Publications

the yiae gene, located at 80.1 minutes on the escherichia coli chromosome, encodes a 2-ketoaldonate reductase.	an open reading frame located in the bisc-cspa intergenic region, or at 80.1 min on the escherichia coli chromosome, encodes a hypothetical 2-hydroxyacid dehydrogenase, which was identified as a result of the e. coli genome sequencing project. we report here that the product of the gene (yiae) is a 2-ketoaldonate reductase (2kr). the gene was cloned and expressed with a c-terminal his tag in e. coli, and the protein was purified by metal-chelate affinity chromatography. the determination of the ...	1998	9811658
distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases.	the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ...	1999	10482517
quantification of hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16s rrna analysis.	the bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rrna analysis. 16s ribosomal dna (rdna) libraries were created from three sludge samples taken on different dates. partial rrna gene sequences were obtained for 46 rdna clones, and nearly complete 16s rrna sequences were obtained for 18 clones. seventeen of these clones were members of the beta subdivision, and their sequences showed high homology t ...	2000	10698787
overproduction of l-lysine from methanol by methylobacillus glycogenes derivatives carrying a plasmid with a mutated dapa gene.	the dapa gene, encoding dihydrodipicolinate synthase (ddps) partially desensitized to inhibition by l-lysine, was cloned from an l-threonine- and l-lysine-coproducing mutant of the obligate methylotroph methylobacillus glycogenes dhl122 by complementation of the nutritional requirement of an escherichia coli dapa mutant. introduction of the dapa gene into dhl122 and al119, which is the parent of dhl122 and an l-threonine producing mutant, elevated the specific activity of ddps 20-fold and l-lysi ...	2001	11425723
duplicate copies of genes encoding methanesulfonate monooxygenase in marinosulfonomonas methylotropha strain tr3 and detection of methanesulfonate utilizers in the environment.	marinosulfonomonas methylotropha strain tr3 is a marine methylotroph that uses methanesulfonic acid (msa) as a sole carbon and energy source. the genes from m. methylotropha strain tr3 encoding methanesulfonate monooxygenase, the enzyme responsible for the initial oxidation of msa to formaldehyde and sulfite, were cloned and sequenced. they were located on two gene clusters on the chromosome of this bacterium. a 5.0-kbp hindiii fragment contained msma, msmb, and msmc, encoding the large and smal ...	2002	11772638
alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of arabidopsis.	plant peroxisomal glyoxylate aminotransferases play central roles within the photorespiratory pathway. genes encoding glyoxylate aminotransferases have been isolated from several animals and microbes, but only recently have plant homologs been identified. three arabidopsis homologs of alanine (ala):glyoxylate aminotransferase 2 (agt2) contain a putative type 1 peroxisomal targeting signal (pts1), but the metabolic significance of these agt2 homologs is unknown. ggt1 and ggt2 are ala aminotransfe ...	2003	12529529
novel archaeal alanine:glyoxylate aminotransferase from thermococcus litoralis.	a novel alanine:glyoxylate aminotransferase was found in a hyperthermophilic archaeon, thermococcus litoralis. the amino acid sequence of the enzyme did not show a similarity to any alanine:glyoxylate aminotransferases reported so far. homologues of the enzyme appear to be present in almost all hyperthermophilic archaea whose whole genomes have been sequenced.	2004	15292154
unique features revealed by the genome sequence of acinetobacter sp. adp1, a versatile and naturally transformation competent bacterium.	acinetobacter sp. strain adp1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized pseudomonas aeruginosa and pseudomonas putida. unlike these bacteria, the acinetobacter adp1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. the circular chromosome of the acinetobacter adp1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence ...	2004	15514110
ctbp contributes quantitatively to knirps repression activity in an nad binding-dependent manner.	transcriptional repressors often employ multiple activities, but the molecular mechanisms and physiological relevance of this functional diversity remain obscure. the drosophila melanogaster knirps repressor uses ctbp corepressor-dependent and -independent pathways. to separately analyze the components of knirps repression activity, we elucidated the specific repression properties of ctbp and of knirps subdomains. like knirps, ctbp represses adjacent transcriptional activators; but unlike knirps ...	2004	15199149
the ctbp2 co-repressor is regulated by nadh-dependent dimerization and possesses a novel n-terminal repression domain.	the c-terminal binding protein 2 (ctbp2) is a 48 kda phosphoprotein reported to function as a co- repressor for a growing list of transcriptional repressors. it was recently demonstrated that ctbp is a dimeric nad+-regulated d-isomer-specific 2-hydroxy acid dehydrogenase. however, the specific substrate(s) of ctbp enzymatic activity and the relationship of this activity to its co-repression function remain unknown. the ability of a human ctbp to bind and serve as a co-repressor of e1a has been s ...	2004	15037661
metabolic engineering of corynebacterium glutamicum for l-serine production.	although l-serine proceeds in just three steps from the glycolytic intermediate 3-phosphoglycerate, and as much as 8% of the carbon assimilated from glucose is directed via l-serine formation, previous attempts to obtain a strain producing l-serine from glucose have not been successful. we functionally identified the genes serc and serb from corynebacterium glutamicum, coding for phosphoserine aminotransferase and phosphoserine phosphatase, respectively. the overexpression of these genes, togeth ...	2005	16269752
glycerate kinase of the hyperthermophilic archaeon thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes.	the presence of the branched entner-doudoroff (ed) pathway in two hyperthermophilic crenarchaea, the anaerobe thermoproteus tenax and the aerobe sulfolobus solfataricus, was suggested. however, so far no enzymatic information of the non-phosphorylative ed branch and especially its key enzyme - glycerate kinase - was available. in the t. tenax genome, a gene homolog with similarity to putative hydroxypyruvate reductase/glycerate dehydrogenase and glycerate kinase was identified.	2007	17764545
the microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures.	the interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. for sediments contaminated with light non-aqueous-phase liquids, anomalous high conductivity values have been observed. vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16s rrna gene libraries. ...	2007	17351087
reduced folate supply as a key to enhanced l-serine production by corynebacterium glutamicum.	the amino acid l-serine is required for pharmaceutical purposes, and the availability of a sugar-based microbial process for its production is desirable. however, a number of intracellular utilization routes prevent overproduction of l-serine, with the essential serine hydroxymethyltransferase (shmt) (glya) probably occupying a key position. we found that constructs of corynebacterium glutamicum strains where chromosomal glya expression is dependent on ptac and laciq are unstable, acquiring muta ...	2007	17142381
reduced folate supply as a key to enhanced l-serine production by corynebacterium glutamicum.	the amino acid l-serine is required for pharmaceutical purposes, and the availability of a sugar-based microbial process for its production is desirable. however, a number of intracellular utilization routes prevent overproduction of l-serine, with the essential serine hydroxymethyltransferase (shmt) (glya) probably occupying a key position. we found that constructs of corynebacterium glutamicum strains where chromosomal glya expression is dependent on ptac and laciq are unstable, acquiring muta ...	2007	17142381
glycerate 2-kinase of thermotoga maritima and genomic reconstruction of related metabolic pathways.	members of a novel glycerate-2-kinase (gk-ii) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the gark (gk-i) family. the recently reported three-dimensional structure of gk-ii from thermotoga maritima (tm1585; pdb code 2b8n) revealed a new fold distinct from other known kinase families. here, we verified the enzymatic activity of tm1585, assessed its kinetic characteristics, and used directed muta ...	2008	18156253
glycerate 2-kinase of thermotoga maritima and genomic reconstruction of related metabolic pathways.	members of a novel glycerate-2-kinase (gk-ii) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the gark (gk-i) family. the recently reported three-dimensional structure of gk-ii from thermotoga maritima (tm1585; pdb code 2b8n) revealed a new fold distinct from other known kinase families. here, we verified the enzymatic activity of tm1585, assessed its kinetic characteristics, and used directed muta ...	2008	18156253
mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5'-phosphate-dependent reaction.	1-aminocyclopropane-1-carboxylic acid (acc) deaminase (accd) is a pyridoxal 5'-phosphate (plp)-dependent enzyme that cleaves the cyclopropane ring of acc, to give α-ketobutyric acid and ammonia as products. the cleavage of the c(α)-c(β) bond of an amino acid substrate is a rare event in plp-dependent enzyme catalysis. potential chemical mechanisms involving nucleophile- or acid-catalyzed cyclopropane ring opening have been proposed for the unusual transformation catalyzed by accd, but the actual ...	2011	21244019
crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration.	the enzyme phosphite dehydrogenase (ptdh) catalyzes the nad(+)-dependent conversion of phosphite to phosphate and represents the first biological catalyst that has been shown to conduct the enzymatic oxidation of phosphorus. despite investigation for more than a decade into both the mechanism of its unusual reaction and its utility in cofactor regeneration, there has been a lack of any structural data for ptdh. here we present the cocrystal structure of an engineered thermostable variant of ptdh ...	2012	22564171
the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments.	the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ...	2013	23451130
a novel serine hydroxymethyltransferase from arthrobacter nicotianae: characterization and improving catalytic efficiency by rational design.	serine hydroxymethyltransferase (shmt) is the key enzyme in l-serine enzymatic production, suggesting the importance of obtaining a shmt with high activity.	2014	25394480
contribution to the prediction of the fold code: application to immunoglobulin and flavodoxin cases.	folding nucleus of globular proteins formation starts by the mutual interaction of a group of hydrophobic amino acids whose close contacts allow subsequent formation and stability of the 3d structure. these early steps can be predicted by simulation of the folding process through a monte carlo (mc) coarse grain model in a discrete space. we previously defined mirs (most interacting residues), as the set of residues presenting a large number of non-covalent neighbour interactions during such simu ...	2015	25915049
deletion of the proposed iron chaperones isca/sufa results in accumulation of a red intermediate cysteine desulfurase iscs in escherichia coli.	in escherichia coli, sulfur in iron-sulfur clusters is primarily derived from l-cysteine via the cysteine desulfurase iscs. however, the iron donor for iron-sulfur cluster assembly remains elusive. previous studies have shown that, among the iron-sulfur cluster assembly proteins in e. coli, isca has a unique and strong iron-binding activity and that the iron-bound isca can efficiently provide iron for iron-sulfur cluster assembly in proteins in vitro, indicating that isca may act as an iron chap ...	2015	25907559
new insights into the mechanism of substrates trafficking in glyoxylate/hydroxypyruvate reductases.	glyoxylate accumulation within cells is highly toxic. in humans, it is associated with hyperoxaluria type 2 (ph2) leading to renal failure. the glyoxylate content within cells is regulated by the nadph/nadh dependent glyoxylate/hydroxypyruvate reductases (grhpr). these are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into d-glycerate. despite the determination of high-resolution x-ray structures, the substrate rec ...	2016	26865263