5WM2

Crystal Structure of CahJ in Complex with Salicylic Acid and AMP

• PDB DOI: https://doi.org/10.2210/pdb5WM2/pdb

• Classification: LIGASE
• Organism(s): Streptomyces gandocaensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-28 Released: 2018-05-23 
• Deposition Author(s): Sikkema, A.P., Smith, J.L.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.159 
• R-Value Work: 0.126 
• R-Value Observed: 0.147 

Starting Model: experimental

Literature

A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ.

Tripathi, A., Park, S.R., Sikkema, A.P., Cho, H.J., Wu, J., Lee, B., Xi, C., Smith, J.L., Sherman, D.H.

(2018) Chembiochem 19: 1595-1600

• PubMed: 29742306 
• DOI: https://doi.org/10.1002/cbic.201800233
• Primary Citation of Related Structures:  
  5WM2, 5WM3, 5WM4, 5WM5, 5WM6, 5WM7


• PubMed Abstract: 
  

  Cahuitamycins are biofilm inhibitors assembled by a convergent nonribosomal peptide synthetase pathway. Previous genetic analysis indicated that a discrete enzyme, CahJ, serves as a gatekeeper for cahuitamycin structural diversification. Here, the CahJ protein was probed structurally and functionally to guide the formation of new analogues by mutasynthetic studies. This analysis enabled the in vivo production of a new cahuitamycin congener through targeted precursor incorporation.

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Organizational Affiliation: 

Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.51 kDa 
• Atom Count: 4,715 
• Modelled Residue Count: 536 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Salicylate-AMP ligase	A	564	Streptomyces gandocaensis	Mutation(s): 0  Gene Names: cahJ
UniProt
Find proteins for A0A140DJY3 (Streptomyces gandocaensis) Explore A0A140DJY3  Go to UniProtKB:  A0A140DJY3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SAL	B [auth A]	2-HYDROXYBENZOIC ACID C7 H6 O3 YGSDEFSMJLZEOE-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.159 
• R-Value Work: 0.126 
• R-Value Observed: 0.147 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.872	α = 90
b = 121.872	β = 90
c = 87.688	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Sikkema, A.P., Smith, J.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK042303
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118101
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM008270

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-07-04
  Changes: Data collection, Database references
• Version 1.2: 2018-08-29
  Changes: Data collection, Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description