types of Rice Bran and Milled Rice' Journal of the Ameri can Oil Chemists’ Society; vol. -
Fulltext01.Pdf
http://www.diva-portal.org This is the published version of a paper published in Cellular and Molecular Life Sciences (CMLS). Citation for the original published paper (version of record): Cava, F., Lam, H., de Pedro, M., Waldor, M. (2011) Emerging knowledge of regulatory roles of D-amino acids in bacteria. Cellular and Molecular Life Sciences (CMLS), 68(5): 817-831 http://dx.doi.org/10.1007/s00018-010-0571-8 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-81861 Cell. Mol. Life Sci. (2011) 68:817–831 DOI 10.1007/s00018-010-0571-8 Cellular and Molecular Life Sciences REVIEW Emerging knowledge of regulatory roles of D-amino acids in bacteria Felipe Cava • Hubert Lam • Miguel A. de Pedro • Matthew K. Waldor Received: 13 July 2010 / Revised: 24 September 2010 / Accepted: 14 October 2010 / Published online: 14 December 2010 Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract The D-enantiomers of amino acids have been Keywords D-amino acid Á Racemase Á Stationary phase Á thought to have relatively minor functions in biological Peptidoglycan Á Biofilm Á Regulation processes. While L-amino acids clearly predominate in nat- ure, D-amino acids are sometimes found in proteins that are Abbreviations not synthesized by ribosomes, and D-Ala and D-Glu are NRP Nonribosomal peptide routinely found in the peptidoglycan cell wall of bacteria. PG Peptidoglycan Here, we review recent findings showing that D-amino acids GlcNAc N-acetyl glucosamine have previously unappreciated regulatory roles in the bac- MurNAc N-acetylmuramic acid terial kingdom. -
Colletotrichum Graminicola</Em>
University of Kentucky UKnowledge Plant Pathology Faculty Publications Plant Pathology 3-8-2016 A Colletotrichum graminicola Mutant Deficient in the Establishment of Biotrophy Reveals Early Transcriptional Events in the Maize Anthracnose Disease Interaction Maria F. Torres University of Kentucky, [email protected] Noushin Ghaffari Texas A&M University Ester A. S. Buiate University of Kentucky, [email protected] Neil Moore University of Kentucky, [email protected] Scott chS wartz Texas A&M University FSeoe nelloxtw pa thige fors aaddndition addal aitutionhorsal works at: https://uknowledge.uky.edu/plantpath_facpub Part of the Bioinformatics Commons, Genomics Commons, Integrative Biology Commons, and Right click to open a feedback form in a new tab to let us know how this document benefits oy u. the Plant Pathology Commons Repository Citation Torres, Maria F.; Ghaffari, Noushin; Buiate, Ester A. S.; Moore, Neil; Schwartz, Scott; Johnson, Charles D.; and Vaillancourt, Lisa J., "A Colletotrichum graminicola Mutant Deficient in the Establishment of Biotrophy Reveals Early Transcriptional Events in the Maize Anthracnose Disease Interaction" (2016). Plant Pathology Faculty Publications. 53. https://uknowledge.uky.edu/plantpath_facpub/53 This Article is brought to you for free and open access by the Plant Pathology at UKnowledge. It has been accepted for inclusion in Plant Pathology Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Authors Maria F. Torres, Noushin Ghaffari, Ester A. S. Buiate, Neil Moore, Scott chS wartz, Charles D. Johnson, and Lisa J. Vaillancourt A Colletotrichum graminicola Mutant Deficient in the Establishment of Biotrophy Reveals Early Transcriptional Events in the Maize Anthracnose Disease Interaction Notes/Citation Information Published in BMC Genomics, v.17, 202, p. -
Nickel-Pincer Cofactor Biosynthesis Involves Larb-Catalyzed Pyridinium
Nickel-pincer cofactor biosynthesis involves LarB- catalyzed pyridinium carboxylation and LarE- dependent sacrificial sulfur insertion Benoît Desguina,b, Patrice Soumillionb, Pascal Holsb, and Robert P. Hausingera,1 aDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824; and bInstitute of Life Sciences, Université catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium Edited by Tadhg P. Begley, Texas A&M University, College Station, TX, and accepted by the Editorial Board March 28, 2016 (received for review January 11, 2016) The lactate racemase enzyme (LarA) of Lactobacillus plantarum proteins) when incubated with ATP (1 mM), MgCl2 (12 mM), harbors a (SCS)Ni(II) pincer complex derived from nicotinic acid. and the other purified proteins, and the activity was stimulated Synthesis of the enzyme-bound cofactor requires LarB, LarC, and fivefold by inclusion of CoA (10 mM) (SI Appendix,Fig.S1A– LarE, which are widely distributed in microorganisms. The functions D). These results are consistent with the requirement of a small of the accessory proteins are unknown, but the LarB C terminus molecule produced by LarB being needed for development of resembles aminoimidazole ribonucleotide carboxylase/mutase, LarC Lar activity. To uncover the substrate of LarB, we replaced the binds Ni and could act in Ni delivery or storage, and LarE is a putative LarB-containing lysates in the LarA activation mixture with ATP-using enzyme of the pyrophosphatase-loop superfamily. Here, purified LarB and potential substrates. Because nicotinic acid is a precursor of the Lar cofactor (1) and LarB features partial we show that LarB carboxylates the pyridinium ring of nicotinic acid sequence identity with PurE, an aminoimidazole ribonucleotide adenine dinucleotide (NaAD) and cleaves the phosphoanhydride (AIR) mutase/carboxylase (4), we tested the possibility that bond to release AMP. -
