6PXI | pdb_00006pxi

The crystal structure of a singly capped HslUV complex with an axial pore plug and a HslU E257Q mutation

PDB DOI: https://doi.org/10.2210/pdb6PXI/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-07-26 Released: 2020-07-29
Deposition Author(s): Baytshtok, V., Grant, R.A., Sauer, R.T.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free:
0.285 (Depositor), 0.263 (DCC)
R-Value Work:
0.257 (Depositor), 0.243 (DCC)
R-Value Observed:
0.261 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Heat activates the AAA+ HslUV protease by melting an axial autoinhibitory plug.

Baytshtok, V., Fei, X., Shih, T.T., Grant, R.A., Santos, J.C., Baker, T.A., Sauer, R.T.

(2021) Cell Rep 34: 108639-108639

PubMed: 33472065 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2020.108639
Primary Citation Related Structures:
6PXI, 6PXK, 6PXL

PubMed Abstract:
At low temperatures, protein degradation by the AAA+ HslUV protease is very slow. New crystal structures reveal that residues in the intermediate domain of the HslU ₆ unfoldase can plug its axial channel, blocking productive substrate binding and subsequent unfolding, translocation, and degradation by the HslV ₁₂ peptidase. Biochemical experiments with wild-type and mutant enzymes support a model in which heat-induced melting of this autoinhibitory plug activates HslUV proteolysis.

Organizational Affiliation

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Macromolecule Content

Total Structure Weight: 177.52 kDa
Atom Count: 11,163
Modeled Residue Count: 1,437
Deposited Residue Count: 1,592
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent protease subunit HslV	A, B, C, D	174	Escherichia coli	Mutation(s): 0 Gene Names: hslV, htpO, yiiC, b3932, JW3903 EC: 3.4.25.2
UniProt
Find proteins for P0A7B8 (Escherichia coli (strain K12)) Explore P0A7B8 Go to UniProtKB: P0A7B8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7B8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent protease ATPase subunit HslU	E, F	448	Escherichia coli	Mutation(s): 1 Gene Names: hslU, htpI, b3931, JW3902
UniProt
Find proteins for P0A6H5 (Escherichia coli (strain K12)) Explore P0A6H5 Go to UniProtKB: P0A6H5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6H5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth F] SDF format, chain J [auth E] MOL2 format, chain K [auth F] MOL2 format, chain J [auth E] mmCIF format, chain K [auth F] mmCIF format, chain J [auth E]	J [auth E], K [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain J [auth E] Focus chain K [auth F] Interactions & Density Focus chain J [auth E] Focus chain K [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth C]	G [auth A], H [auth A], I [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.285 (Depositor), 0.263 (DCC)
R-Value Work: 0.257 (Depositor), 0.243 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.604	α = 90
b = 168.604	β = 90
c = 162.886	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Baytshtok, V.

Grant, R.A.

Sauer, R.T.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2021-02-10
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-06-19
Changes: Database references, Source and taxonomy