6IYK

The structure of EntE with 2-nitrobenzoyl adenylate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket.

Ishikawa, F.Miyanaga, A.Kitayama, H.Nakamura, S.Nakanishi, I.Kudo, F.Eguchi, T.Tanabe, G.

(2019) Angew Chem Int Ed Engl 58: 6906-6910

  • DOI: 10.1002/anie.201900318
  • Primary Citation of Related Structures:  
    6IYK, 6IYL

  • PubMed Abstract: 
  • Adenylation (A) domains act as the gatekeepers of non-ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron-chelating siderophores, but are not limited to them ...

    Adenylation (A) domains act as the gatekeepers of non-ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron-chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A-domains. We show that a single asparagine-to-glycine mutation in an aryl acid A-domain leads to an enzyme that tolerates a wide range of non-native aryl acids. The engineered catalyst is capable of activating non-native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild-type enzyme was observed toward these substrates. Co-crystal structures with non-hydrolysable aryl-AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.


    Organizational Affiliation

    Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-, 8502, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complexA, B556Escherichia coli 1303Mutation(s): 1 
Gene Names: entEEC1303_c05680
EC: 2.7.7.58 (PDB Primary Data), 6.3.2.14 (UniProt), 6.2.1.71 (UniProt)
UniProt
Find proteins for P10378 (Escherichia coli (strain K12))
Explore P10378 
Go to UniProtKB:  P10378
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10378
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B1U
Query on B1U

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5'-O-[(2-nitrobenzene-1-carbonyl)sulfamoyl]adenosine
C17 H17 N7 O9 S
OCXRXKRXIAIGOE-CNEMSGBDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B1U Binding MOAD:  6IYK Ki: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.503α = 90
b = 57.22β = 96.31
c = 171.648γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17H05438
Japan Society for the Promotion of ScienceJapan16H06451

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references