6QSU

Helicobacter pylori urease with BME bound in the active site

  • Classification: HYDROLASE
  • Organism(s): Helicobacter pylori
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-02-22 Released: 2021-01-20 
  • Deposition Author(s): Luecke, H., Cunha, E.
  • Funding Organization(s): Research Council of Norway, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 angstrom resolution.

Cunha, E.S.Chen, X.Sanz-Gaitero, M.Mills, D.J.Luecke, H.

(2021) Nat Commun 12: 230-230

  • DOI: https://doi.org/10.1038/s41467-020-20485-6
  • Primary Citation of Related Structures:  
    6QSU, 6ZJA

  • PubMed Abstract: 

    Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 Å resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.5 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.


  • Organizational Affiliation

    Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318, Oslo, Norway. cunha@uio.no.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit alpha238Helicobacter pyloriMutation(s): 0 
Gene Names: ureABGL58_00110D2C78_00705DD749_00755
EC: 3.5.1.5
UniProt
Find proteins for P14916 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P14916 
Go to UniProtKB:  P14916
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14916
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Urease subunit beta569Helicobacter pyloriMutation(s): 0 
Gene Names: 
EC: 3.5.1.5
UniProt
Find proteins for P69996 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P69996 
Go to UniProtKB:  P69996
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69996
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download Ideal Coordinates CCD File 
AA [auth B]
BB [auth T]
DA [auth J]
EB [auth V]
GA [auth D]
AA [auth B],
BB [auth T],
DA [auth J],
EB [auth V],
GA [auth D],
HB [auth X],
JA [auth F],
MA [auth H],
PA [auth L],
SA [auth N],
VA [auth P],
YA [auth R]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
AB [auth T]
BA [auth J]
CA [auth J]
CB [auth V]
DB [auth V]
AB [auth T],
BA [auth J],
CA [auth J],
CB [auth V],
DB [auth V],
EA [auth D],
FA [auth D],
FB [auth X],
GB [auth X],
HA [auth F],
IA [auth F],
KA [auth H],
LA [auth H],
NA [auth L],
OA [auth L],
QA [auth N],
RA [auth N],
TA [auth P],
UA [auth P],
WA [auth R],
XA [auth R],
Y [auth B],
Z [auth B],
ZA [auth T]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
B
N [auth J]
O [auth D]
P [auth F]
Q [auth H]
B,
N [auth J],
O [auth D],
P [auth F],
Q [auth H],
R [auth L],
S [auth N],
T [auth P],
U [auth R],
V [auth T],
W [auth V],
X
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0 beta
MODEL REFINEMENTPHENIX1.13

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway--
Research Council of NorwayNorway275207
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI78000

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references