7VOC | pdb_00007voc

The crystal structure of a Radical SAM Enzyme BlsE involved in the Biosynthesis of Blasticidin S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Radical S -Adenosyl Methionine Enzyme BlsE Catalyzes a Radical-Mediated 1,2-Diol Dehydration during the Biosynthesis of Blasticidin S.

Lee, Y.H.Hou, X.Chen, R.Feng, J.Liu, X.Ruszczycky, M.W.Gao, J.M.Wang, B.Zhou, J.Liu, H.W.

(2022) J Am Chem Soc 144: 4478-4486

  • DOI: https://doi.org/10.1021/jacs.1c12010
  • Primary Citation Related Structures: 
    7VOB, 7VOC

  • PubMed Abstract: 

    The biosynthesis of blasticidin S has drawn attention due to the participation of the radical S -adenosyl methionine (SAM) enzyme BlsE. The original assignment of BlsE as a radical-mediated, redox-neutral decarboxylase is unusual because this reaction appears to serve no biosynthetic purpose and would need to be reversed by a subsequent carboxylation step. Furthermore, with the exception of BlsE, all other radical SAM decarboxylases reported to date are oxidative in nature. Careful analysis of the BlsE reaction, however, demonstrates that BlsE is not a decarboxylase but instead a lyase that catalyzes the dehydration of cytosylglucuronic acid (CGA) to form cytosyl-4'-keto-3'-deoxy-d-glucuronic acid, which can rapidly decarboxylate nonenzymatically in vitro . Analysis of substrate isotopologs, fluorinated analogues, as well as computational models based on X-ray crystal structures of the BlsE·SAM (2.09 Å) and BlsE·SAM·CGA (2.62 Å) complexes suggests that BlsE catalysis likely proceeds via direct elimination of water from the CGA C4' α-hydroxyalkyl radical as opposed to 1,2-migration of the C3'-hydroxyl prior to dehydration. Biosynthetic and mechanistic implications of the revised assignment of BlsE are discussed.


  • Organizational Affiliation
    • Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.

Macromolecule Content 

  • Total Structure Weight: 41.81 kDa 
  • Atom Count: 2,633 
  • Modeled Residue Count: 327 
  • Deposited Residue Count: 364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytosylglucuronate decarboxylaseA [auth C]364Streptomyces griseochromogenesMutation(s): 0 
Gene Names: AVL59_19980
UniProt
Find proteins for A0A1B1AYF2 (Streptomyces griseochromogenes)
Explore A0A1B1AYF2 
Go to UniProtKB:  A0A1B1AYF2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B1AYF2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM

Query on SAM



Download:Ideal Coordinates CCD File
D [auth C]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
B [auth C],
C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
7QO

Query on 7QO



Download:Ideal Coordinates CCD File
E [auth C](2~{S},3~{S},4~{S},5~{R},6~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid
C10 H13 N3 O7
CHKIQPXDGYGCHW-YOWKYNACSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.92α = 90
b = 163.92β = 90
c = 158.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description