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- EMDB-60849: Apo-state E.coli PatZ -

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Basic information

Entry
Database: EMDB / ID: EMD-60849
TitleApo-state E.coli PatZ
Map data
Sample
  • Complex: Acetyltransferase
    • Protein or peptide: Protein acetyltransferase
  • Ligand: water
KeywordsAcetyltransferase / TRANSFERASE
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
Protein lysine acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsPark JB / Roh SH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: 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 18, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60849.png

Downloads & links

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Map

FileDownload / File: emd_60849.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 448 pix.
= 340.48 Å		0.76 Å/pix.
x 448 pix.
= 340.48 Å		0.76 Å/pix.
x 448 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.038891837 - 0.53410596
Average (Standard dev.)0.0012375576 (±0.008289846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-223-223-223
Dimensions448448448
Spacing448448448
CellA=B=C: 340.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Acetyltransferase

EntireName: Acetyltransferase
Components
  • Complex: Acetyltransferase
    • Protein or peptide: Protein acetyltransferase
  • Ligand: water

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Supramolecule #1: Acetyltransferase

SupramoleculeName: Acetyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Protein acetyltransferase

MacromoleculeName: Protein acetyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 96.907102 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GLEALLRPKS IAVIGASMKP NRAGYLMMRN LLAGGFNGPV LPVTPAWKAV LGVLAWPDIA SLPFTPDLAV LCTNASRNLA LLEELGEKG CKTCIILSAP ASQHEDLRAC ALRHNMRLLG PNSLGLLAPW QGLNASFSPV PIKRGKLAFI SQSAAVSNTI L DWAQQRKM ...String:
GLEALLRPKS IAVIGASMKP NRAGYLMMRN LLAGGFNGPV LPVTPAWKAV LGVLAWPDIA SLPFTPDLAV LCTNASRNLA LLEELGEKG CKTCIILSAP ASQHEDLRAC ALRHNMRLLG PNSLGLLAPW QGLNASFSPV PIKRGKLAFI SQSAAVSNTI L DWAQQRKM GFSYFIALGD SLDIDVDELL DYLARDSKTS AILLYLEQLS DARRFVSAAR SASRNKPILV IKSGRSPAAQ RL LNTTAGM DPAWDAAIQR AGLLRVQDTH ELFSAVETLS HMRPLRGDRL MIISNGAAPA ALALDALWSR NGKLATLSEA TCQ KLRDAL PEHVAISNPL DLRDDASSEH YIKTLDILLH SQDFDALMVI HSPSAAAPAT ESAQVLIEAV KHHPRSKYVS LLTN WCGEH SSQEARRLFS EAGLPTYRTP EGTITAFMHM VEYRRNQKQL RETPALPSNL TSNTAEAHLL LQQAIAEGAT SLDTH EVQP ILQAYGMNTL PTWIASDSTE AVHIAEQIGY PVALKLRSPD IPHKSEVQGV MLYLRTANEV QQAANAIFDR VKMAWP QAR VHGLLVQSMA NRAGAQELRV VVEHDPVFGP LIMLGEGGVE WRPEDQAVVA LPPLNMNLAR YLVIQGIKSK KIRARSA LR PLDVAGLSQL LVQVSNLIVD CPEIQRLDIH PLLASGSEFT ALDVTLDISP FEGDNESRLA VRPYPHQLEE WVELKNGE R CLFRPILPED EPQLQQFISR VTKEDLYYRY FSEINEFTHE DLANMTQIDY DREMAFVAVR RIDQTEEILG VTRAISDPD NIDAEFAVLV RSDLKGLGLG RRLMEKLITY TRDHGLQRLN GITMPNNRGM VALARKLGFN VDIQLEEGIV GLTLNLA

UniProtKB: Protein lysine acetyltransferase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 40 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 548962
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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