1FWG

KLEBSIELLA AEROGENES UREASE, C319S VARIANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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
  • Structures With Same Primary Citation

  • 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 activity (C319Y), indicating Cys is not required at this position, but its presence is highly influential [Martin, P ...

    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: 
    • Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants
      Jabri, E., Karplus, P.A.
      (1996) Biochemistry 35: 10616
    • 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 the Active Site Cysteine in Klebsiella Aerogenes Urease
      Martin, P.R., Hausinger, R.P.
      (1992) J Biol Chem 267: 20024
    • Identification of the Essential Cysteine Residue in Klebsiella Aerogenes Urease
      Todd, M.J., Hausinger, R.P.
      (1991) J Biol Chem 266: 24327

    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UREASEA100Klebsiella aerogenesMutation(s): 0 
Gene Names: ureA
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
UREASEB106Klebsiella aerogenesMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
Find proteins for P18315 (Klebsiella aerogenes)
Explore P18315 
Go to UniProtKB:  P18315
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UREASEC567Klebsiella aerogenesMutation(s): 2 
Gene Names: ureC
EC: 3.5.1.5
Find proteins for P18314 (Klebsiella aerogenes)
Explore P18314 
Go to UniProtKB:  P18314
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
CL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • 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
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    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