6FD2

Radical SAM 1,2-diol dehydratase AprD4 in complex with its substrate paromamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

1,2-Diol Dehydration by the Radical SAM Enzyme AprD4: A Matter of Proton Circulation and Substrate Flexibility.

Liu, W.Q.Amara, P.Mouesca, J.M.Ji, X.Renoux, O.Martin, L.Zhang, C.Zhang, Q.Nicolet, Y.

(2018) J Am Chem Soc 140: 1365-1371

  • DOI: https://doi.org/10.1021/jacs.7b10501
  • Primary Citation of Related Structures:  
    6FD2

  • PubMed Abstract: 

    Regiospecific dehydration of vicinal diols by enzymes is a difficult reaction that usually requires activation by dedicated organic cofactors. The enzymatic use of radical-based chemistry is an effective but challenging alternative as radical intermediates are difficult to control. Here we report the X-ray structure of the radical S-adenosyl-l-methionine (SAM) dehydratase AprD4 involved in the biosynthesis of the aminoglycoside (AG) antibiotic apramycin. Using in vitro characterizations and theoretical calculations based on our crystal structure, we have been able to propose a detailed mechanism of AprD4 catalysis, which involves a complex partially substrate-induced proton relay network in the enzyme active site and highlights the key role of the protein matrix in driving high-energy intermediates.


  • Organizational Affiliation

    Department of Chemistry, Fudan University , Shanghai 200433, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative apramycin biosynthetic oxidoreductase 4A [auth B],
B [auth A]
457Streptoalloteichus tenebrariusMutation(s): 0 
Gene Names: aprD4
UniProt
Find proteins for Q2MFI7 (Streptoalloteichus tenebrarius (strain ATCC 17920 / DSM 40477 / JCM 4838 / CBS 697.72 / NBRC 16177 / NCIMB 11028 / NRRL B-12390 / A12253. 1 / ISP 5477))
Explore Q2MFI7 
Go to UniProtKB:  Q2MFI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2MFI7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth B],
H [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
D5E
Query on D5E

Download Ideal Coordinates CCD File 
C [auth B],
G [auth A]
paromamine
C12 H25 N3 O7
JGSMDVGTXBPWIM-HKEUSBCWSA-N
5AD
Query on 5AD

Download Ideal Coordinates CCD File 
F [auth B],
J [auth A]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
MET
Query on MET

Download Ideal Coordinates CCD File 
E [auth B],
I [auth A]
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.82α = 90
b = 121.82β = 90
c = 233.78γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Key Research and Development ProgramChina2016 Y F A0501302
National Natural Science Foundation of ChinaChina1500028
National Natural Science Foundation of ChinaChina31670060
French National Research AgencyFranceANR-10-INSB-05-02
French National Research AgencyFranceANR-10-LABX-49-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description