1IE7

PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 778-790

  • DOI: 10.1007/s007750100254
  • Also Cited By: 4CEX, 4CEU, 4AC7

  • PubMed Abstract: 
  • The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate was solved and refined using synchrotron X-ray diffraction data from a vitrified crystal (1.85 A resolution, 99.3% completeness, data redundancy 4.6, R-factor 17.3%, PDB code 6 ...

    The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate was solved and refined using synchrotron X-ray diffraction data from a vitrified crystal (1.85 A resolution, 99.3% completeness, data redundancy 4.6, R-factor 17.3%, PDB code 6UBP). A distance of 3.5 A separates the two Ni ions in the active site. The binding mode of the inhibitor involves the formation of four coordination bonds with the two Ni ions: one phosphate oxygen atom symmetrically bridges the two metal ions (1.9-2.0 A), while two of the remaining phosphate oxygen atoms bind to the Ni atoms at 2.4 A. The fourth phosphate oxygen is directed into the active site channel. Analysis of the H-bonding network around the bound inhibitor indicates that phosphate is bound as the H2PO4- anion, and that an additional proton is present on the Odelta2 atom of Asp(alpha363), an active site residue involved in Ni coordination through Odelta1. The flexible flap flanking the active site cavity is in the open conformation. Analysis of the complex reveals why phosphate is a relatively weak inhibitor and why sulfate does not bind to the nickels in the active site. The implications of the results for the understanding of the urease catalytic mechanism are reviewed. A novel alternative for the proton donor is presented.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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

    EMBL, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.489α = 90.00
b = 131.489β = 90.00
c = 189.489γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance