5WMM

Crystal structure of an adenylation domain interrupted by a methylation domain (AMA4) from nonribosomal peptide synthetase TioS

• PDB DOI: https://doi.org/10.2210/pdb5WMM/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Micromonospora sp. ML1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-30 Released: 2018-03-14 
• Deposition Author(s): Pang, A.H., Mori, S., Garneau-Tsodikova, S., Tsodikov, O.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.253 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Starting Model: experimental

Literature

Structural basis for backbone N-methylation by an interrupted adenylation domain.

Mori, S., Pang, A.H., Lundy, T.A., Garzan, A., Tsodikov, O.V., Garneau-Tsodikova, S.

(2018) Nat Chem Biol 14: 428-430

• PubMed: 29556104 
• DOI: https://doi.org/10.1038/s41589-018-0014-7
• Primary Citation of Related Structures:  
  5WMM


• PubMed Abstract: 
  

  Interrupted adenylation domains are enigmatic fusions, in which one enzyme is inserted into another to form a highly unusual bifunctional enzyme. We present the first crystal structure of an interrupted adenylation domain that reveals a unique embedded methyltransferase. The structure and functional data provide insight into how these enzymes N-methylate amino acid precursors en route to nonribosomal peptides.

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Organizational Affiliation: 

Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 112.95 kDa 
• Atom Count: 7,342 
• Modelled Residue Count: 934 
• Deposited Residue Count: 1,013 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRPS	A	926	Micromonospora sp. ML1	Mutation(s): 0  Gene Names: tioS
UniProt
Find proteins for Q333U7 (Micromonospora sp. ML1) Explore Q333U7  Go to UniProtKB:  Q333U7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MbtH homologue	B	87	Micromonospora sp. ML1	Mutation(s): 0  Gene Names: tioT
UniProt
Find proteins for Q333U6 (Micromonospora sp. ML1) Explore Q333U6  Go to UniProtKB:  Q333U6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B6G	C [auth A]	(2S)-2-amino-3-methylbutanoyl (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl hydrogen (S)-phosphate C14 H21 N6 O8 P PJUFCHCQTYUTMG-JDUCOKCXSA-N
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CA	H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.253 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.712	α = 90
b = 136.712	β = 90
c = 228.234	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Pang, A.H., Mori, S., Garneau-Tsodikova, S., Tsodikov, O.V.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2018-04-25
  Changes: Data collection, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description