8UZW

Selenocysteine synthase- SelA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bacterial selenocysteine synthase structure revealed by single-particle cryoEM.

Balasco Serrao, V.H.Minari, K.Pereira, H.D.Thiemann, O.H.

(2024) Curr Res Struct Biol 7: 100143-100143

  • DOI: https://doi.org/10.1016/j.crstbi.2024.100143
  • Primary Citation of Related Structures:  
    8UZW

  • PubMed Abstract: 

    The 21st amino acid, selenocysteine (Sec), is synthesized on its dedicated transfer RNA (tRNA Sec ). In bacteria, Sec is synthesized from Ser-tRNA [Ser]Sec by Selenocysteine Synthase (SelA), which is a pivotal enzyme in the biosynthesis of Sec. The structural characterization of bacterial SelA is of paramount importance to decipher its catalytic mechanism and its role in the regulation of the Sec-synthesis pathway. Here, we present a comprehensive single-particle cryo-electron microscopy (SPA cryoEM) structure of the bacterial SelA with an overall resolution of 2.69 Å. Using recombinant Escherichia coli SelA, we purified and prepared samples for single-particle cryoEM. The structural insights from SelA, combined with previous in vivo and in vitro knowledge, underscore the indispensable role of decamerization in SelA's function. Moreover, our structural analysis corroborates previous results that show that SelA adopts a pentamer of dimers configuration, and the active site architecture, substrate binding pocket, and key K295 catalytic residue are identified and described in detail. The differences in protein architecture and substrate coordination between the bacterial enzyme and its counterparts offer compelling structural evidence supporting the independent molecular evolution of the bacterial and archaea/eukarya Ser-Sec biosynthesis present in the natural world.


  • Organizational Affiliation

    Biomolecular Cryoelectron Microscopy Facility, University of California - Santa Cruz, Santa Cruz, CA, 95064, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-seryl-tRNA(Sec) selenium transferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
463Escherichia coli K-12Mutation(s): 0 
Gene Names: selAfdhAb3591JW3564
EC: 2.9.1.1
UniProt
Find proteins for P0A821 (Escherichia coli (strain K12))
Explore P0A821 
Go to UniProtKB:  P0A821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A821
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil12/23730-1
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesU24GM129547
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10OD02509
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil232251/2014-2
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil140636/2013-7

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references, Experimental preparation
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2024-06-26
    Changes: Data collection, Database references