[English] 日本語
Yorodumi
- EMDB-60853: Liganded-state E.coli PatZ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60853
TitleLiganded-state E.coli PatZ
Map data
Sample
  • Complex: Acetyltransferase
    • Protein or peptide: Protein acetyltransferase
  • Ligand: ACETYL COENZYME *A
  • Ligand: PHOSPHATE ION
  • 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 acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 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 19, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60853.png

Downloads & links

-
Map

FileDownload / File: emd_60853.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: 0.12
Minimum - Maximum0.0 - 1.3145499
Average (Standard dev.)0.0098446235 (±0.020175207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 340.47998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Acetyltransferase

EntireName: Acetyltransferase
Components
  • Complex: Acetyltransferase
    • Protein or peptide: Protein acetyltransferase
  • Ligand: ACETYL COENZYME *A
  • Ligand: PHOSPHATE ION
  • Ligand: water

-
Supramolecule #1: Acetyltransferase

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

-
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: 98.099375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSQRGLEALL RPKSIAVIGA SMKPNRAGYL MMRNLLAGGF NGPVLPVTPA WKAVLGVLAW PDIASLPFTP DLAVLCTNAS RNLALLEEL GEKGCKTCII LSAPASQHED LRACALRHNM RLLGPNSLGL LAPWQGLNAS FSPVPIKRGK LAFISQSAAV S NTILDWAQ ...String:
MSQRGLEALL RPKSIAVIGA SMKPNRAGYL MMRNLLAGGF NGPVLPVTPA WKAVLGVLAW PDIASLPFTP DLAVLCTNAS RNLALLEEL GEKGCKTCII LSAPASQHED LRACALRHNM RLLGPNSLGL LAPWQGLNAS FSPVPIKRGK LAFISQSAAV S NTILDWAQ QRKMGFSYFI ALGDSLDIDV DELLDYLARD SKTSAILLYL EQLSDARRFV SAARSASRNK PILVIKSGRS PA AQRLLNT TAGMDPAWDA AIQRAGLLRV QDTHELFSAV ETLSHMRPLR GDRLMIISNG AAPAALALDA LWSRNGKLAT LSE ETCQKL RDALPEHVAI SNPLDLRDDA SSEHYIKTLD ILLHSQDFDA LMVIHSPSAA APATESAQVL IEAVKHHPRS KYVS LLTNW CGEHSSQEAR RLFSEAGLPT YRTPEGTITA FMHMVEYRRN QKQLRETPAL PSNLTSNTAE AHLLLQQAIA EGATS LDTH EVQPILQAYG MNTLPTWIAS DSTEAVHIAE QIGYPVALKL RSPDIPHKSE VQGVMLYLRT ANEVQQAANA IFDRVK MAW PQARVHGLLV QSMANRAGAQ ELRVVVEHDP VFGPLIMLGE GGVEWRPEDQ AVVALPPLNM NLARYLVIQG IKSKKIR AR SALRPLDVAG LSQLLVQVSN LIVDCPEIQR LDIHPLLASG SEFTALDVTL DISPFEGDNE SRLAVRPYPH QLEEWVEL K NGERCLFRPI LPEDEPQLQQ FISRVTKEDL YYRYFSEINE FTHEDLANMT QIDYDREMAF VAVRRIDQTE EILGVTRAI SDPDNIDAEF AVLVRSDLKG LGLGRRLMEK LITYTRDHGL QRLNGITMPN NRGMVALARK LGFNVDIQLE EGIVGLTLNL AQREES

UniProtKB: Protein acetyltransferase

-
Macromolecule #2: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 2 / Number of copies: 8 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

-
Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 507 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5121944
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more