3MDW

The structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-formimino-L-Aspartate

Summary for 3MDW

• Entry DOI: 10.2210/pdb3mdw/pdb
• Related: 3MDU
• Descriptor: N-formimino-L-Glutamate Iminohydrolase, N-[(E)-iminomethyl]-L-aspartic acid, ZINC ION, ... (6 entities in total)
• Functional Keywords: aminohydrolase family, n-formimino-l-glutamate iminohydrolase, hydrolase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 4
• Total formula weight: 198796.18

Authors

Fedorov, A.A.,Fedorov, E.V.,Marti-Arbona, R.,Raushel, F.M.,Almo, S.C. (deposition date: 2010-03-30, release date: 2011-03-09, Last modification date: 2024-02-21)

Primary citation

Fedorov, A.A.,Marti-Arbona, R.,Nemmara, V.V.,Hitchcock, D.,Fedorov, E.V.,Almo, S.C.,Raushel, F.M.
Structure of N-Formimino-l-glutamate Iminohydrolase from Pseudomonas aeruginosa.
Biochemistry, 54:890-897, 2015

PubMed 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 Å, 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 Å 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.

PubMed: 25559274
DOI: 10.1021/bi501299y

Experimental method

X-RAY DIFFRACTION (1.8979 Å)