9IT0 | pdb_00009it0

Liganded-state E.coli PatZ

PDB DOI: https://doi.org/10.2210/pdb9IT0/pdb
EM Map EMD-60853: EMDB EMDataResource

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

Deposited: 2024-07-19 Released: 2025-06-04
Deposition Author(s): Park, J.B., Roh, S.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ.

Park, J.B., Lee, G., Han, Y.Y., Kim, D., Heo, K., Kim, J., Park, J., Yun, H., Lee, C.W., Cho, H.S., Kim, J.S., Steinegger, M., Seok, Y.J., Roh, S.H.

(2025) Proc Natl Acad Sci U S A 122: e2419096122-e2419096122

PubMed: 40498448 Search on PubMed
DOI: https://doi.org/10.1073/pnas.2419096122
Primary Citation of Related Structures:
9ISB, 9ISQ, 9IT0

PubMed Abstract:
GCN5-related N -acetyltransferases (GNATs) are essential for regulating bacterial metabolism by acetylating specific target proteins. Despite their importance in bacterial physiology, the mechanisms behind their enzymatic and regulatory functions remain poorly understood. In this study, we investigated the structures of Escherichia coli protein acetyltransferase Z (PatZ), a Type I GNAT, and examined its ligand interactions, catalytic mechanism, and allosteric regulation. PatZ functions as a homotetramer, with each subunit comprising a catalytic and a regulatory domain. Our results demonstrate that the regulatory domain is vital for acetyltransferase activity, as it triggers cooperative conformational changes in the catalytic domain and directly aids in the formation of substrate-binding pockets. Additionally, a protein structure-based evolutionary analysis of bacterial GNAT types revealed a distinct regulatory domain pattern across phyla, highlighting its crucial role in responding to cellular energy levels.

Organizational Affiliation

School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.

Macromolecule Content

Total Structure Weight: 399.25 kDa
Atom Count: 28,311
Modeled Residue Count: 3,524
Deposited Residue Count: 3,544
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein acetyltransferase	A, B, C, D	886	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: pat, yfiQ, ACU57_10170, BGM66_000644, BJI68_02105, C0P57_000002, CG831_000342, CIG67_15390, CTR35_002231, CV83915_03530... 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 EC: 2.3.1
UniProt
Find proteins for P76594 (Escherichia coli (strain K12)) Explore P76594 Go to UniProtKB: P76594
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76594
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] K [auth C] E [auth A], F [auth A], G [auth B], H [auth B], K [auth C], L [auth C], O [auth D], P [auth D]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B], M [auth C], N [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]