1S3T

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1S3T/pdb

• Classification: HYDROLASE
• Organism(s): Sporosarcina pasteurii
• Mutation(s): Yes 


• Deposited: 2004-01-14 Released: 2004-04-06 
• Deposition Author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism.

Benini, S., Rypniewski, W.R., Wilson, K.S., Mangani, S., Ciurli, S.

(2004) J Am Chem Soc 126: 3714-3715

• PubMed: 15038715 
• DOI: https://doi.org/10.1021/ja049618p
• Primary Citation of Related Structures:  
  1S3T


• PubMed Abstract: 
  

  The structure of the complex of urease, a Ni-containing metalloenzyme, with boric acid was determined at 2.10 A resolution. The complex shows the unprecedented binding mode of the competitive inhibitor to the dinuclear metal center, with the B(OH)3 molecule bridging the Ni ions and leaving in place the bridging hydroxide. Boric acid can be considered a substrate analogue of urea, and the structure supports the proposal that the Ni-bridging hydroxide acts as the nucleophile in the enzymatic process of urea hydrolysis.

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Organizational Affiliation: 

York Structural Biology Laboratory, University of York, York, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 87.1 kDa 
• Atom Count: 6,376 
• Modelled Residue Count: 792 
• Deposited Residue Count: 796 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease gamma subunit	A	100	Sporosarcina pasteurii	Mutation(s): 1  EC: 3.5.1.5
UniProt
Find proteins for P41022 (Sporosarcina pasteurii) Explore P41022  Go to UniProtKB:  P41022

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease beta subunit	B	126	Sporosarcina pasteurii	Mutation(s): 0  EC: 3.5.1.5
UniProt
Find proteins for P41021 (Sporosarcina pasteurii) Explore P41021  Go to UniProtKB:  P41021

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease alpha subunit	C	570	Sporosarcina pasteurii	Mutation(s): 1  EC: 3.5.1.5
UniProt
Find proteins for P41020 (Sporosarcina pasteurii) Explore P41020  Go to UniProtKB:  P41020

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BO3	G [auth C]	BORIC ACID B H3 O3 KGBXLFKZBHKPEV-UHFFFAOYSA-N
NI	D [auth C], E [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM	A	L-PEPTIDE LINKING	C6 H11 N O4 S		MET
KCX	C	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.906	α = 90
b = 130.906	β = 90
c = 189.366	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-06 
Deposition Author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

Revision History  

• Version 1.0: 2004-04-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2015-07-08
  Changes: Source and taxonomy
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection