3UBP

DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 205-216

  • DOI: 10.1016/S0969-2126(99)80026-4
  • Primary Citation of Related Structures:  
    2UBP, 3UBP

  • PubMed Abstract: 
  • Urease catalyzes the hydrolysis of urea, the final step of organic nitrogen mineralization, using a bimetallic nickel centre. The role of the active site metal ions and amino acid residues has not been elucidated to date. Many pathologies are associated with the activity of ureolytic bacteria, and the efficiency of soil nitrogen fertilization with urea is severely decreased by urease activity ...

    Urease catalyzes the hydrolysis of urea, the final step of organic nitrogen mineralization, using a bimetallic nickel centre. The role of the active site metal ions and amino acid residues has not been elucidated to date. Many pathologies are associated with the activity of ureolytic bacteria, and the efficiency of soil nitrogen fertilization with urea is severely decreased by urease activity. Therefore, the development of urease inhibitors would lead to a reduction of environmental pollution, to enhanced efficiency of nitrogen uptake by plants, and to improved therapeutic strategies for treatment of infections due to ureolytic bacteria. Structure-based design of urease inhibitors would require knowledge of the enzyme mechanism at the molecular level.


    Related Citations: 
    • 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
    • The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65A Resolution
      Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.
      (1998) J Biol Inorg Chem 3: 268
    • Bacillus Pasteurii Urease: A Heteropolimeric Enzyme with a Binuclear Nickel Active Site
      Benini, S., Gessa, C., Ciurli, S.
      (1996) Soil Biol Biochem 28: 819
    • X-Ray Absorption Spectroscopy Study of Native and Phenylphosphorodiamidate- Inhibited Bacillus Pasteurii Urease
      Benini, S., Ciurli, S., Nolting, H.F., Mangani, S.
      (1996) Eur J Biochem 239: 61

    Organizational Affiliation

    European Molecular Biology Laboratory, DESY, Notkestrasse 85 D-22603, Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UREASE GAMMA SUBUNIT)A101Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureA
EC: 3.5.1.5
UniProt
Find proteins for P41022 (Sporosarcina pasteurii)
Explore P41022 
Go to UniProtKB:  P41022
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UREASE BETA SUBUNIT)B126Sporosarcina pasteuriiMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
UniProt
Find proteins for P41021 (Sporosarcina pasteurii)
Explore P41021 
Go to UniProtKB:  P41021
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UREASE ALPHA SUBUNIT)C570Sporosarcina pasteuriiMutation(s): 7 
Gene Names: ureC
EC: 3.5.1.5
UniProt
Find proteins for P41020 (Sporosarcina pasteurii)
Explore P41020 
Go to UniProtKB:  P41020
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PA
Query on 2PA

Download Ideal Coordinates CCD File 
F [auth C]DIAMIDOPHOSPHATE
H5 N2 O2 P
ANCLJVISBRWUTR-UHFFFAOYSA-N
 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  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 Free: 0.200 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.532α = 90
b = 131.532β = 90
c = 188.451γ = 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: 1999-12-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance