5JXM

Crystal Structure of Prenyltransferase PriB Apo Form

PDB DOI: https://doi.org/10.2210/pdb5JXM/pdb

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

Deposited: 2016-05-13 Released: 2016-06-08
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), National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.211
R-Value Work: 0.179
R-Value Observed: 0.179

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 43.55 kDa
Atom Count: 3,538
Modelled Residue Count: 356
Deposited Residue Count: 405
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PriB	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A182DWE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF 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: 1.15 Å
R-Value Free: 0.211
R-Value Work: 0.179
R-Value Observed: 0.179
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.526	α = 90
b = 83.723	β = 106.27
c = 41.527	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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	R01CA203257
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI52188
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	UL1TR000117

Revision History (Full details and data files)

Version 1.0: 2016-06-08
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: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description