5YGK

Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.

Malwal, S.R.Gao, J.Hu, X.Yang, Y.Liu, W.Huang, J.W.Ko, T.P.Li, L.Chen, C.C.O'Dowd, B.Khade, R.L.Zhang, Y.Zhang, Y.Oldfield, E.Guo, R.T.

(2018) ACS Catal 8: 4299-4312

  • DOI: 10.1021/acscatal.8b00543
  • Primary Citation of Related Structures:  
    5YGK, 5YGJ

  • PubMed Abstract: 
  • We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl ...

    We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl ( S )-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other ζ-fold ( cis - head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg 2+ in the so-called S1 site (which is typically the allylic binding site in ζ-fold proteins) while the second diphosphate binds to Mg 2+ in the so-called S2 site (which is typically the homoallylic binding site in ζ-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H + , which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in ζ-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many "head-to-head" prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H + elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg 2+ can act as a general (imine-like) base, while Gln, Tyr and H 2 O form a proton channel that is adjacent to the conventional (Asp-rich) "active site". Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H 2 O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg 2+ , and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis.


    Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclolavandulyl diphosphate synthaseA, B, C, D, E, F, G, H217Streptomyces sp. CL190Mutation(s): 0 
Find proteins for X5IYJ5 (Streptomyces sp. (strain CL190))
Explore X5IYJ5 
Go to UniProtKB:  X5IYJ5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DST
Query on DST

Download CCD File 
A, B, C, D, E, F, G, H
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.09α = 90
b = 119.308β = 117.35
c = 93.133γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 2.0: 2019-10-16
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-25
    Changes: Database references