Crystal Structure of<i>Escherichia coli</i>ArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-<scp>l</scp>-arabinose and Polymyxin Resistance<sup>,</sup>

Gatzeva-Topalova, § Petia Z.; May, and Andrew P.; Sousa, Marcelo C.

doi:10.1021/bi048551f

Cited by 52 publications

(101 citation statements)

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“…2B69) is unpublished; however, two research groups have independently published analyses of the structure (PDB ID no. 1U9J and 2BLL) of the C-terminal portion of E. coli ArnA (18,42). The C-terminal portion of this bifunctional enzyme catalyzes the NAD ϩ -dependent oxidative decarboxylation of UDPGlcA as part of a pathway leading to production of UDP-4-amino-4-deoxy-L-arabinose (7,18,42).…”

Section: Resultsmentioning

confidence: 99%

“…The C-terminal portion of this bifunctional enzyme catalyzes the NAD ϩ -dependent oxidative decarboxylation of UDPGlcA as part of a pathway leading to production of UDP-4-amino-4-deoxy-L-arabinose (7,18,42). Analysis of the crystal structure of the C-terminal decarboxylase region of ArnA revealed that R 619 and S 433 are important for decarboxylase activity (7,18,42). In addition, site-directed mutations of S433A, E434A, and E434Q of ArnA affected UDP-GlcA decarboxylase activity.…”

Section: Resultsmentioning

confidence: 99%

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UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria

et al. 2011

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Xylose is rarely described as a component of bacterial glycans. UDP-xylose is the nucleotide-activated form necessary for incorporation of xylose into glycans and is synthesized by the decarboxylation of UDP-glucuronic acid (UDP-GlcA). Enzymes with UDP-GlcA decarboxylase activity include those that lead to the formation of UDP-xylose as the end product (Uxs type) and those synthesizing UDP-xylose as an intermediate (ArnA and RsU4kpxs types). In this report, we identify and confirm the activities of two Uxs-type UDP-GlcA decarboxylases of Bacteroides fragilis, designated BfUxs1 and BfUxs2. Bfuxs1 is located in a conserved region of the B. fragilis genome, whereas Bfuxs2 is in the heterogeneous capsular polysaccharide F (PSF) biosynthesis locus. Deletion of either gene separately does not result in the loss of a detectable phenotype, but deletion of both genes abrogates PSF synthesis, strongly suggesting that they are functional paralogs and that the B. fragilis NCTC 9343 PSF repeat unit contains xylose. UDP-GlcA decarboxylases are often annotated incorrectly as NAD-dependent epimerases/dehydratases; therefore, their prevalence in bacteria is underappreciated. Using available structural and mutational data, we devised a sequence pattern to detect bacterial genes encoding UDP-GlcA decarboxylase activity. We identified 826 predicted UDP-GlcA decarboxylase enzymes in diverse bacterial species, with the ArnA and RsU4kpxs types confined largely to proteobacterial species. These data suggest that xylose, or a monosaccharide requiring a UDP-xylose intermediate, is more prevalent in bacterial glycans than previously appreciated. Genes encoding BfUxs1-like enzymes are highly conserved in Bacteroides species, indicating that these abundant intestinal microbes may synthesize a conserved xylose-containing glycan.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria

et al. 2011

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“…This protein is found in most Gram-negative bacteria and catalyzes the decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose by adding a formyl group. The modified arabinose, which is then attached to lipid A, is essential for resistance to cationic antimicrobial peptides such as polymyxin (66)(67)(68). The second protein is an outer membrane protein (OmpF), and its function is limited to the passive diffusion of small molecules across the outer membrane pores (69).…”

Section: Discussionmentioning

confidence: 99%

Biodegradation of the Organic Disulfide 4,4′-Dithiodibutyric Acid by Rhodococcus spp

Khairy

Wübbeler

Steinbüchel

2015

Appl Environ Microbiol

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c Four Rhodococcus spp. exhibited the ability to use 4,4=-dithiodibutyric acid (DTDB) as a sole carbon source for growth. The most important step for the production of a novel polythioester (PTE) using DTDB as a precursor substrate is the initial cleavage of DTDB. Thus, identification of the enzyme responsible for this step was mandatory. Because Rhodococcus erythropolis strain MI2 serves as a model organism for elucidation of the biodegradation of DTDB, it was used to identify the genes encoding the enzymes involved in DTDB utilization. To identify these genes, transposon mutagenesis of R. erythropolis MI2 was carried out using transposon pTNR-TA. Among 3,261 mutants screened, 8 showed no growth with DTDB as the sole carbon source. In five mutants, the insertion locus was mapped either within a gene coding for a polysaccharide deacetyltransferase, a putative ATPase, or an acetyl coenzyme A transferase, 1 bp upstream of a gene coding for a putative methylase, or 176 bp downstream of a gene coding for a putative kinase. In another mutant, the insertion was localized between genes encoding a putative transcriptional regulator of the TetR family (noxR) and an NADH:flavin oxidoreductase (nox). Moreover, in two other mutants, the insertion loci were mapped within a gene encoding a hypothetical protein in the vicinity of noxR and nox. The interruption mutant generated, R. erythropolis MI2 nox⍀tsr, was unable to grow with DTDB as the sole carbon source. Subsequently, nox was overexpressed and purified, and its activity with DTDB was measured. The specific enzyme activity of Nox amounted to 1.2 ؎ 0.15 U/mg. Therefore, we propose that Nox is responsible for the initial cleavage of DTDB into 2 molecules of 4-mercaptobutyric acid (4MB).T he genus Rhodococcus has attracted great interest in recent years due to the ability of many of its species to degrade and transform a wide range of xenobiotic substances (1). Rhodococci are described as aerobic, Gram-positive, mycolate-containing actinomycetes with high genomic GϩC contents. They have a diverse set of genetic and catabolic features, because of the presence of large linear plasmids in addition to their large chromosomes (2). The number of publications and patents involving Rhodococcus spp. has increased significantly in recent years (3).Rhodococcus spp. have been isolated from a variety of sources. They are ubiquitous in soils contaminated with crude oil and/or other xenobiotic compounds. The ability of Rhodococcus species to degrade substituted hydrocarbons and other chemicals allows them to play a role in the natural degradation and bioremediation of such compounds (4). Many Rhodococcus species are characterized by broad metabolic diversity and an array of unique enzymatic capabilities; therefore, they are also of interest for pharmaceutical, environmental, chemical, and energy studies. They play a significant role in the process of desulfurization of fossil fuels (5) and in the industrial production of acrylamide (6). Strains of Rhodococcus erythropolis have been identi...

