3MDU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4003 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1021/bi501299y
  • Primary Citation of Related Structures:  

  • 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-gluta ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-formimino-L-Glutamate Iminohydrolase
A
453Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9HU77 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HU77
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NGQ
Query on NGQ

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Download CCD File 
A
N-carbamimidoyl-L-glutamic acid
N-Guanidino-L-Glutamate
C6 H11 N3 O4
RHVVRMJOHATSPD-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4003 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.179 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 133.208α = 90.00
b = 133.208β = 90.00
c = 124.835γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
ADSCdata collection
SCALEPACKdata scaling
PHENIXrefinement
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-01-21
    Type: Database references
  • Version 1.3: 2015-01-28
    Type: Database references
  • Version 1.4: 2015-02-11
    Type: Database references