Cloning and nucleotide sequences of histidase and regulatory genes in the Bacillus subtilis hut operon and positive regulation of the operon

Oda, Masanao; Sugishita, Akio; Furukawa, Koichi

doi:10.1128/jb.170.7.3199-3205.1988

Cited by 76 publications

(66 citation statements)

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“…The second structure was of urocanase or HutU, also from P. putida, and the structure was determined by the same group who solved the histidase in 2004 (9). The third structure solved was the last enzyme in the histidine degradation pathway, formiminoglutamase or HutG from Vibrio cholerae, which was determined by Wu et al 5 and deposited in the Protein Data Bank under accession number 1XFK. The imidazolonepropionase or HutI is the only enzyme left in this pathway that has no published structural information so far, although some properties of this enzyme have been studied in Salmonella typhimurium (10), Pseudomonas fluorescens ATCC 11299 (11), rat liver (12), and other organisms during 1960s and 1970s.…”

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confidence: 99%

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A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

Bröstromer

et al. 2006

Journal of Biological Chemistry

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Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-L-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-Å resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small ␤-sandwich domain. The TIM barrel domain is quite similar to the members of the ␣/␤ barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 Å away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.The histidine degradation pathway is highly conserved from prokaryotes to eukaryotes (1, 2). In bacteria, the histidine degradation pathway is operated by the hut (histidine utilization) genes, and the Bacillus subtilis hut operon encodes proteins in the order of HutP, HutH, HutU, HutI, HutG, HutM (3-6).There (Fig. 1A); 4) N-formimino-L-glutamic acid ϩ H 2 O 3 glutamate ϩ HCONH 2 (catalyzed by formiminoglutamase, EC 3.5.3.8).Among the four enzymes, the first three-dimensional structure determined was the 2.1-Å resolution crystal structure of histidase or HutH from Pseudomonas putida by Schulz and co-workers in 1999 (7,8). It was found that there was a polypeptide modification, forming a novel catalytically essential electrophilic group. The second structure was of urocanase or HutU, also from P. putida, and the structure was determined by the same group who solved the histidase in 2004 (9). The third structure solved was the last enzyme in the histidine degradation pathway, formiminoglutamase or HutG from Vibrio cholerae, which was determined by Wu et al. 5 and deposited in the Protein Data Bank under accession number 1XFK. The imidazolonepropionase or HutI is the only enzyme left in this pathway that has no published structural information so far, although some properties of this enzyme have been studied in Salmonella typhimurium (10), Pseudomonas fluorescens ATCC 11299 (11), rat liver (12), and other organisms during 1960s and 1970s. The maximal activity of this enzyme occurred at pH 7.4 with a narrow pH optimum, and its Michaelis constant was calculated to be 7 M (12). It was also mentioned in the literature that 1 mM EDTA could...

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“…In bacteria, the histidine degradation pathway is operated by the hut (histidine utilization) genes, and the Bacillus subtilis hut operon encodes proteins in the order of HutP, HutH, HutU, HutI, HutG, HutM (3)(4)(5)(6).…”

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confidence: 99%

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

Bröstromer

et al. 2006

Journal of Biological Chemistry

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“…5) encodes enzymes for the catabolism of L-histidine (Kimhi and Magasanik, 1970). It is regulated by an antiterminator protein, HutP, which is not similar to other antiterminator proteins (Oda et al, 1988;Wray and Fisher, 1994). The operon contains a potential transcription terminator but, as yet, no antiterminator sequence has been identified.…”

Section: The Hut Operon Of B Subtilismentioning

confidence: 99%

Antitermination of transcription of catabolic operons

Rutberg¹

1997

Molecular Microbiology

102

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SummaryAntitermination of transcription mediated by proteins interacting with mRNA sequences is described for nine operons/regulons. Eight of the systems are catabolic, while the ninth, the Klebsiella pneumoniae nas regulon, is involved in the assimilation of nitrate and nitrite. Six of the catabolic operons/regulons are found in Bacillus subtilis, one is found in Escherichia coli, and one in Pseudomonas aeruginosa. The antitermination system of five of the operons/regulons (E. coli blg, and sacPA, sacB, bgl, and lic from B. subtilis) are assigned to the bgl-sac family on the basis of extensive similarities with regard to antiterminator proteins and the sequences of the antiterminators. Other members of the bgl-sac family are the arb operon of Erwinia chrysanthemi and a presumed bgl operon of Lactococcus lactis. The antitermination systems of the other four operons/regulons (B. subtilis glp, B. subtilis hut, P. aeruginosa ami, and K. pneumoniae nas) seem to be unrelated both to the bgl-sac family and to each other. The antiterminator protein of the B. subtilis glp regulon has been found not only to cause antitermination but also to stabilize the resultant mRNA and to mediate glucose repression. If other antiterminator proteins, and antitermination factors, also prove to have additional functions, it will broaden the impact of antitermination as a means of controlling gene expression.

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“…It is responsible for regulating the expression of the hut structural genes in response to changes in the intracellular levels of L-histidine [10,11]. In the hut operon, HutP is located just downstream from the promoter, while the five other subsequent structural genes, hutH, hutU, hutI, hutG and hutM, are positioned far downstream from the promoter [12][13][14][15]. In the presence of Lhistidine and divalent metal ions, HutP binds to the nascent hut mRNA leader transcript.…”

Section: Description Of the Hutpmentioning

confidence: 99%

Studies of the Activation Steps Concurrent to Ligand Binding in δOR and κOR Opioid Receptors Based on Molecular Dynamics Simulations

Kumarevel¹

2009

TOSBJ

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Regulating gene expression directly at the mRNA level represents a novel approach in the control of cellular processes in all organisms. In this respect, RNA-binding proteins, while in the presence of their cognate ligands, play a key role by targeting the mRNA to regulate its expression through attenuation or anti-termination mechanisms. Although many proteins are known to use these mechanisms in the regulation of gene expression, no structural insights have been revealed, to date, to explain how these proteins trigger the conformation for the recognition of RNA. This review describes the HutP mediated anti-termination mechanism by combining the in vivo, in vitro and X-ray analyses of the activated conformation of HutP, initiated by the coordination of L-histidine and Mg 2+ ions, based on our previous and recently solved crystal structures (uncomplexed HutP, HutP-Mg -Lhistidine-RNA (21-mer and 55-mer)). In this anti-termination process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first UAG-rich region and then accesses the second UAG-rich region, located downstream of the stable G-C-rich segment of the terminator stem. By this mode of action, HutP appears to disrupt the G-C rich terminator stem loop, and allow the RNA polymerase to pass through the destabilized terminator, thus it prevents premature termination of transcription in the RNA segment preceding the regions encoding for the genes responsible for histidine degradation.

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Cloning and nucleotide sequences of histidase and regulatory genes in the Bacillus subtilis hut operon and positive regulation of the operon

Cited by 76 publications

References 34 publications

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis

Antitermination of transcription of catabolic operons

Studies of the Activation Steps Concurrent to Ligand Binding in δOR and κOR Opioid Receptors Based on Molecular Dynamics Simulations

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