1XIM

ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS

• PDB DOI:  https://doi.org/10.2210/pdb1XIM/pdb

• Classification: ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
• Organism(s): Actinoplanes missouriensis
• Mutation(s): No 


• Deposited: 1991-05-29 Released: 1993-04-15 
• Deposition Author(s): Mrabet, N.T., Van Denbroek, A., Van Den Brande, I., Stanssens, P., Laroche, Y., Lambeir, A.-M., Matthyssens, G., Jenkins, J., Chiadmi, M., Vantilbeurgh, H., Rey, F., Janin, J., Quax, W.J., Lasters, I., Demaeyer, M., Wodak, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Observed: 0.152 

Literature

Arginine residues as stabilizing elements in proteins.

Mrabet, N.T., Van den Broeck, A., Van den brande, I., Stanssens, P., Laroche, Y., Lambeir, A.M., Matthijssens, G., Jenkins, J., Chiadmi, M., van Tilbeurgh, H., Rey, F., Janin, J., Quax, W.J., Lasters, I., Demaeyer, M., Wodak, S.J.

(1992) Biochemistry 31: 2239-2253

• PubMed: 1540579 
• DOI: https://doi.org/10.1021/bi00123a005
• Primary Citation of Related Structures:  
  1XIM, 2XIM, 3XIM


• PubMed Abstract: 
  

Site-specific substitutions of arginine for lysine in the thermostable D-xylose isomerase (XI) from Actinoplanes missouriensis are shown to impart significant heat stability enhancement in the presence of sugar substrates most probably by interfering with nonenzymatic glycation. The same substitutions are also found to increase heat stability in the absence of any sugar derivatives, where a mechanism based on prevention of glycation can no longer be invoked. This rather conservative substitution is moreover shown to improve thermostability in two other structurally unrelated proteins, human copper, zinc-superoxide dismutase (CuZnSOD) and D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus subtilis. The stabilizing effect of Lys----Arg substitutions is rationalized on the basis of a detailed analysis of the crystal structures of wild-type XI and of engineered variants with Lys----Arg substitution at four distinct locations, residues 253, 309, 319, and 323. Molecular model building analysis of the structures of wild-type and mutant CuZnSOD (K9R) and GAPDH (G281K and G281R) is used to explain the observed stability enhancement in these proteins. In addition to demonstrating that even thermostable proteins can lend themselves to further stability improvement, our findings provide direct evidence that arginine residues are important stabilizing elements in proteins. Moreover, the stabilizing role of electrostatic interactions, particularly between subunits in oligomeric proteins, is documented.

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Related Citations: 

• Structural Analysis of the 2.8 Angstroms Model of Xylose Isomerase from Actinoplanes Missouriensis
  Rey, F., Jenkins, J., Janin, J., Lasters, I., Alard, P., Claessens, M., Matthyssens, G., Wodak, S.
  (1988) Proteins 4: 165

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Organizational Affiliation: 

Protein Engineering Department, Plant Genetic Systems, Gent, Belgium.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 174.77 kDa 
• Atom Count: 13,141 
• Modelled Residue Count: 1,568 
• Deposited Residue Count: 1,572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-XYLOSE ISOMERASE	A, B, C, D	393	Actinoplanes missouriensis	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P12851 (Actinoplanes missouriensis (strain ATCC 14538 / DSM 43046 / CBS 188.64 / JCM 3121 / NBRC 102363 / NCIMB 12654 / NRRL B-3342 / UNCC 431)) Explore P12851  Go to UniProtKB:  P12851

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYL	E [auth A], H [auth B], K [auth C], N [auth D]	Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N
CO	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Observed: 0.152 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.45	α = 90
b = 143.45	β = 90
c = 231.5	γ = 120

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-04-15 
Deposition Author(s): Mrabet, N.T., Van Denbroek, A., Van Den Brande, I., Stanssens, P., Laroche, Y., Lambeir, A.-M., Matthyssens, G., Jenkins, J., Chiadmi, M., Vantilbeurgh, H., Rey, F., Janin, J., Quax, W.J., Lasters, I., Demaeyer, M., Wodak, S.J.

Revision History  

• Version 1.0: 1993-04-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Other, Structure summary