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

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Structure of N-Formimino-l-glutamate Iminohydrolase from Pseudomonas aeruginosa.

Fedorov, A.A.Marti-Arbona, R.Nemmara, V.V.Hitchcock, D.Fedorov, E.V.Almo, S.C.Raushel, F.M.

(2015) Biochemistry 54: 890-897

  • DOI: https://doi.org/10.1021/bi501299y
  • Primary Citation of Related Structures:  
    3MDU, 3MDW, 4RZB

  • 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.

  • Organizational Affiliation

    Department of Chemistry and ‡Department of Biochemistry & Biophysics, Texas A&M University , College Station, Texas 77843, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-formimino-L-Glutamate Iminohydrolase453Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA5106
Find proteins for Q9HU77 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HU77 
Go to UniProtKB:  Q9HU77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HU77
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.208α = 90
b = 133.208β = 90
c = 124.835γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-01-21
    Changes: Database references
  • Version 1.3: 2015-01-28
    Changes: Database references
  • Version 1.4: 2015-02-11
    Changes: Database references
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Derived calculations