4NAG | pdb_00004nag

Xanthomonins I III are a New Class of Lasso Peptides Featuringa Seven-Membered Macrolactam Ring

• PDB DOI: https://doi.org/10.2210/pdb4NAG/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Xanthomonas hortorum ATCC 19865
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-22 Released: 2014-04-30 
• Deposition Author(s): Hegemann, J.D., Zimmermann, M., Zhu, S., Steuber, H., Harms, K., Xie, X., Marahiel, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.81 Å
• R-Value Work: 
  0.080 (DCC) 

Literature

Xanthomonins I-III: A New Class of Lasso Peptides with a Seven-Residue Macrolactam Ring.

Hegemann, J.D., Zimmermann, M., Zhu, S., Steuber, H., Harms, K., Xie, X., Marahiel, M.A.

(2014) Angew Chem Int Ed Engl 53: 2230-2234

• PubMed: 24446383 
• DOI: https://doi.org/10.1002/anie.201309267
• Primary Citation Related Structures: 
  4NAG


• PubMed Abstract: 
  

  Lasso peptides belong to the class of ribosomally synthesized and post-translationally modified peptides. Their common distinguishing feature is an N-terminal macrolactam ring that is threaded by the C-terminal tail. This lasso fold is maintained through steric interactions. The isolation and characterization of xanthomonins I-III, the first lasso peptides featuring macrolactam rings consisting of only seven amino acids, is now presented. The crystal structure of xanthomonin I and the NMR structure of xanthomonin II were also determined. A total of 25 variants of xanthomonin II were generated to probe different aspects of the biosynthesis, stability, and fold maintenance. These mutational studies reveal the limits such a small ring imposes on the threading and show that every plug amino acid larger than serine is able to maintain a heat-stable lasso fold in the xanthomonin II scaffold.

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Organizational Affiliation: 
• Fachbereich Chemie, Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische, Mikrobiologie, Philipps-Universität Marburg, Meerwein-Strasse 4, 35032 Marburg (Germany).

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.06 kDa 
• Atom Count: 253 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthomonin I	A, B	16	Xanthomonas hortorum ATCC 19865	Mutation(s): 0  Gene Names: XGA_4058

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	C [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.81 Å
• R-Value Work:  0.080 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 13.804	α = 90
b = 45.096	β = 91.42
c = 13.89	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Hegemann, J.D., Zimmermann, M., Zhu, S., Steuber, H., Harms, K., Xie, X., Marahiel, M.A.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary