5WM4

Crystal Structure of CahJ in Complex with 6-Methylsalicyl Adenylate

PDB DOI: https://doi.org/10.2210/pdb5WM4/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.196
R-Value Work: 0.154
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 61.83 kDa
Atom Count: 5,005
Modelled Residue Count: 534
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A140DJY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B5M Query on B5M Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	9-(5-O-{(S)-hydroxy[(2-hydroxy-6-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine C₁₈ H₂₀ N₅ O₉ P YIFBGYAAIZMTKM-NBCLGQJJSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.196
R-Value Work: 0.154
R-Value Observed: 0.207
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.188	α = 90
b = 122.188	β = 90
c = 88.174	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-23

Deposition Author(s):

Sikkema, A.P.

Smith, J.L.

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 (Full details and data files)

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, Derived calculations, Refinement description