8UXU

Cryo-EM structure of a bacterial nitrilase filament with a covalent adduct derived from benzonitrile hydrolysis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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Literature

Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis.

Aguirre-Sampieri, S.Casanal, A.Emsley, P.Garza-Ramos, G.

(2024) J Struct Biol 216: 108093-108093

  • DOI: https://doi.org/10.1016/j.jsb.2024.108093
  • Primary Citation of Related Structures:  
    8UXU

  • PubMed Abstract: 

    Many enzymes can self-assemble into higher-order structures with helical symmetry. A particularly noteworthy example is that of nitrilases, enzymes in which oligomerization of dimers into spiral homo-oligomers is a requirement for their enzymatic function. Nitrilases are widespread in nature where they catalyze the hydrolysis of nitriles into the corresponding carboxylic acid and ammonia. Here, we present the Cryo-EM structure, at 3 Å resolution, of a C-terminal truncate nitrilase from Rhodococcus sp. V51B that assembles in helical filaments. The model comprises a complete turn of the helical arrangement with a substrate-intermediate bound to the catalytic cysteine. The structure was solved having added the substrate to the protein. The length and stability of filaments was made more substantial in the presence of the aromatic substrate, benzonitrile, but not for aliphatic nitriles or dinitriles. The overall structure maintains the topology of the nitrilase family, and the filament is formed by the association of dimers in a chain-like mechanism that stabilizes the spiral. The active site is completely buried inside each monomer, while the substrate binding pocket was observed within the oligomerization interfaces. The present structure is in a closed configuration, judging by the position of the lid, suggesting that the intermediate is one of the covalent adducts. The proximity of the active site to the dimerization and oligomerization interfaces, allows the dimer to sense structural changes once the benzonitrile was bound, and translated to the rest of the filament, stabilizing the helical structure.


  • Organizational Affiliation

    Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrilase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
327Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 0 
UniProt
Find proteins for A4LA85 (Rhodococcus rhodochrous)
Explore A4LA85 
Go to UniProtKB:  A4LA85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4LA85
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HBX
Query on HBX

Download Ideal Coordinates CCD File 
AA [auth M]
BA [auth N]
O [auth A]
P [auth B]
Q [auth C]
AA [auth M],
BA [auth N],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
benzaldehyde
C7 H6 O
HUMNYLRZRPPJDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONRELION3.0.8

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentMexicoDGAPA-PAPIIT UNAM IN218318

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release