1FWI

KLEBSIELLA AEROGENES UREASE, H134A VARIANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of the mononickel metallocenter in H134A mutant urease.

Park, I.S.Michel, L.O.Pearson, M.A.Jabri, E.Karplus, P.A.Wang, S.Dong, J.Scott, R.A.Koehler, B.P.Johnson, M.K.Hausinger, R.P.

(1996) J.Biol.Chem. 271: 18632-18637


  • PubMed Abstract: 
  • A mutant form of Klebsiella aerogenes urease possessing Ala instead of His at position 134 (H134A) is inactive and binds approximately half the normal complement of nickel (Park, I.-S., and Hausinger, R. P.(1993) Protein Sci. 2, 1034-1041). The cryst ...

    A mutant form of Klebsiella aerogenes urease possessing Ala instead of His at position 134 (H134A) is inactive and binds approximately half the normal complement of nickel (Park, I.-S., and Hausinger, R. P.(1993) Protein Sci. 2, 1034-1041). The crystal structure of the H134A protein was obtained at 2.0-A resolution, and it confirms that only Ni-1 of the two nickel ions found in the native enzyme is present. In contrast to the pseudotetrahedral geometry observed for Ni-1 in native urease (where it is liganded by His-246, His-272, one oxygen atom of carbamylated Lys-217, and a water molecule at partial occupancy), the mononickel metallocenter in the H134A protein was found to possess octahedral geometry and was coordinated by the above protein ligands plus three water molecules. The nickel site of H134A urease was probed by UV-visible, variable temperature magnetic circular dichroism, and x-ray absorption spectroscopies. The spectroscopic data are consistent with the presence of Ni(II) in octahedral geometry coordinated by two histidylimidazoles and additional oxygen and/or nitrogen donors. These data underscore the requirement of Ni-2 for formation of active urease and demonstrate the important role of Ni-2 in establishing the proper Ni-1 coordination geometry.


    Related Citations: 
    • The Crystal Structure of Urease from Klebsiella Aerogenes
      Jabri, E.,Carr, M.B.,Hausinger, R.P.,Karplus, P.A.
      (1995) Science 268: 998
    • Site-Directed Mutagenesis of Klebsiella Aerogenes Urease: Identification of Histidine Residues that Appear to Function in Nickel Ligation, Substrate Binding, and Catalysis
      Park, I.S.,Hausinger, R.P.
      (1993) Protein Sci. 2: 1034
    • Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants
      Jabri, E.,Karplus, P.A.
      (1996) Biochemistry 35: 10616


    Organizational Affiliation

    Department of Microbiology, Michigan State University, East Lansing, Michigan 48824-1101, 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 1 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
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: 0.170 
  • 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
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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