5US1 | pdb_00005us1

Crystal structure of aminoglycoside acetyltransferase AAC(2')-Ia in complex with N2'-acetylgentamicin C1A and coenzyme A

PDB DOI: https://doi.org/10.2210/pdb5US1/pdb

Classification: TRANSFERASE
Organism(s): Providencia stuartii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-13 Released: 2017-03-15
Deposition Author(s): Stogios, P.J., Evdokimova, E., Xu, Z., Wawrzak, Z., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.230 (Depositor), 0.233 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes.

Cox, G., Ejim, L., Stogios, P.J., Koteva, K., Bordeleau, E., Evdokimova, E., Sieron, A.O., Savchenko, A., Serio, A.W., Krause, K.M., Wright, G.D.

(2018) ACS Infect Dis 4: 980-987

PubMed: 29634241 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsinfecdis.8b00001
Primary Citation Related Structures:
5US1, 6CD7

PubMed Abstract:
Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural product sisomicin to provide protection from common aminoglycoside modifying enzymes that chemically alter these drugs via N-acetylation, O-adenylylation, or O-phosphorylation. In this study, plazomicin was profiled against a panel of isogenic strains of Escherichia coli individually expressing twenty-one aminoglycoside resistance enzymes. Plazomicin retained antibacterial activity against 15 of the 17 modifying enzyme-expressing strains tested. Expression of only two of the modifying enzymes, aac(2')-Ia and aph(2″)-IVa, decreased plazomicin potency. On the other hand, expression of 16S rRNA ribosomal methyltransferases results in a complete lack of plazomicin potency. In vitro enzymatic assessment confirmed that AAC(2')-Ia and APH(2'')-IVa (aminoglycoside acetyltransferase, AAC; aminoglycoside phosphotransferase, APH) were able to utilize plazomicin as a substrate. AAC(2')-Ia and APH(2'')-IVa are limited in their distribution to Providencia stuartii and Enterococci, respectively. These data demonstrate that plazomicin is not modified by a broad spectrum of common aminoglycoside modifying enzymes including those commonly found in Enterobacteriaceae. However, plazomicin is inactive in the presence of 16S rRNA ribosomal methyltransferases, which should be monitored in future surveillance programs.

Organizational Affiliation

M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine , McMaster University , 1280 Main Street West , Hamilton , Ontario L8N 4K1 , Canada.

Macromolecule Content

Total Structure Weight: 263.33 kDa
Atom Count: 18,350
Modeled Residue Count: 2,163
Deposited Residue Count: 2,268
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside 2'-N-acetyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	189	Providencia stuartii	Mutation(s): 0 Gene Names: aac EC: 2.3.1.59
UniProt
Find proteins for Q52424 (Providencia stuartii) Explore Q52424 Go to UniProtKB: Q52424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q52424
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain HA [auth L] SDF format, chain U [auth E] MOL2 format, chain BA [auth I] MOL2 format, chain HA [auth L] MOL2 format, chain U [auth E] mmCIF format, chain BA [auth I] mmCIF format, chain HA [auth L] mmCIF format, chain U [auth E]	BA [auth I], HA [auth L], U [auth E]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain BA [auth I] Focus chain HA [auth L] Focus chain U [auth E] Interactions & Density Focus chain BA [auth I] Focus chain HA [auth L] Focus chain U [auth E]
8MM Query on 8MM Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain EA [auth K] SDF format, chain GA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain EA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain AA [auth I] mmCIF format, chain EA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth H]	AA [auth I] EA [auth K] GA [auth L] M [auth A] O [auth B] AA [auth I], EA [auth K], GA [auth L], M [auth A], O [auth B], R [auth D], T [auth E], V [auth F], X [auth G], Y [auth H]	(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-(acetylamino)-6-amino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside C₂₁ H₄₁ N₅ O₈ RLGSXXMFPPOROB-JOYMZIHVSA-N		Interactions Focus chain AA [auth I] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H]
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain DA [auth J] SDF format, chain N [auth A] SDF format, chain S [auth D] SDF format, chain W [auth F] SDF format, chain Z [auth H] MOL2 format, chain DA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain S [auth D] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth H] mmCIF format, chain DA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain S [auth D] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth H]	DA [auth J], N [auth A], S [auth D], W [auth F], Z [auth H]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain DA [auth J] Focus chain N [auth A] Focus chain S [auth D] Focus chain W [auth F] Focus chain Z [auth H] Interactions & Density Focus chain DA [auth J] Focus chain N [auth A] Focus chain S [auth D] Focus chain W [auth F] Focus chain Z [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain FA [auth K] SDF format, chain Q [auth C] MOL2 format, chain CA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain Q [auth C] mmCIF format, chain CA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain Q [auth C]	CA [auth I], FA [auth K], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth I] Focus chain FA [auth K] Focus chain Q [auth C] Interactions & Density Focus chain CA [auth I] Focus chain FA [auth K] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.230 (Depositor), 0.233 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 340.17	α = 90
b = 340.17	β = 90
c = 62.77	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PHENIX	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSCN27220120026C

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2018-04-25
Changes: Data collection, Database references
Version 1.3: 2018-06-20
Changes: Data collection, Database references
Version 1.4: 2019-12-11
Changes: Author supporting evidence
Version 1.5: 2023-10-04
Changes: Data collection, Database references, Refinement description