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“…This is consistent with the function of ArnA in the oxidative decarboxylation of UDP-GlcUA. All three proteins possess the conserved glycine-rich "Rossmann fold," located within the first 13 amino acids of the dTDP-D-glucose 4,6-dehydratase and UDP-galactose epimerase (52,53) and between Arg-317 and Gly-330 of ArnA (55).…”

Section: One-dimensional 1 H Nmr Spectroscopy Of the Formylated Produmentioning

confidence: 99%

A Formyltransferase Required for Polymyxin Resistance in Escherichia coli and the Modification of Lipid A with 4-Amino-4-deoxy-l-arabinose

Breazeale

Ribeiro

McClerren

et al. 2005

Journal of Biological Chemistry

154

178

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Modification of the phosphate groups of lipid A with 4-amino-4-deoxy-L-arabinose (L-Ara4N Lipopolysaccharide (LPS)1 is an immunogenic glycolipid that constitutes most of the outer leaflet of the outer membrane of Gram-negative bacteria (1-4). LPS consists of three domains, which are the O-antigen, the core oligosaccharide, and the lipid A moiety (1-4). The O-antigen functions as a protective barrier, whereas the core sugars maintain outer membrane integrity and provide an attachment site for the O-antigen (1-4). Lipid A is the hydrophobic membrane anchor of LPS, and it is the active (endotoxin) component of LPS, accounting for many of the pathophysiological effects associated with Gram-negative sepsis (5-7).The Kdo 2 -lipid A portion of LPS is sufficient to support growth in Escherichia coli and Salmonella typhimurium (2). Covalent modifications to Kdo 2 -lipid A can be induced by environmental stimuli, such as low Mg 2ϩ concentrations or low pH (8 -10). As shown in Fig. 1 for S. typhimurium, these modifications include the incorporation of palmitate (11, 12), the addition of phosphoethanolamine (pEtN) (13-15), and/or the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) moieties (13,16,17). The modification of at least one phosphate residue with L-Ara4N is required for maintaining resistance to certain cationic antimicrobial peptides of the innate immune system and to the antibiotic polymyxin (18,19). Resistance is due, in part, to the neutralization of the negative charges of lipid A by L-Ara4N, reducing the affinity of lipid A for cationic substances (20) and preventing these anti-microbial compounds from penetrating the outer membrane.The addition of pEtN and L-Ara4N groups to lipid A is controlled by the PmrA/PmrB two-component regulatory system, which is activated by low pH, high Fe 3ϩ levels, or indirectly, by low concentrations of Mg 2ϩ via the PhoP/PhoQ system through the action of PmrD (9). Activated PmrA stimulates transcription at the pmrCAB, pmrE(ugd) , and pmrHFIJKLM loci (19,21). Constitutive pmrA (pmrA c ) mutants of E. coli and S. typhimurium are polymyxin-resistant, and they modify their lipid A with L-Ara4N and pEtN groups under all growth conditions (17,18,22). Inactivation of either pmrE or the genes in the pmrHFIJKLM operon results in complete loss of polymyxin resistance and of L-Ara4N-modified lipid A in pmrA c bacterial cells (19,21,23). Similarly, pmrA c mutants harboring a nonpolar disruption of the pmrC(eptA) gene are unable * This research was supported by National Institutes of Health Grant GM-51310 (to C. R. H. R.). The Duke University NMR Center is partially supported by P30-CA-14236. NMR instrumentation in the Center was funded by the National Science Foundation, the National Institutes of Health, the North Carolina Biotechnology Center, and Duke University. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fac...

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Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

Cited by 52 publications

References 54 publications

UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria

UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria

Biodegradation of the Organic Disulfide 4,4′-Dithiodibutyric Acid by Rhodococcus spp

A Formyltransferase Required for Polymyxin Resistance in Escherichia coli and the Modification of Lipid A with 4-Amino-4-deoxy-l-arabinose

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Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance,

Cited by 52 publications

References 54 publications

UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria

UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria

Biodegradation of the Organic Disulfide 4,4′-Dithiodibutyric Acid by Rhodococcus spp

A Formyltransferase Required for Polymyxin Resistance in Escherichia coli and the Modification of Lipid A with 4-Amino-4-deoxy-l-arabinose

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Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,