1FWA

KLEBSIELLA AEROGENES UREASE, C319A VARIANT AT PH 7.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease.

Pearson, M.A., Michel, L.O., Hausinger, R.P., Karplus, P.A.

(1997) Biochemistry 36: 8164-8172

  • DOI: 10.1021/bi970514j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Cys319 is located on a mobile flap covering the active site of Klebsiella aerogenes urease but does not play an essential role in catalysis. Four urease variants altered at position C319 range from having high activity (C319A) to no measurable activi ...

    Cys319 is located on a mobile flap covering the active site of Klebsiella aerogenes urease but does not play an essential role in catalysis. Four urease variants altered at position C319 range from having high activity (C319A) to no measurable activity (C319Y), indicating Cys is not required at this position, but its presence is highly influential [Martin, P. R., & Hausinger, R. P. (1992) J. Biol. Chem. 267, 20024-20027]. Here, we present 2.0 A resolution crystal structures of C319A, C319S, C319D, and C319Y proteins and the C319A variant inhibited by acetohydroxamic acid. These structures show changes in the hydration of the active site nickel ions and in the position and flexibility of the active site flap. The C319Y protein exhibits an alternate conformation of the flap, explaining its lack of activity. The changes in hydration and conformation suggest that there are suboptimal protein-solvent and protein-protein interactions in the empty urease active site which contribute to urease catalysis. Specifically, we hypothesize that the suboptimal interactions may provide a significant source of substrate binding energy, and such hidden energy may be a common phenomenon for enzymes that contain mobile active site loops and undergo an induced fit. The acetohydroxamic acid-bound structure reveals a chelate interaction similar to those seen in other metalloenzymes and in a small molecule nickel complex. The inhibitor binding mode supports the proposed mode of urea binding. We complement these structural studies with extended functional studies of C319A urease to show that it has enhanced stability and resistance to inhibition by buffers containing nickel ions. The near wild-type activity and enhanced stability of the C319A variant make it useful for further studies of urease structure-function relationships.

    Related Citations: 
    • Site-Directed Mutagenesis of the Active Site Cysteine in Klebsiella Aerogenes Urease
      Martin, P.R.,Hausinger, R.P.
      (1992) J.Biol.Chem. 267: 20024
    • The Crystal Structure of Urease from Klebsiella Aerogenes
      Jabri, E.,Carr, M.B.,Hausinger, R.P.,Karplus, P.A.
      (1995) Science 268: 998
    • Identification of the Essential Cysteine Residue in Klebsiella Aerogenes Urease
      Todd, M.J.,Hausinger, R.P.
      (1991) J.Biol.Chem. 266: 24327
    • Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants
      Jabri, E.,Karplus, P.A.
      (1996) Biochemistry 35: 10616

    Organizational Affiliation: 

    Section of Biochemistry, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASE
A
100Klebsiella aerogenesMutation(s): 0 
Gene Names: ureA
EC: 3.5.1.5
Find proteins for P18316 (Klebsiella aerogenes)
Go to UniProtKB:  P18316
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UREASE
B
106Klebsiella aerogenesMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
Find proteins for P18315 (Klebsiella aerogenes)
Go to UniProtKB:  P18315
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UREASE
C
567Klebsiella aerogenesMutation(s): 1 
Gene Names: ureC
EC: 3.5.1.5
Find proteins for P18314 (Klebsiella aerogenes)
Go to UniProtKB:  P18314
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI
Download SDF File 
Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3
Download SDF File 
Download CCD File 
C
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
C
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.169 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 170.800α = 90.00
b = 170.800β = 90.00
c = 170.800γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance