6YL3 image
Entry Detail
PDB ID:
6YL3
EMDB ID:
Title:
High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica
Biological Source:
PDB Version:
Deposition Date:
2020-04-06
Release Date:
2020-05-06
Method Details:
Experimental Method:
Resolution:
1.98 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Urease subunit gamma
Chain IDs:A, D, G, J, M, P, S, V (auth: W), Y (auth: Z), BA (auth: 2), EA (auth: 5), HA (auth: 8)
Chain Length:100
Number of Molecules:12
Biological Source:Yersinia enterocolitica W22703
Polymer Type:polypeptide(L)
Description:Urease subunit beta
Chain IDs:B, E, H, K, N, Q, T, W (auth: X), Z (auth: 0), CA (auth: 3), FA (auth: 6), IA (auth: 9)
Chain Length:132
Number of Molecules:12
Biological Source:Yersinia enterocolitica W22703
Polymer Type:polypeptide(L)
Description:Urease subunit alpha
Chain IDs:C, F, I, L, O, R, U (auth: V), X (auth: Y), AA (auth: 1), DA (auth: 4), GA (auth: 7), JA (auth: U)
Chain Length:571
Number of Molecules:12
Biological Source:Yersinia enterocolitica W22703
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX C LYS modified residue
Ligand Molecules
Primary Citation
High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica.
Nat Commun 11 5101 5101 (2020)
PMID: 33037208 DOI: 10.1038/s41467-020-18870-2

Abstact

Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. The obtained structure is of sufficient quality to support drug development efforts.

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Primary Citation of related structures