6PXK | pdb_00006pxk

3.65 Angstroms resolution structure of HslU with an axial-channel plug

• PDB DOI: https://doi.org/10.2210/pdb6PXK/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 
  0.271 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

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 
• 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.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A6B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A5B1C1 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A5B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 619.65 kDa 
• Atom Count: 37,523 
• Modeled Residue Count: 4,728 
• Deposited Residue Count: 5,392 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent protease ATPase subunit HslU	A [auth G], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	448	Escherichia coli	Mutation(s): 0  Gene Names: hslU
UniProt
Find proteins for P0A6H5 (Escherichia coli (strain K12)) Explore P0A6H5  Go to UniProtKB:  P0A6H5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
unidentified alpha helical sequence	M [auth X]	16	Escherichia coli	Mutation(s): 0  Gene Names: HslU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	BA [auth L], DA [auth A], FA [auth B], HA [auth C], IA [auth D], LA [auth E], N [auth G], NA [auth F], P [auth H], S [auth I], V [auth J], Y [auth K]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	AA [auth K], CA [auth L], EA [auth A], GA [auth B], JA [auth D], KA [auth D], MA [auth E], O [auth G], OA [auth F], Q [auth H], R [auth H], T [auth I], U [auth I], W [auth J], X [auth J], Z [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth G], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
UNK	M [auth X]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.03	α = 90
b = 91.2	β = 99.43
c = 201.8	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Baytshtok, V., Grant, R.A., Sauer, R.T.

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

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Data collection
• Version 1.2: 2021-02-10
  Changes: Database references
• Version 1.3: 2022-03-16
  Changes: Author supporting evidence, Database references
• Version 1.4: 2023-10-11
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-11-06
  Changes: Structure summary