5INJ | pdb_00005inj

Crystal Structure of Prenyltransferase PriB Ternary Complex with L-Tryptophan and Dimethylallyl thiolodiphosphate (DMSPP)

PDB DOI: https://doi.org/10.2210/pdb5INJ/pdb

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

Deposited: 2016-03-07 Released: 2016-05-11
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 Center for Advancing Translational Sciences (NIH/NCATS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.197 (Depositor), 0.199 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.2285
Primary Citation 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: 43.99 kDa
Atom Count: 3,403
Modeled Residue Count: 355
Deposited Residue Count: 405
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A182DWE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DST Query on DST Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C₅ H₁₂ O₆ P₂ S ZWFWSISPSBLNGO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
TRP Query on TRP 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]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.197 (Depositor), 0.199 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.396	α = 90
b = 83.422	β = 106.74
c = 41.618	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-05-11

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	GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA84374
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: 2016-05-11
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 2.0: 2019-10-02
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2019-12-04
Changes: Author supporting evidence
Version 2.2: 2020-09-23
Changes: Structure summary
Version 2.3: 2024-03-06
Changes: Data collection, Database references