6ZRX

Crystal structure of 6-dimethylallyltryptophan synthase from Micromonospora olivasterospora in complex with DMASPP and Trp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 

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Ligand Structure Quality Assessment 


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Literature

Reprogramming Substrate and Catalytic Promiscuity of Tryptophan Prenyltransferases.

Ostertag, E.Zheng, L.Broger, K.Stehle, T.Li, S.M.Zocher, G.

(2020) J Mol Biol 433: 166726-166726

  • DOI: https://doi.org/10.1016/j.jmb.2020.11.025
  • Primary Citation of Related Structures:  
    6ZRX, 6ZRY, 6ZRZ, 6ZS0

  • PubMed Abstract: 

    Prenylation is a process widely prevalent in primary and secondary metabolism, contributing to functionality and chemical diversity in natural systems. Due to their high regio- and chemoselectivities, prenyltransferases are also valuable tools for creation of new compounds by chemoenzymatic synthesis and synthetic biology. Over the last ten years, biochemical and structural investigations shed light on the mechanism and key residues that control the catalytic process, but to date crucial information on how certain prenyltransferases control regioselectivity and chemoselectivity is still lacking. Here, we advance a general understanding of the enzyme family by contributing the first structure of a tryptophan C5-prenyltransferase 5-DMATS. Additinally, the structure of a bacterial tryptophan C6-prenyltransferase 6-DMATS was solved. Analysis and comparison of both substrate-bound complexes led to the identification of key residues for catalysis. Next, site-directed mutagenesis was successfully implemented to not only modify the prenyl donor specificity but also to redirect the prenylation, thereby switching the regioselectivity of 6-DMATS to that of 5-DMATS. The general strategy of structure-guided protein engineering should be applicable to other related prenyltransferases, thus enabling the production of novel prenylated compounds.


  • Organizational Affiliation

    Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DMATS type aromatic prenyltransferaseA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
362Micromonospora olivasterosporaMutation(s): 0 
Gene Names: MolI14.36JD77_02062
UniProt
Find proteins for Q2MFY2 (Micromonospora olivasterospora)
Explore Q2MFY2 
Go to UniProtKB:  Q2MFY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2MFY2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6C7 (Subject of Investigation/LOI)
Query on 6C7

Download Ideal Coordinates CCD File 
E [auth AAA],
I [auth BBB],
M [auth CCC],
R [auth DDD]
S-(3-methylbut-2-en-1-yl) trihydrogen thiodiphosphate
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
TRP (Subject of Investigation/LOI)
Query on TRP

Download Ideal Coordinates CCD File 
F [auth AAA],
J [auth BBB],
N [auth CCC],
S [auth DDD]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth AAA]
H [auth AAA]
K [auth BBB]
L [auth BBB]
O [auth CCC]
G [auth AAA],
H [auth AAA],
K [auth BBB],
L [auth BBB],
O [auth CCC],
P [auth CCC],
Q [auth CCC],
U [auth DDD]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
T [auth DDD]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.021α = 90
b = 98.471β = 107.487
c = 89.185γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB -TR 261

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description