1A5O

K217C VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand.

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

(1998) Biochemistry 37: 6214-6220

  • DOI: 10.1021/bi980021u
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Klebsiella aerogenes urease possesses a dinuclear metallocenter in which two nickel atoms are bridged by carbamylated Lys217. To assess whether carbamate-specific chemistry is required for urease activity, site-directed mutagenesis and chemical rescu ...

    Klebsiella aerogenes urease possesses a dinuclear metallocenter in which two nickel atoms are bridged by carbamylated Lys217. To assess whether carbamate-specific chemistry is required for urease activity, site-directed mutagenesis and chemical rescue strategies were combined in efforts to place a carboxylate group at the location of this metal ligand. Urease variants with Lys217 replaced by Glu, Cys, and Ala (K217E, K217C/C319A, and K217A proteins) were purified, shown to be activated by incubation with small organic acids plus Ni(II), and structurally characterized. K217C/C319A urease possessed a second change in which Cys319 was replaced by Ala in order to facilitate efforts to chemically modify Cys217; however, this covalent modification approach did not produce active urease. Chemical rescue of the K217E, K217C/C319A, and K217A variants required 2, 2, and 10 h, respectively, to reach maximal activity levels. The highest activity generated [224 micromol of urea degraded.min-1.(mg of protein)-1, for K217C/C319A urease incubated with 500 mM formic acid and 10 mM Ni at pH 6.5] corresponded to 56% of that measured for in vitro activation of the wild-type apoprotein. While the K217E apoprotein showed minimal structural perturbations, the K217C/C319A apoprotein showed a disordering of some active site residues, and the K217A apoprotein revealed a repositioning of His219 to allow the formation of a hydrogen bond with Thr169, thus replacing the hydrogen bond between the amino group of Lys217 and Thr169 in the native enzyme. Importantly, these structures allow rationalization of the relative rates and yields of chemical rescue experiments. The crystal structures of chemically rescued K217A and K217C/C319A ureases revealed a return of the active site residues to their wild-type positions. In both cases, noncovalently bound formate was structurally equivalent to the Lys-carbamate as the bridging metallocenter ligand. We conclude that carbamate-specific chemistry is not required for urease catalysis.


    Related Citations: 
    • 70 Years of Crystalline Urease: What Have We Learned?
      Karplus, P.A., Pearson, M.A., Hausinger, R.P.
      (1997) Acc Chem Res 30: 330
    • The Crystal Structure of Urease from Klebsiella Aerogenes
      Jabri, E., Carr, M.B., Hausinger, R.P., Karplus, P.A.
      (1995) Science 268: 998

    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UREASE (ALPHA SUBUNIT)C566Klebsiella aerogenesMutation(s): 1 
Gene Names: UREAUREBureC
EC: 3.5.1.5
Find proteins for P18314 (Klebsiella aerogenes)
Explore P18314 
Go to UniProtKB:  P18314
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASE (GAMMA SUBUNIT)A100Klebsiella aerogenesMutation(s): 0 
Gene Names: ureAUREBUREC
EC: 3.5.1.5
Find proteins for P18316 (Klebsiella aerogenes)
Explore P18316 
Go to UniProtKB:  P18316
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UREASE (BETA SUBUNIT)B101Klebsiella aerogenesMutation(s): 0 
Gene Names: UREAureBUREC
EC: 3.5.1.5
Find proteins for P18315 (Klebsiella aerogenes)
Explore P18315 
Go to UniProtKB:  P18315
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.8α = 90
b = 170.8β = 90
c = 170.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance