4UBP

STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 110-118

  • DOI: 10.1007/s007750050014
  • Primary Citation of Related Structures:  
    4UBP

  • PubMed Abstract: 
  • The structure of Bacillus pasteurii urease inhibited with acetohydroxamic acid was solved and refined anisotropically using synchrotron X-ray cryogenic diffraction data (1.55 A resolution, 99.5% completeness, data redundancy = 26, R-factor = 15.1%, PDB code 4UBP) ...

    The structure of Bacillus pasteurii urease inhibited with acetohydroxamic acid was solved and refined anisotropically using synchrotron X-ray cryogenic diffraction data (1.55 A resolution, 99.5% completeness, data redundancy = 26, R-factor = 15.1%, PDB code 4UBP). The two Ni ions in the active site are separated by a distance of 3.53 A. The structure clearly shows the binding mode of the inhibitor anion, symmetrically bridging the two Ni ions in the active site through the hydroxamate oxygen and chelating one Ni ion through the carbonyl oxygen. The flexible flap flanking the active site cavity is in the open conformation. The possible implications of the results on structure-based molecular design of new urease inhibitors are discussed.


    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
    • 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 1.65 A 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

    EMBL c/o DESY, Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UREASE (CHAIN A))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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41022
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UREASE (CHAIN B))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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41021
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UREASE (CHAIN C))C570Sporosarcina pasteuriiMutation(s): 8 
Gene Names: ureCNCTC4822_02163
EC: 3.5.1.5
UniProt
Find proteins for P41020 (Sporosarcina pasteurii)
Explore P41020 
Go to UniProtKB:  P41020
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41020
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAE
Query on HAE

Download Ideal Coordinates CCD File 
F [auth C]ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-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
C L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
HAE Binding MOAD:  4UBP Ki: 2600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.88α = 90
b = 130.88β = 90
c = 189γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-06
    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
  • Version 1.3: 2019-11-06
    Changes: Advisory, Data collection, Database references, Derived calculations