6MW2 | pdb_00006mw2

cyclo-Mle-Phe-Mle-D-Phe. D-Phe analogue of pseudoxylallemycin A.

• PDB DOI: https://doi.org/10.2210/pdb6MW2/pdb

• Classification: ANTIBIOTIC
• Organism(s): Xylaria
• Mutation(s): No 


• Deposited: 2018-10-29 Released: 2019-09-11 
• Deposition Author(s): Cameron, A.J., Harris, P.W.R., Brimble, M.A., Squire, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.77 Å
• R-Value Work: 
  0.042 (Depositor), 0.072 (DCC) 

Literature

Investigations of the key macrolactamisation step in the synthesis of cyclic tetrapeptide pseudoxylallemycin A.

Cameron, A.J., Squire, C.J., Gerenton, A., Stubbing, L.A., Harris, P.W.R., Brimble, M.A.

(2019) Org Biomol Chem 17: 3902-3913

• PubMed: 30941386 
• DOI: https://doi.org/10.1039/c9ob00227h
• Primary Citation Related Structures: 
  6MVZ, 6MW0, 6MW1, 6MW2


• PubMed Abstract: 
  

  The total synthesis and structural confirmation of naturally occurring all l-cyclic tetrapeptide pseudoxylallemycin A is reported. X-ray crystallography revealed that the linear precursor adopted an all-trans (ttt) extended linear conformation, while its cyclic derivative adopts a trans,cis,trans,cis (tctc) conformation. Two kinetically favoured cyclic conformers prone to hydrolysis initially formed rapidly during cyclisation, with subsequent conversion to the thermodynamically stable tctc macrocycle taking place slowly. We postulate the initial unstable cyclic product undergoes an unprecedented nucleophilic ring opening with either the T3P or PyAOP by-products to give the linear ttt structure as a reactivated species and through a series of equilibria is slowly consumed by cyclisation to the thermodynamic product pseudoxylallemycin A. Consumption of the reactivated species by formation of pseudoxylallemycin A requires a trans-cis isomerism to occur and necessitates moderately increased reaction temperatures. Cyclisation with T3P was found to provide the greatest stereoretention. Synthesis and X-ray crystallography of the C-terminal epimer demonstrated its cyclisation to be kinetically favoured and to proceed without epimerisation despite also bearing an all-trans backbone.

---

Organizational Affiliation: 
• School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1010, New Zealand. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 0.57 kDa 
• Atom Count: 40 
• Modeled Residue Count: 4 
• Deposited Residue Count: 4 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pseudoxylallemycin A	A	4	Xylaria	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPN	A	D-PEPTIDE LINKING	C9 H11 N O2		--
MLE	A	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002368	A	cyclo-Mle-Phe-Mle-D-Phe. D-Phe analogue of pseudoxylallemycin A	Cyclic peptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.77 Å
• R-Value Work:  0.042 (Depositor), 0.072 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 10.928	α = 90
b = 13.552	β = 90
c = 20.488	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
XDS	data reduction
Aimless	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Cameron, A.J., Harris, P.W.R., Brimble, M.A., Squire, C.J.

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary