7XBU | pdb_00007xbu

Crystal structure of the adenylation domain of CmnG in complex with capreomycidine

• PDB DOI: https://doi.org/10.2210/pdb7XBU/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Saccharothrix mutabilis subsp. capreolus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-22 Released: 2023-03-01 
• Deposition Author(s): Chen, I.H., Wang, Y.L., Chang, C.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Characterization and Structural Determination of CmnG-A, the Adenylation Domain That Activates the Nonproteinogenic Amino Acid Capreomycidine in Capreomycin Biosynthesis.

Chen, I.H., Cheng, T., Wang, Y.L., Huang, S.J., Hsiao, Y.H., Lai, Y.T., Toh, S.I., Chu, J., Rudolf, J.D., Chang, C.Y.

(2022) Chembiochem 23: e202200563-e202200563

• PubMed: 36278314 
• DOI: https://doi.org/10.1002/cbic.202200563
• Primary Citation of Related Structures:  
  7XBS, 7XBT, 7XBU, 7XBV


• PubMed Abstract: 
  

  Capreomycidine (Cap) is a nonproteinogenic amino acid and building block of nonribosomal peptide (NRP) natural products. We report the formation and activation of Cap in capreomycin biosynthesis. CmnC and CmnD catalyzed hydroxylation and cyclization, respectively, of l-Arg to form l-Cap. l-Cap is then adenylated by CmnG-A before being incorporated into the nonribosomal peptide. The co-crystal structures of CmnG-A with l-Cap and adenosine nucleotides provide insights into the specificity and engineering opportunities of this unique adenylation domain.

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Organizational Affiliation: 

Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.41 kDa 
• Atom Count: 3,816 
• Modelled Residue Count: 483 
• Deposited Residue Count: 513 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CmnG	A	513	Saccharothrix mutabilis subsp. capreolus	Mutation(s): 0  Gene Names: cmnG
UniProt
Find proteins for A6YEH8 (Saccharothrix mutabilis subsp. capreolus) Explore A6YEH8  Go to UniProtKB:  A6YEH8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYN (Subject of Investigation/LOI)	B [auth A]	(2S)-amino[(4R)-2-amino-1,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid C6 H12 N4 O2 XHNWDEHKMJLKGG-DMTCNVIQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.04	α = 90
b = 77.04	β = 90
c = 192.201	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-01 
Deposition Author(s): Chen, I.H., Wang, Y.L., Chang, C.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	110-2113-M-A49-026-MY3

Revision History  

• Version 1.0: 2023-03-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description