5VDB

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with bisubstrate analog 3

PDB DOI: https://doi.org/10.2210/pdb5VDB/pdb

Classification: transferase/transferase inhibitor
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-01 Released: 2017-07-26
Deposition Author(s): Majorek, K.A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.170
R-Value Work: 0.145
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases.

Reidl, C., Majorek, K.A., Dang, J., Tran, D., Jew, K., Law, M., Payne, Y., Minor, W., Becker, D.P., Kuhn, M.L.

(2017) FEBS Lett 591: 2348-2361

PubMed: 28703494 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.12753
Primary Citation of Related Structures:
5VD6, 5VDB

PubMed Abstract:
Gcn5-related N-acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor-bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X-ray induced radical-mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely applicable across the GNAT superfamily and can be used to improve the success rate of obtaining liganded structures of other acyltransferases.

Organizational Affiliation

Department of Chemistry, Loyola University Chicago, IL, USA.

Macromolecule Content

Total Structure Weight: 19.61 kDa
Atom Count: 1,598
Modelled Residue Count: 159
Deposited Residue Count: 161
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acetyltransferase PA4794	A	161	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA4794
UniProt
Find proteins for Q9HV14 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HV14 Go to UniProtKB: Q9HV14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HV14
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
93M Query on 93M Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	(3R,5S,9R,26S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,20-trioxo-26-({[(phenylacetyl)amino]acetyl}amino)-2,4,6-trioxa-18-thia-11,15,21-triaza-3,5-diphosphaheptacosan-27-oic acid 3,5-dioxide (non-preferred name) C₃₉ H₅₉ N₁₀ O₂₁ P₃ S UWVFJLUZBIMSSQ-RYFVFCQRSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [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]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.170
R-Value Work: 0.145
R-Value Observed: 0.146
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.335	α = 90
b = 76.121	β = 90
c = 39.149	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	data reduction
HKL-3000	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Majorek, K.A.

Joachimiak, A.

Minor, W.

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54 GM094585

Revision History (Full details and data files)

Version 1.0: 2017-07-26
Type: Initial release
Version 1.1: 2017-08-23
Changes: Database references
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description