Title Non-Stereospecific Transamination Catalyzed by Pyridoxal Phosphate-Dependent Amino Acid Racemases of Broad Substrate Speci
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Non-stereospecific Transamination Catalyzed by Pyridoxal Phosphate-dependent Amino Acid Racemases of Broad Title Substrate Specificity (MOLECULAR BIOFUNCTION- Molecular Microbial Science) Esaki, Nobuyoshi; Yoshimura, Tohru; Soda, Kenji; Lim, Author(s) Young Hee Citation ICR annual report (1999), 5: 46-47 Issue Date 1999-03 URL http://hdl.handle.net/2433/65185 Right Type Article Textversion publisher Kyoto University 46 ICR Annual Report, Vol. 5, 1998 Non-stereospecific Transamination Catalyzed by Pyridoxal Phosphate-dependent Amino Acid Racemases of Broad Substrate Specificity Nobuyoshi Esaki, Tohru Yoshimura, Kenji Soda and Young Hee Lim Pyridoxal 5’-phosphate-dependent amino acid racemases of broad substrate specificity catalyze transamination as a side-reaction. We studied the stereospecificities for hydrogen abstraction from C-4’ of the bound pyridoxamine 5’-phosphate during transamination from pyridoxamine 5’-phosphate to pyruvate catalyzed by three amino acid racemases of broad substrate specificity. When the enzymes were incubated with (4’S)- or (4’R)-[4’-3H]- pyridoxamine 5’-phosphate in the presence of pyruvate, tritium was released into the solvent from both pyridoxamine 5’-phosphates. Thus, these enzymes abstract a hydrogen non-stereospecifically from C-4’ of the coenzyme in contrast to the other pyridoxal 5’-phosphate-dependent enzymes so far studied which catalyze the stereospecific hydrogen removal. Amino acid racemase of broad substrate specificity from Pseudomonas putida produced D- and L-glutamate from α-ketoglutarate through the transamination with L-ornithine. Because glutamate does not serve as a substrate for racemization, the enzyme catalyzed the non-stereospecific overall transamination between L-ornithine and α-ketoglutarate. -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Expression of a Phosphoglucomutase Gene in Rainbow Trout (Polymorphism/Developmental Rate/Glycolysis/Salmo Gairdneri) FRED W
Proc. Natt Acad. Sci. USA Vol. 80, pp. 1397-1400, March 1983 Genetics Adaptive significance of differences in the tissue-specific expression of a phosphoglucomutase gene in rainbow trout (polymorphism/developmental rate/glycolysis/Salmo gairdneri) FRED W. ALLENDORF, KATHY L. KNUDSEN, AND ROBB F. LEARY Department of Zoology,, University of Montana, Missoula, Montana 59812 Communicated by G. Ledyard Stebbins, November 17, 1982 ABSTRACT We have investigated the phenotypic effects of fold increase in the expression of a phosphoglucomutase (PGM; a mutant allele that results in the expression of a phosphogluco- a-D-glucose-1,6-bisphosphate:a-D-glucose-l-phosphate phos- mutase locus (Pgml) in the liver of rainbow trout. Embryos with photransferase EC 2.7.5. 1) locus, Pgml, in liver tissue (14, 15). liver Pgml expression hatch earlier than embryos without liver The results of inheritance experiments are consistent with a sin- Pgml expression. These differences apparently result from in- gle regulatory gene, Pgml-t, with additive inheritance being re- creased flux through glycolysis in embryos with liver PGM1 ac- sponsible for the differences in the expression of this locus (15). tivity while they are dependent on the yolk for energy. Fish with We report here that the presence or absence of PGM1 in the liver PGM1 activity are also more developmentally buffered, as liver rise to indicated by less fluctuating asymmetry of five bilateral meristic gives important differences in several phenotypic traits. The more rapidly developing individuals begin exogenous characteristics of adaptive significance (developmental rate, de- feeding earlier and achieve a size advantage that is maintained velopmental stability, body size, and age at first maturity). -
Supplementary Table 9. Functional Annotation Clustering Results for the Union (GS3) of the Top Genes from the SNP-Level and Gene-Based Analyses (See ST4)
Supplementary Table 9. Functional Annotation Clustering Results for the union (GS3) of the top genes from the SNP-level and Gene-based analyses (see ST4) Column Header Key Annotation Cluster Name of cluster, sorted by descending Enrichment score Enrichment Score EASE enrichment score for functional annotation cluster Category Pathway Database Term Pathway name/Identifier Count Number of genes in the submitted list in the specified term % Percentage of identified genes in the submitted list associated with the specified term PValue Significance level associated with the EASE enrichment score for the term Genes List of genes present in the term List Total Number of genes from the submitted list present in the category Pop Hits Number of genes involved in the specified term (category-specific) Pop Total Number of genes in the human genome background (category-specific) Fold Enrichment Ratio of the proportion of count to list total and population hits to population total Bonferroni Bonferroni adjustment of p-value Benjamini Benjamini adjustment of p-value FDR False Discovery Rate of p-value (percent form) Annotation Cluster 1 Enrichment Score: 3.8978262119731335 Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR GOTERM_CC_DIRECT GO:0005886~plasma membrane 383 24.33290978 5.74E-05 SLC9A9, XRCC5, HRAS, CHMP3, ATP1B2, EFNA1, OSMR, SLC9A3, EFNA3, UTRN, SYT6, ZNRF2, APP, AT1425 4121 18224 1.18857065 0.038655922 0.038655922 0.086284383 UP_KEYWORDS Membrane 626 39.77128335 1.53E-04 SLC9A9, HRAS,