5G4H

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.154
R-Value Work: 0.121
R-Value Observed: 0.123

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.jinorgbio.2016.11.016
Primary Citation of 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.

Organizational Affiliation

Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41022
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41021
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAQ Query on CAQ Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	CATECHOL C₆ H₆ O₂ YCIMNLLNPGFGHC-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth C]	BA [auth C] D [auth A] G [auth B] I [auth B] M [auth C] 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		Interactions Focus chain BA [auth C] Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth C] Interactions & Density Focus chain BA [auth C] Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] E [auth A] F [auth A] H [auth B] P [auth C] 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		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	J [auth C], K [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain J [auth C] Focus chain K [auth C]
OH Query on OH Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM Query on CXM	A	L-PEPTIDE LINKING	C₆ H₁₁ N O₄ S		MET
KCX Query on 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
R-Value Work: 0.121
R-Value Observed: 0.123
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Revision History (Full details and data files)

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