8ITG | pdb_00008itg

Crystal structure of lasso peptide epimerase MslH in complexed with precursor peptide variant MslAW21G

• PDB DOI: https://doi.org/10.2210/pdb8ITG/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces griseorubiginosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-22 Released: 2023-06-21 
• Deposition Author(s): Nakashima, Y., Hiroyuki, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism.

Nakashima, Y., Kawakami, A., Ogasawara, Y., Maeki, M., Tokeshi, M., Dairi, T., Morita, H.

(2023) Nat Commun 14: 4752-4752

• PubMed: 37550286 
• DOI: https://doi.org/10.1038/s41467-023-40232-x
• Primary Citation Related Structures: 
  8GQ9, 8GQA, 8GQB, 8ITG, 8ITH


• PubMed Abstract: 
  

  The lasso peptide MS-271 is a ribosomally synthesized and post-translationally modified peptide (RiPP) consisting of 21 amino acids with D-tryptophan at the C-terminus, and is derived from the precursor peptide MslA. MslH, encoded in the MS-271 biosynthetic gene cluster (msl), catalyzes the epimerization at the Cα center of the MslA C-terminal Trp21, leading to epi-MslA. The detailed catalytic process, including the catalytic site and cofactors, has remained enigmatic. Herein, based on X-ray crystallographic studies in association with MslA core peptide analogues, we show that MslH is a metallo-dependent peptide epimerase with a calcineurin-like fold. The crystal structure analysis, followed by site-directed mutagenesis, docking simulation, and ICP-MS studies demonstrate that MslH employs acid/base chemistry to facilitate the reversible epimerization of the C-terminal Trp21 of MslA, by utilizing two pairs of His/Asp catalytic residues that are electrostatically tethered to a six-coordination motif with a Ca(II) ion via water molecules.

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Organizational Affiliation: 
• Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan.
Graduate School of Chemical Sciences and Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan. [e-mail].
Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A8B8 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A8B1C1D1E1F1G1H1I1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.92 kDa 
• Atom Count: 3,627 
• Modeled Residue Count: 446 
• Deposited Residue Count: 482 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)	A	440	Streptomyces griseorubiginosus	Mutation(s): 0  Gene Names: EV578_104528

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tricyclic peptide MS-271	B	42	Streptomyces griseorubiginosus	Mutation(s): 0  Gene Names: DWG14_02265

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.232	α = 90
b = 127.232	β = 90
c = 170.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Nakashima, Y., Hiroyuki, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H02777
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K15303

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2023-08-23
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Structure summary