PDBsum entry 2xim

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protein ligands metals Protein-protein interface(s) links
Isomerase(intramolecular oxidoreductse) PDB id
Protein chains
392 a.a. *
XYL ×4
_MG ×8
Waters ×919
* Residue conservation analysis
PDB id:
Name: Isomerase(intramolecular oxidoreductse)
Title: Arginine residues as stabilizing elements in proteins
Structure: D-xylose isomerase. Chain: a, b, c, d. Engineered: yes
Source: Actinoplanes missouriensis. Organism_taxid: 1866
Biol. unit: Tetramer (from PQS)
2.30Å     R-factor:   0.149    
Authors: N.T.Mrabet,A.Van Denbroek,I.Van Den Brande,P.Stanssens, Y.Laroche,A.-M.Lambeir,G.Matthyssens,J.Jenkins,M.Chiadmi, H.Vantilbeurgh,F.Rey,J.Janin,W.J.Quax,I.Lasters,M.Demaeyer, S.J.Wodak
Key ref:
N.T.Mrabet et al. (1992). Arginine residues as stabilizing elements in proteins. Biochemistry, 31, 2239-2253. PubMed id: 1540579 DOI: 10.1021/bi00123a005
29-May-91     Release date:   15-Apr-93    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P12851  (XYLA_ACTMI) -  Xylose isomerase
394 a.a.
392 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
Bound ligand (Het Group name = XYL)
corresponds exactly
= D-xylulose
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     isomerase activity     4 terms  


    Key reference    
DOI no: 10.1021/bi00123a005 Biochemistry 31:2239-2253 (1992)
PubMed id: 1540579  
Arginine residues as stabilizing elements in proteins.
N.T.Mrabet, A.Van den Broeck, I.Van den brande, P.Stanssens, Y.Laroche, A.M.Lambeir, G.Matthijssens, J.Jenkins, M.Chiadmi, H.van Tilbeurgh.
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.

Literature references that cite this PDB file's key reference

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PDB codes: 1zin 1zio 1zip
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Crystallization and preliminary crystallographic analysis of glyceraldehyde 3-phosphate dehydrogenase from Sacchromyces cerevisiae (baker's yeast).
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Asparaginyl-tRNA synthetase from Thermus thermophilus HB8. Sequence of the gene and crystallization of the enzyme expressed in Escherichia coli.
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Molecular dynamics simulations of adipocyte lipid-binding protein: effect of electrostatics and acyl chain unsaturation.
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A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design.
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Crystal structure of recombinant triosephosphate isomerase from Bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three-dimensional structures points to the importance of hydrophobic interactions.
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PDB code: 1btm
  7773178 L.Shimoni, and J.P.Glusker (1995).
Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.
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A review of protein engineering for the food industry.
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Stability and structural analysis of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
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A single carboxy-terminal arginine determines the amino-terminal helix conformation of an alanine-based peptide.
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Sequence and expression of the gene for N10-formyltetrahydrofolate synthetase from Clostridium cylindrosporum.
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Solubility and secretability.
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Protein engineering for unusual environments.
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Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases.
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X- and Q-band EPR studies on the two Mn(2+)-substituted metal-binding sites of D-xylose isomerase.
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Purification and characterization of a highly thermostable glucose isomerase produced by the extremely thermophilic eubacterium, Thermotoga maritima.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.