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 
  • R-Value Observed: 0.190 

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
  • Primary Citation of Related Structures:  
    1IE7

  • 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 6UBP) ...

    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 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
    • 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 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 D Biol Crystallogr 54: 409

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UREASE GAMMA SUBUNITA100Sporosarcina pasteuriiMutation(s): 1 
Gene Names: ureA
EC: 3.5.1.5
Find proteins for P41022 (Sporosarcina pasteurii)
Explore P41022 
Go to UniProtKB:  P41022
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UREASE BETA SUBUNITB126Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
Find proteins for P41021 (Sporosarcina pasteurii)
Explore P41021 
Go to UniProtKB:  P41021
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UREASE ALPHA SUBUNITC570Sporosarcina pasteuriiMutation(s): 1 
Gene Names: ureC
EC: 3.5.1.5
Find proteins for P41020 (Sporosarcina pasteurii)
Explore P41020 
Go to UniProtKB:  P41020
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth C], E [auth C]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
AL-PEPTIDE LINKINGC6 H11 N O4 SMET
KCX
Query on KCX
CL-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 
  • R-Value Observed: 0.190 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.489α = 90
b = 131.489β = 90
c = 189.489γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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