5WMM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/s41589-018-0014-7

  • 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 embedd ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NRPS
A
926Micromonospora sp. ML1Mutation(s): 0 
Gene Names: tioS
Find proteins for Q333U7 (Micromonospora sp. ML1)
Go to UniProtKB:  Q333U7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MbtH homologue
B
87Micromonospora sp. ML1Mutation(s): 0 
Gene Names: tioT
Find proteins for Q333U6 (Micromonospora sp. ML1)
Go to UniProtKB:  Q333U6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
B6G
Query on B6G

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Download CCD File 
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
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.236 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.712α = 90.00
b = 136.712β = 90.00
c = 228.234γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references