3UBP

DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 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 Fold.Des. 7: 205-216

  • DOI: 10.1016/S0969-2126(99)80026-4
  • Primary Citation of Related Structures:  2UBP
  • Also Cited By: 4AC7, 4CEU, 4CEX

  • 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 associa ...

    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: 
    • 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
    • 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
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (UREASE GAMMA SUBUNIT)
A
101Sporosarcina pasteuriiGene Names: ureA
EC: 3.5.1.5
Find proteins for P41022 (Sporosarcina pasteurii)
Go to UniProtKB:  P41022
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (UREASE BETA SUBUNIT)
B
126Sporosarcina pasteuriiGene Names: ureB
EC: 3.5.1.5
Find proteins for P41021 (Sporosarcina pasteurii)
Go to UniProtKB:  P41021
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (UREASE ALPHA SUBUNIT)
C
570Sporosarcina pasteuriiGene 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
NI
Query on NI

Download SDF File 
Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
2PA
Query on 2PA

Download SDF File 
Download CCD File 
C
DIAMIDOPHOSPHATE
H5 N2 O2 P
ANCLJVISBRWUTR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
C
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.532α = 90.00
b = 131.532β = 90.00
c = 188.451γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance