6YL3 image
Deposition Date 2020-04-06
Release Date 2020-05-06
Last Version Date 2025-04-09
Entry Detail
PDB ID:
6YL3
Title:
High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.98 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Urease subunit gamma
Gene (Uniprot):ureA
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Urease subunit beta
Gene (Uniprot):ureB
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Urease subunit alpha
Gene (Uniprot):ureC
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
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