5G4H | pdb_00005g4h

1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporosarcina pasteurii urease

• PDB DOI: https://doi.org/10.2210/pdb5G4H/pdb

• Classification: HYDROLASE
• Organism(s): Sporosarcina pasteurii
• Mutation(s): No 


• Deposited: 2016-05-13 Released: 2016-12-07 
• Deposition Author(s): Mazzei, L., Cianci, M., Musiani, F., Ciurli, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.154 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

Literature

Inactivation of Urease by Catechol: Kinetics and Structure.

Mazzei, L., Cianci, M., Musiani, F., Lente, G., Palombo, M., Ciurli, S.

(2016) J Inorg Biochem 166: 182

• PubMed: 27888701 
• DOI: https://doi.org/10.1016/j.jinorgbio.2016.11.016
• Primary Citation Related Structures: 
  5G4H


• PubMed Abstract: 
  

  Urease is a Ni(II)-containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbamate at a rate 10 ¹⁵ times higher than the uncatalyzed reaction. Urease is a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Therefore, efficient urease inhibitors are actively sought. In this study, we describe a molecular characterization of the interaction between urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) with catechol, a model polyphenol. In particular, catechol irreversibly inactivates both SPU and JBU with a complex radical-based autocatalytic multistep mechanism. The crystal structure of the SPU-catechol complex, determined at 1.50Å resolution, reveals the structural details of the enzyme inhibition.

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Organizational Affiliation: 
• Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy.
European Molecular Biology Laboratory, DESY, Hamburg, Germany.
Department of Inorganic and Analytical Chemistry, University of Debrecen, Hungary.
Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy. Electronic address: [e-mail].

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 (software)

Macromolecule Content 

• Total Structure Weight: 88.44 kDa 
• Atom Count: 7,020 
• Modeled Residue Count: 792 
• Deposited Residue Count: 796 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UREASE SUBUNIT GAMMA	A	100	Sporosarcina pasteurii	Mutation(s): 0  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 SUBUNIT BETA	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 SUBUNIT ALPHA	C	570	Sporosarcina pasteurii	Mutation(s): 0  EC: 3.5.1.5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAQ	L [auth C]	CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N
SO4	BA [auth C], D [auth A], G [auth B], I [auth B], M [auth C], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AA [auth C], E [auth A], F [auth A], H [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	J [auth C], K [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
OH	N [auth C]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M

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: 1.50 Å
• R-Value Free:  0.154 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.276	α = 90
b = 131.276	β = 90
c = 189.017	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Mazzei, L., Cianci, M., Musiani, F., Ciurli, S.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description