6H1B

Structure of amide bond synthetase Mcba K483A mutant from Marinactinospora thermotolerans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Broad Aryl Acid Specificity of the Amide Bond Synthetase McbA Suggests Potential for the Biocatalytic Synthesis of Amides.

Petchey, M.Cuetos, A.Rowlinson, B.Dannevald, S.Frese, A.Sutton, P.W.Lovelock, S.Lloyd, R.C.Fairlamb, I.J.S.Grogan, G.

(2018) Angew. Chem. Int. Ed. Engl. 57: 11584-11588

  • DOI: 10.1002/anie.201804592

  • PubMed Abstract: 
  • Amide bond formation is one of the most important reactions in pharmaceutical synthetic chemistry. The development of sustainable methods for amide bond formation, including those that are catalyzed by enzymes, is therefore of significant interest. T ...

    Amide bond formation is one of the most important reactions in pharmaceutical synthetic chemistry. The development of sustainable methods for amide bond formation, including those that are catalyzed by enzymes, is therefore of significant interest. The ATP-dependent amide bond synthetase (ABS) enzyme McbA, from Marinactinospora thermotolerans, catalyzes the formation of amides as part of the biosynthetic pathway towards the marinacarboline secondary metabolites. The reaction proceeds via an adenylate intermediate, with both adenylation and amidation steps catalyzed within one active site. In this study, McbA was applied to the synthesis of pharmaceutical-type amides from a range of aryl carboxylic acids with partner amines provided at 1-5 molar equivalents. The structure of McbA revealed the structural determinants of aryl acid substrate tolerance and differences in conformation associated with the two half reactions catalyzed. The catalytic performance of McbA, coupled with the structure, suggest that this and other ABS enzymes may be engineered for applications in the sustainable synthesis of pharmaceutically relevant (chiral) amides.


    Organizational Affiliation

    Department of Chemistry, University of York, York, YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty acid CoA ligase
A, B, C, E
497Marinactinospora thermotoleransMutation(s): 1 
Find proteins for R4R1U5 (Marinactinospora thermotolerans)
Go to UniProtKB:  R4R1U5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fatty acid CoA ligase
D
499Marinactinospora thermotoleransMutation(s): 1 
Find proteins for R4R1U5 (Marinactinospora thermotolerans)
Go to UniProtKB:  R4R1U5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EQ2
Query on EQ2

Download SDF File 
Download CCD File 
A, B, C, D, E
1-ethanoyl-9~{H}-pyrido[3,4-b]indole-3-carboxylic acid
C14 H10 N2 O3
RMLMLEMGHAUXDM-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B, C, D, E
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.234α = 90.00
b = 130.738β = 90.00
c = 196.383γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release