5WCZ | pdb_00005wcz

Crystal Structure of Wild-Type MalL from Bacillus subtilis with TS analogue 1-deoxynojirimycin

• PDB DOI: https://doi.org/10.2210/pdb5WCZ/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-07-03 Released: 2018-03-28 
• Deposition Author(s): Arcus, V.L., Prentice, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.197 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Dynamical origins of heat capacity changes in enzyme-catalysed reactions.

van der Kamp, M.W., Prentice, E.J., Kraakman, K.L., Connolly, M., Mulholland, A.J., Arcus, V.L.

(2018) Nat Commun 9: 1177-1177

• PubMed: 29563521 
• DOI: https://doi.org/10.1038/s41467-018-03597-y
• Primary Citation Related Structures: 
  5WCZ


• PubMed Abstract: 
  

  Heat capacity changes are emerging as essential for explaining the temperature dependence of enzyme-catalysed reaction rates. This has important implications for enzyme kinetics, thermoadaptation and evolution, but the physical basis of these heat capacity changes is unknown. Here we show by a combination of experiment and simulation, for two quite distinct enzymes (dimeric ketosteroid isomerase and monomeric alpha-glucosidase), that the activation heat capacity change for the catalysed reaction can be predicted through atomistic molecular dynamics simulations. The simulations reveal subtle and surprising underlying dynamical changes: tightening of loops around the active site is observed, along with changes in energetic fluctuations across the whole enzyme including important contributions from oligomeric neighbours and domains distal to the active site. This has general implications for understanding enzyme catalysis and demonstrating a direct connection between functionally important microscopic dynamics and macroscopically measurable quantities.

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Organizational Affiliation: 
• School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK. [e-mail].
Centre of Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail].
School of Science, University of Waikato, Hamilton, 3216, New Zealand.
Centre of Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
Centre of Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail].
School of Science, University of Waikato, Hamilton, 3216, New Zealand. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 139.07 kDa 
• Atom Count: 10,395 
• Modeled Residue Count: 1,110 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligo-1,6-glucosidase 1	A, B	586	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: malL, yvdL, BSU34560 EC: 3.2.1.10
UniProt
Find proteins for O06994 (Bacillus subtilis (strain 168)) Explore O06994  Go to UniProtKB:  O06994

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOJ	C [auth A], F [auth B]	1-DEOXYNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-JGWLITMVSA-N
GOL	D [auth A], E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.197 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.585	α = 90
b = 98.835	β = 103.08
c = 101.345	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Arcus, V.L., Prentice, E.J.

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description