4RYF | pdb_00004ryf

ClpP1/2 heterocomplex from Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb4RYF/pdb

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

Deposited: 2014-12-15 Released: 2014-12-31
Deposition Author(s): Dahmen, M., Vielberg, M.-T., Groll, M., Sieber, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure and mechanism of the caseinolytic protease ClpP1/2 heterocomplex from Listeria monocytogenes.

Dahmen, M., Vielberg, M.T., Groll, M., Sieber, S.A.

(2015) Angew Chem Int Ed Engl 54: 3598-3602

PubMed: 25630955 Search on PubMed
DOI: https://doi.org/10.1002/anie.201409325
Primary Citation Related Structures:
4RYF

PubMed Abstract:
Listeria monocytogenes is a devastating bacterial pathogen. Its virulence and intracellular stress tolerance are supported by caseinolytic protease P (ClpP), an enzyme that is conserved among bacteria. L. monocytogenes expresses two ClpP isoforms that are only distantly related by sequence and differ in catalysis, oligomerization, active-site composition, and N-terminal interaction sites for associated AAA(+) chaperones. The crystal structure of the ClpP1/2 heterocomplex from L. monocytogenes was solved, and in combination with biochemical studies, it provides insights into the mode of action. The results demonstrate that structural interlocking of LmClpP1 with LmClpP2 leads to the formation of a tetradecamer, aligns all 14 active sites, and enhances proteolytic activity. Furthermore, the catalytic center was identified as being responsible for the transient stability of ClpPs.

Organizational Affiliation

Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching (Germany).

Macromolecule Content

Total Structure Weight: 317.23 kDa
Atom Count: 19,892
Modeled Residue Count: 2,533
Deposited Residue Count: 2,835
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A, B, C, D, E A, B, C, D, E, F, G	201	Listeria monocytogenes	Mutation(s): 0 Gene Names: clpP EC: 3.4.21.92
UniProt
Find proteins for Q8Y7Y1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y7Y1 Go to UniProtKB: Q8Y7Y1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y7Y1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	H, I, J, K, L H, I, J, K, L, M, N	204	Listeria monocytogenes	Mutation(s): 0 Gene Names: clpP EC: 3.4.21.92
UniProt
Find proteins for Q9RQI6 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q9RQI6 Go to UniProtKB: Q9RQI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RQI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain X [auth I] SDF format, chain V [auth H] SDF format, chain HA [auth N] SDF format, chain FA [auth M] SDF format, chain DA [auth L] SDF format, chain BA [auth K] MOL2 format, chain Z [auth J] MOL2 format, chain X [auth I] MOL2 format, chain V [auth H] MOL2 format, chain HA [auth N] MOL2 format, chain FA [auth M] MOL2 format, chain DA [auth L] MOL2 format, chain BA [auth K] mmCIF format, chain Z [auth J] mmCIF format, chain X [auth I] mmCIF format, chain V [auth H] mmCIF format, chain HA [auth N] mmCIF format, chain FA [auth M] mmCIF format, chain DA [auth L] mmCIF format, chain BA [auth K]	BA [auth K] DA [auth L] FA [auth M] HA [auth N] V [auth H] BA [auth K], DA [auth L], FA [auth M], HA [auth N], V [auth H], X [auth I], Z [auth J]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain BA [auth K] Focus chain DA [auth L] Focus chain FA [auth M] Focus chain HA [auth N] Focus chain V [auth H] Focus chain X [auth I] Focus chain Z [auth J] Interactions & Density Focus chain BA [auth K] Focus chain DA [auth L] Focus chain FA [auth M] Focus chain HA [auth N] Focus chain V [auth H] Focus chain X [auth I] Focus chain Z [auth J]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain U [auth G] SDF format, chain W [auth H] SDF format, chain Y [auth I] SDF format, chain T [auth F] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain IA [auth N] SDF format, chain GA [auth M] SDF format, chain EA [auth L] SDF format, chain CA [auth K] SDF format, chain AA [auth J] MOL2 format, chain S [auth E] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain T [auth F] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain IA [auth N] MOL2 format, chain GA [auth M] MOL2 format, chain EA [auth L] MOL2 format, chain CA [auth K] MOL2 format, chain AA [auth J] mmCIF format, chain S [auth E] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain T [auth F] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain IA [auth N] mmCIF format, chain GA [auth M] mmCIF format, chain EA [auth L] mmCIF format, chain CA [auth K] mmCIF format, chain AA [auth J]	AA [auth J] CA [auth K] EA [auth L] GA [auth M] IA [auth N] AA [auth J], CA [auth K], EA [auth L], GA [auth M], IA [auth N], O [auth A], P [auth B], Q [auth C], R [auth D], S [auth E], T [auth F], U [auth G], W [auth H], Y [auth I]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain CA [auth K] Focus chain EA [auth L] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain Y [auth I] Interactions & Density Focus chain AA [auth J] Focus chain CA [auth K] Focus chain EA [auth L] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain Y [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.23	α = 90
b = 127.15	β = 90
c = 265.5	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-31
Type: Initial release
Version 1.1: 2020-05-06
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4RYF | pdb_00004ryf

ClpP1/2 heterocomplex from Listeria monocytogenes

Literature

Structure and mechanism of the caseinolytic protease ClpP1/2 heterocomplex from Listeria monocytogenes.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2