4QHI | pdb_00004qhi

Crystal structure of Methanocaldococcus jannaschii selecase mutant R36W

PDB DOI: https://doi.org/10.2210/pdb4QHI/pdb

Classification: HYDROLASE
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-05-28 Released: 2014-07-16
Deposition Author(s): Lopez-pelegrin, M., Cerda-costa, N., Cintas-pedrola, A., Herranz-trillo, F., Bernado, P., Peinado, J.R., Arolas, J.L., Gomis-ruth, F.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.247 (Depositor), 0.254 (DCC)
R-Value Work:
0.222 (Depositor), 0.230 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Multiple stable conformations account for reversible concentration-dependent oligomerization and autoinhibition of a metamorphic metallopeptidase

Lopez-Pelegrin, M., Cerda-Costa, N., Cintas-Pedrola, A., Herranz-Trillo, F., Bernado, P., Peinado, J.R., Arolas, J.L., Gomis-Ruth, F.X.

(2014) Angew Chem Int Ed Engl 53: 10624-10630

PubMed: 25159620 Search on PubMed
DOI: https://doi.org/10.1002/anie.201405727
Primary Citation Related Structures:
4QHF, 4QHG, 4QHH, 4QHI, 4QHJ

PubMed Abstract:
Molecular plasticity controls enzymatic activity: the native fold of a protein in a given environment is normally unique and at a global free-energy minimum. Some proteins, however, spontaneously undergo substantial fold switching to reversibly transit between defined conformers, the "metamorphic" proteins. Here, we present a minimal metamorphic, selective, and specific caseinolytic metallopeptidase, selecase, which reversibly transits between several different states of defined three-dimensional structure, which are associated with loss of enzymatic activity due to autoinhibition. The latter is triggered by sequestering the competent conformation in incompetent but structured dimers, tetramers, and octamers. This system, which is compatible with a discrete multifunnel energy landscape, affords a switch that provides a reversible mechanism of control of catalytic activity unique in nature.

Organizational Affiliation

Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park c/Baldiri Reixac, 15-21, 08028 Barcelona (Spain) http://www.ibmb.csic.es/home/xgomis.

Macromolecule Content

Total Structure Weight: 53.2 kDa
Atom Count: 3,796
Modeled Residue Count: 430
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ1213	A, B, C, D	110	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 1 Gene Names: MJ1213
UniProt
Find proteins for Q58610 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58610 Go to UniProtKB: Q58610
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58610
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], J [auth B], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247 (Depositor), 0.254 (DCC)
R-Value Work: 0.222 (Depositor), 0.230 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.69	α = 90
b = 101.09	β = 99.83
c = 76.47	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2014-10-22
Changes: Database references
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-04-03
Changes: Refinement description