2KAU

THE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES AT 2.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of urease from Klebsiella aerogenes.

Jabri, E.Carr, M.B.Hausinger, R.P.Karplus, P.A.

(1995) Science 268: 998-1004


  • PubMed Abstract: 
  • The crystal structure of urease from Klebsiella aerogenes has been determined at 2.2 A resolution and refined to an R factor of 18.2 percent. The enzyme contains four structural domains: three with novel folds playing structural roles, and an (alpha ...

    The crystal structure of urease from Klebsiella aerogenes has been determined at 2.2 A resolution and refined to an R factor of 18.2 percent. The enzyme contains four structural domains: three with novel folds playing structural roles, and an (alpha beta)8 barrel domain, which contains the bi-nickel center. The two active site nickels are 3.5 A apart. One nickel ion is coordinated by three ligands (with low occupancy of a fourth ligand) and the second is coordinated by five ligands. A carbamylated lysine provides an oxygen ligand to each nickel, explaining why carbon dioxide is required for the activation of urease apoenzyme. The structure is compatible with a catalytic mechanism whereby urea ligates Ni-1 to complete its tetrahedral coordination and a hydroxide ligand of Ni-2 attacks the carbonyl carbon. A surprisingly high structural similarity between the urease catalytic domain and that of the zinc-dependent adenosine deaminase reveals a remarkable example of active site divergence.


    Related Citations: 
    • Preliminary Crystallographic Studies of Urease from Jack Bean and from Klebsiella Aerogenes
      Jabri, E.,Lee, M.H.,Hausinger, R.P.,Karplus, P.A.
      (1992) J.Mol.Biol. 227: 934
    • Requirement of Carbon Dioxide for in Vitro Assembly of the Urease Nickel Metallocenter
      Park, I.-S.,Hausinger, R.P.
      (1995) Science 267: 1156


    Organizational Affiliation

    Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASE (GAMMA CHAIN)
A
100Enterobacter aerogenesGene Names: ureA
EC: 3.5.1.5
Find proteins for P18316 (Enterobacter aerogenes)
Go to UniProtKB:  P18316
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UREASE (BETA CHAIN)
B
106Enterobacter aerogenesGene Names: ureB
EC: 3.5.1.5
Find proteins for P18315 (Enterobacter aerogenes)
Go to UniProtKB:  P18315
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UREASE (ALPHA CHAIN)
C
567Enterobacter aerogenesGene Names: ureC
EC: 3.5.1.5
Find proteins for P18314 (Enterobacter 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 Free: 0.225 
  • R-Value Work: 0.185 
  • 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
SDMSdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance