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- PDB-9isb: Ligand bound AGD of enzyme -

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Basic information

Entry
Database: PDB / ID: 9isb
TitleLigand bound AGD of enzyme
ComponentsProtein acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / ATP binding / metal ion binding
Similarity search - Function
Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, subdomain 1 / Acetyltransferase (GNAT) family / ATP-grasp fold ...Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, subdomain 1 / Acetyltransferase (GNAT) family / ATP-grasp fold / ATP-grasp fold profile. / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Protein acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPark, J.B. / Roh, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Ligand bound AGD of enzyme
Authors: Park, J.B. / Roh, S.H.
#1: Journal: mBio / Year: 2018
Title: Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli.
Authors: David G Christensen / Jesse G Meyer / Jackson T Baumgartner / Alexandria K D'Souza / William C Nelson / Samuel H Payne / Misty L Kuhn / Birgit Schilling / Alan J Wolfe /
Abstract: Posttranslational modifications, such as ε-lysine acetylation, regulate protein function. ε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses ...Posttranslational modifications, such as ε-lysine acetylation, regulate protein function. ε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an ε-lysine residue of a protein. The enzymatic mechanism uses ε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to ε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Here, we demonstrate the existence of 4 additional KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria.ε-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, ε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an strain that lacked both known acetylation mechanisms to identify four new ε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.
History
DepositionJul 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein acetyltransferase
B: Protein acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8894
Polymers50,9552
Non-polymers9342
Water1,51384
1
A: Protein acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9052
Polymers25,4771
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9852
Polymers25,4771
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.050, 76.050, 199.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Protein acetyltransferase / Protein lysine acetyltransferase / Putative acyl-CoA synthetase


Mass: 25477.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria)
Gene: pat, yfiQ, ACU57_10170, BGM66_000644, BJI68_02105, C0P57_000002, CG831_000342, CIG67_15390, CTR35_002231, CV83915_03530, DTL43_02095, EIZ93_15170, FOI11_000020, FOI11_20030, FWK02_03775, G3V95_ ...Gene: pat, yfiQ, ACU57_10170, BGM66_000644, BJI68_02105, C0P57_000002, CG831_000342, CIG67_15390, CTR35_002231, CV83915_03530, DTL43_02095, EIZ93_15170, FOI11_000020, FOI11_20030, FWK02_03775, G3V95_05750, G4A38_06870, G4A47_19960, GNW61_15560, GOP25_16215, GQM21_00025, GRW05_03440, HMV95_11440, J0541_000369, JNP96_20710, QDW62_06300, SAMEA3752557_00912
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8T0A9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium sodium tartrate, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.24→99.57 Å / Num. obs: 28802 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 36.26 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 20.2
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.834 / Num. unique obs: 2880

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLM7.4.0data reduction
pointless1.2.16data scaling
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AGD

Resolution: 2.24→71.05 Å / SU ML: 0.2601 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2702 1405 4.88 %
Rwork0.2359 27397 -
obs0.2375 28802 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.89 Å2
Refinement stepCycle: LAST / Resolution: 2.24→71.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 58 84 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933606
X-RAY DIFFRACTIONf_angle_d1.14564926
X-RAY DIFFRACTIONf_chiral_restr0.0648590
X-RAY DIFFRACTIONf_plane_restr0.0111632
X-RAY DIFFRACTIONf_dihedral_angle_d15.46221326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.320.31551220.26222656X-RAY DIFFRACTION99.75
2.32-2.420.28991320.26922670X-RAY DIFFRACTION99.75
2.42-2.530.29381590.26812701X-RAY DIFFRACTION99.65
2.53-2.660.35471470.25422672X-RAY DIFFRACTION99.58
2.66-2.830.28751470.25772712X-RAY DIFFRACTION99.62
2.83-3.040.25881290.25392734X-RAY DIFFRACTION99.79
3.04-3.350.30631370.2512721X-RAY DIFFRACTION99.79
3.35-3.840.2891450.23322768X-RAY DIFFRACTION99.83
3.84-4.830.21881350.20692785X-RAY DIFFRACTION99.49
4.83-71.050.24671520.22082978X-RAY DIFFRACTION99.59

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