5K9M

Crystal Structure of PriB Binary Complex with Product Diphosphate

• PDB DOI: https://doi.org/10.2210/pdb5K9M/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces sp. RM-5-8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2016-06-15 
• Deposition Author(s): Cao, H., Elshahawi, S., Benach, J., Wasserman, S.R., Morisco, L.L., Koss, J.W., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.227 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Structure and specificity of a permissive bacterial C-prenyltransferase.

Elshahawi, S.I., Cao, H., Shaaban, K.A., Ponomareva, L.V., Subramanian, T., Farman, M.L., Spielmann, H.P., Phillips, G.N., Thorson, J.S., Singh, S.

(2017) Nat Chem Biol 13: 366-368

• PubMed: 28166207 
• DOI: https://doi.org/10.1038/nchembio.2285
• Primary Citation of Related Structures:  
  5INJ, 5JXM, 5K9M


• PubMed Abstract: 
  

  This study highlights the biochemical and structural characterization of the L-tryptophan C6 C-prenyltransferase (C-PT) PriB from Streptomyces sp. RM-5-8. PriB was found to be uniquely permissive to a diverse array of prenyl donors and acceptors including daptomycin. Two additional PTs also produced novel prenylated daptomycins with improved antibacterial activities over the parent drug.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 43.7 kDa 
• Atom Count: 3,256 
• Modelled Residue Count: 353 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PriB Prenyltransferase	A	405	Streptomyces sp. RM-5-8	Mutation(s): 0
UniProt
Find proteins for A0A182DWE5 (Streptomyces sp. RM-5-8) Explore A0A182DWE5  Go to UniProtKB:  A0A182DWE5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	B [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.227 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.727	α = 90
b = 83.02	β = 90
c = 95.304	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Cao, H., Elshahawi, S., Benach, J., Wasserman, S.R., Morisco, L.L., Koss, J.W., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA84374
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI52188

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2017-02-22
  Changes: Database references
• Version 1.3: 2017-03-29
  Changes: Database references
• Version 1.4: 2017-09-27
  Changes: Author supporting evidence
• Version 1.5: 2019-12-04
  Changes: Author supporting evidence
• Version 1.6: 2020-09-23
  Changes: Structure summary
• Version 1.7: 2023-09-27
  Changes: Data collection, Database references, Refinement description