Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa

Alexander A. Fedorov, Ricardo Martí-Arbona, Venkatesh V. Nemmara, Daniel Hitchcock, Elena V. Fedorov, Steven C. Almo, Frank M. Raushel

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

N-Formimino-l-glutamate iminohydrolase (HutF), from Pseudomonas aeruginosa with a locus tag of Pa5106 (gi|15600299), is a member of the amidohydrolase superfamily. This enzyme catalyzes the deamination of N-formimino-l-glutamate to N-formyl-l-glutamate and ammonia in the histidine degradation pathway. The crystal structure of Pa5106 was determined in the presence of the inhibitors N-formimino-l-aspartate and N-guanidino-l-glutaric acid at resolutions of 1.9 and 1.4 A˚, respectively. The structure of an individual subunit is composed of two domains with the larger domain folding as a distorted (β/α)8-barrel. The (β/α)8-barrel domain is composed of eight β-strands flanked by 11 α-helices, whereas the smaller domain is made up of eight β-strands. The active site of Pa5106 contains a single zinc atom that is coordinated by His-56, His-58, His-232, and Asp-320. The nucleophilic solvent water molecule coordinates with the zinc atom at a distance of 2.0 A˚ and is hydrogen bonded to Asp-320 and His-269. The α-carboxylate groups of both inhibitors are hydrogen bonded to the imidazole moiety of His-206, the hydroxyl group of Tyr-121, and the side chain amide group of Gln-61. The side chain carboxylate groups of the two inhibitors are ion-paired with the guanidino groups of Arg-209 and Arg-82. Computational docking of high-energy tetrahedral intermediate forms of the substrate, N-formimino-l-glutamate, to the three-dimensional structure of Pa5106 suggests that this compound likely undergoes a re-faced nucleophilic attack at the formimino group by the metal-bound hydroxide. A catalytic mechanism of the reaction catalyzed by Pa5106 is proposed. (Chemical Equation Presented).

Original languageEnglish (US)
Pages (from-to)890-897
Number of pages8
JournalBiochemistry
Volume54
Issue number3
DOIs
StatePublished - Jan 27 2015

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Pseudomonas aeruginosa
Glutamic Acid
Zinc
Hydrogen
Amidohydrolases
Atoms
Deamination
Ammonia
Histidine
Aspartic Acid
Amides
Hydroxyl Radical
Catalytic Domain
Crystal structure
Metals
Ions
Degradation
Molecules
Water
Substrates

ASJC Scopus subject areas

  • Biochemistry

Cite this

Fedorov, A. A., Martí-Arbona, R., Nemmara, V. V., Hitchcock, D., Fedorov, E. V., Almo, S. C., & Raushel, F. M. (2015). Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa. Biochemistry, 54(3), 890-897. https://doi.org/10.1021/bi501299y

Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa. / Fedorov, Alexander A.; Martí-Arbona, Ricardo; Nemmara, Venkatesh V.; Hitchcock, Daniel; Fedorov, Elena V.; Almo, Steven C.; Raushel, Frank M.

In: Biochemistry, Vol. 54, No. 3, 27.01.2015, p. 890-897.

Research output: Contribution to journalArticle

Fedorov, AA, Martí-Arbona, R, Nemmara, VV, Hitchcock, D, Fedorov, EV, Almo, SC & Raushel, FM 2015, 'Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa', Biochemistry, vol. 54, no. 3, pp. 890-897. https://doi.org/10.1021/bi501299y
Fedorov AA, Martí-Arbona R, Nemmara VV, Hitchcock D, Fedorov EV, Almo SC et al. Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa. Biochemistry. 2015 Jan 27;54(3):890-897. https://doi.org/10.1021/bi501299y
Fedorov, Alexander A. ; Martí-Arbona, Ricardo ; Nemmara, Venkatesh V. ; Hitchcock, Daniel ; Fedorov, Elena V. ; Almo, Steven C. ; Raushel, Frank M. / Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa. In: Biochemistry. 2015 ; Vol. 54, No. 3. pp. 890-897.
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N2 - N-Formimino-l-glutamate iminohydrolase (HutF), from Pseudomonas aeruginosa with a locus tag of Pa5106 (gi|15600299), is a member of the amidohydrolase superfamily. This enzyme catalyzes the deamination of N-formimino-l-glutamate to N-formyl-l-glutamate and ammonia in the histidine degradation pathway. The crystal structure of Pa5106 was determined in the presence of the inhibitors N-formimino-l-aspartate and N-guanidino-l-glutaric acid at resolutions of 1.9 and 1.4 A˚, respectively. The structure of an individual subunit is composed of two domains with the larger domain folding as a distorted (β/α)8-barrel. The (β/α)8-barrel domain is composed of eight β-strands flanked by 11 α-helices, whereas the smaller domain is made up of eight β-strands. The active site of Pa5106 contains a single zinc atom that is coordinated by His-56, His-58, His-232, and Asp-320. The nucleophilic solvent water molecule coordinates with the zinc atom at a distance of 2.0 A˚ and is hydrogen bonded to Asp-320 and His-269. The α-carboxylate groups of both inhibitors are hydrogen bonded to the imidazole moiety of His-206, the hydroxyl group of Tyr-121, and the side chain amide group of Gln-61. The side chain carboxylate groups of the two inhibitors are ion-paired with the guanidino groups of Arg-209 and Arg-82. Computational docking of high-energy tetrahedral intermediate forms of the substrate, N-formimino-l-glutamate, to the three-dimensional structure of Pa5106 suggests that this compound likely undergoes a re-faced nucleophilic attack at the formimino group by the metal-bound hydroxide. A catalytic mechanism of the reaction catalyzed by Pa5106 is proposed. (Chemical Equation Presented).

AB - N-Formimino-l-glutamate iminohydrolase (HutF), from Pseudomonas aeruginosa with a locus tag of Pa5106 (gi|15600299), is a member of the amidohydrolase superfamily. This enzyme catalyzes the deamination of N-formimino-l-glutamate to N-formyl-l-glutamate and ammonia in the histidine degradation pathway. The crystal structure of Pa5106 was determined in the presence of the inhibitors N-formimino-l-aspartate and N-guanidino-l-glutaric acid at resolutions of 1.9 and 1.4 A˚, respectively. The structure of an individual subunit is composed of two domains with the larger domain folding as a distorted (β/α)8-barrel. The (β/α)8-barrel domain is composed of eight β-strands flanked by 11 α-helices, whereas the smaller domain is made up of eight β-strands. The active site of Pa5106 contains a single zinc atom that is coordinated by His-56, His-58, His-232, and Asp-320. The nucleophilic solvent water molecule coordinates with the zinc atom at a distance of 2.0 A˚ and is hydrogen bonded to Asp-320 and His-269. The α-carboxylate groups of both inhibitors are hydrogen bonded to the imidazole moiety of His-206, the hydroxyl group of Tyr-121, and the side chain amide group of Gln-61. The side chain carboxylate groups of the two inhibitors are ion-paired with the guanidino groups of Arg-209 and Arg-82. Computational docking of high-energy tetrahedral intermediate forms of the substrate, N-formimino-l-glutamate, to the three-dimensional structure of Pa5106 suggests that this compound likely undergoes a re-faced nucleophilic attack at the formimino group by the metal-bound hydroxide. A catalytic mechanism of the reaction catalyzed by Pa5106 is proposed. (Chemical Equation Presented).

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