1S3T

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism.

Benini, S.Rypniewski, W.R.Wilson, K.S.Mangani, S.Ciurli, S.

(2004) J.Am.Chem.Soc. 126: 3714-3715

  • DOI: 10.1021/ja049618p
  • Also Cited By: 4CEX, 4CEU, 4AC7

  • PubMed Abstract: 
  • The structure of the complex of urease, a Ni-containing metalloenzyme, with boric acid was determined at 2.10 A resolution. The complex shows the unprecedented binding mode of the competitive inhibitor to the dinuclear metal center, with the B(OH)3 m ...

    The structure of the complex of urease, a Ni-containing metalloenzyme, with boric acid was determined at 2.10 A resolution. The complex shows the unprecedented binding mode of the competitive inhibitor to the dinuclear metal center, with the B(OH)3 molecule bridging the Ni ions and leaving in place the bridging hydroxide. Boric acid can be considered a substrate analogue of urea, and the structure supports the proposal that the Ni-bridging hydroxide acts as the nucleophile in the enzymatic process of urea hydrolysis.


    Related Citations: 
    • A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme from Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Miletti, S.,Ciurli, S.,Mangani, S.
      (1999) Structure 7: 205
    • Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Ciurli, S.,Mangani, S.
      (2001) J.Biol.Inorg.Chem. 6: 778
    • Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and Beta-Mercaptoethanol-Inhibited Urease from Bacillus Pasteurii
      Benini, S.,Ciurli, S.,Rypniewski, W.R.,Wilson, K.S.,Mangani, S.
      (1998) Acta Crystallogr.,Sect.D 54: 409
    • The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65 A Resolution
      Benini, S.,Ciurli, S.,Rypniewski, W.R.,Wilson, K.S.,Mangani, S.
      (1998) J.Biol.Inorg.Chem. 3: 268
    • The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 A Resolution
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Miletti, S.,Ciurli, S.,Mangani, S.
      (2000) J.Biol.Inorg.Chem. 5: 110


    Organizational Affiliation

    York Structural Biology Laboratory, University of York, York, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urease gamma subunit
A
100Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureA
EC: 3.5.1.5
Find proteins for P41022 (Sporosarcina pasteurii)
Go to UniProtKB:  P41022
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Urease beta subunit
B
126Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
Find proteins for P41021 (Sporosarcina pasteurii)
Go to UniProtKB:  P41021
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Urease alpha subunit
C
570Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureC
EC: 3.5.1.5
Find proteins for P41020 (Sporosarcina pasteurii)
Go to UniProtKB:  P41020
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BO3
Query on BO3

Download SDF File 
Download CCD File 
C
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A
L-PEPTIDE LINKINGC6 H11 N O4 SMET
KCX
Query on KCX
C
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 130.906α = 90.00
b = 130.906β = 90.00
c = 189.366γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2015-07-08
    Type: Source and taxonomy