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- PDB-8d1r: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 8d1r
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT520
ComponentsN-acetyltransferase Eis
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / resistance / aminoglycoside / enzyme / inhibitor / acetyl transfer / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / N-acetyltransferase activity ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / N-acetyltransferase activity / biological process involved in interaction with host / host cell cytoplasmic vesicle / peptide-lysine-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / host extracellular space / response to antibiotic / identical protein binding / cytosol
Similarity search - Function
N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
1-{3-[(4-chlorophenyl)methoxy]phenyl}methanamine / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsPang, A.H. / Punetha, A. / Garneau-Tsodikova, S. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI090048 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Discovery of substituted benzyloxy-benzylamine inhibitors of acetyltransferase Eis and their anti-mycobacterial activity.
Authors: Pang, A.H. / Green, K.D. / Chandrika, N.T. / Garzan, A. / Punetha, A. / Holbrook, S.Y.L. / Willby, M.J. / Posey, J.E. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3393
Polymers45,9991
Non-polymers3402
Water2,792155
1
A: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)278,03418
Polymers275,9956
Non-polymers2,03912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area23020 Å2
ΔGint-54 kcal/mol
Surface area89670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.102, 175.102, 124.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein N-acetyltransferase Eis / Aminoglycoside N-acetyltransferase / Enhanced intracellular survival protein / Protein-lysine N- ...Aminoglycoside N-acetyltransferase / Enhanced intracellular survival protein / Protein-lysine N-acetyltransferase


Mass: 45999.113 Da / Num. of mol.: 1 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PVF / 1-{3-[(4-chlorophenyl)methoxy]phenyl}methanamine


Mass: 247.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClNO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 8.5, 9.5-10% w/v PEG 8000, and 500 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 37172 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.8
Reflection shellResolution: 2.19→2.24 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 1835 / CC1/2: 0.952 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.19→43.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1893 5.1 %RANDOM
Rwork0.1732 ---
obs0.1748 35276 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.33 Å2 / Biso mean: 36.864 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0.56 Å2-0 Å2
2---1.13 Å2-0 Å2
3---3.66 Å2
Refinement stepCycle: final / Resolution: 2.19→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 23 155 3225
Biso mean--61.65 37.42 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133150
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172979
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6454281
X-RAY DIFFRACTIONr_angle_other_deg2.351.5766807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.38218.743183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1091541
X-RAY DIFFRACTIONr_chiral_restr0.0810.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023588
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02779
LS refinement shellResolution: 2.195→2.252 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 122 -
Rwork0.246 2527 -
all-2649 -
obs--96.96 %

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