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PDBsum entry 2xim

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protein ligands metals Protein-protein interface(s) links
Isomerase(intramolecular oxidoreductse) PDB id
2xim
Jmol
Contents
Protein chains
392 a.a. *
Ligands
XYL ×4
Metals
_MG ×8
Waters ×919
* Residue conservation analysis
PDB id:
2xim
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)
Resolution:
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
Date:
29-May-91     Release date:   15-Apr-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12851  (XYLA_ACTMI) -  Xylose isomerase
Seq:
Struc:
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.5.3.1.5  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
D-xylopyranose
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.
 
  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.
 

Literature references that cite this PDB file's key reference

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PDB code: 2vu5
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PDB code: 2zhx
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PDB code: 1okb
12626496 M.J.Buch-Pedersen, and M.G.Palmgren (2003).
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12752432 R.Griessler, A.Schwarz, J.Mucha, and B.Nidetzky (2003).
Tracking interactions that stabilize the dimer structure of starch phosphorylase from Corynebacterium callunae. Roles of Arg234 and Arg242 revealed by sequence analysis and site-directed mutagenesis.
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PDB code: 1iwd
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PDB codes: 1b20 1b21 1b2x 1b2z
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Electrostatic interactions in an integral membrane protein.
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Proteasomal inhibition by misfolded mutant superoxide dismutase 1 induces selective motor neuron death in familial amyotrophic lateral sclerosis.
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PDB code: 1f9c
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Arginine activity in the proton-motive photocycle of bacteriorhodopsin: solid-state NMR studies of the wild-type and D85N proteins.
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Structural organization of the human eukaryotic initiation factor 5A precursor and its site-directed variant Lys50-->Arg.
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Further improvement of the thermal stability of a partially stabilized Bacillus subtilis 3-isopropylmalate dehydrogenase variant by random and site-directed mutagenesis.
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Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.
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PDB code: 1qez
10024022 V.Prasanna, B.Gopal, M.R.Murthy, D.V.Santi, and P.Balaram (1999).
Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase.
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Formation of native disulfide bonds in endothelin-1. Structural evidence for the involvement of a highly specific salt bridge between the prosequence and the endothelin-1 sequence.
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Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
10089540 R.Gilboa, A.J.Bauer, and G.Shoham (1998).
Crystallization and preliminary crystallographic analysis of glyceraldehyde 3-phosphate dehydrogenase from Sacchromyces cerevisiae (baker's yeast).
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Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability.
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Structure and expression of a pyrimidine gene cluster from the extreme thermophile Thermus strain ZO5.
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Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.
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Importance of two buried salt bridges in the stability and folding pathway of barnase.
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Peptide rescue of an N-terminal truncation of the Stoffel fragment of taq DNA polymerase.
  Protein Sci, 5, 1785-1792.  
8706760 L.Seignovert, M.Härtlein, and R.Leberman (1996).
Asparaginyl-tRNA synthetase from Thermus thermophilus HB8. Sequence of the gene and crystallization of the enzyme expressed in Escherichia coli.
  Eur J Biochem, 239, 501-508.  
8634281 M.R.Rich, and J.S.Evans (1996).
Molecular dynamics simulations of adipocyte lipid-binding protein: effect of electrostatics and acyl chain unsaturation.
  Biochemistry, 35, 1506-1515.  
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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.
  Protein Sci, 4, 2594-2604.
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.
  Protein Sci, 4, 65-74.  
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A review of protein engineering for the food industry.
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8060493 A.Magalhaes, B.Maigret, J.Hoflack, J.N.Gomes, and H.A.Scheraga (1994).
Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins.
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  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
8020481 G.Feller, F.Payan, F.Theys, M.Qian, R.Haser, and C.Gerday (1994).
Stability and structural analysis of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
  Eur J Biochem, 222, 441-447.  
7664050 W.R.Fiori, K.M.Lundberg, and G.L.Millhauser (1994).
A single carboxy-terminal arginine determines the amino-terminal helix conformation of an alanine-based peptide.
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  8443597 C.A.Rankin, G.C.Haslam, and R.H.Himes (1993).
Sequence and expression of the gene for N10-formyltetrahydrofolate synthetase from Clostridium cylindrosporum.
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7763977 C.H.Schein (1993).
Solubility and secretability.
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7763976 F.H.Arnold (1993).
Protein engineering for unusual environments.
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8229092 G.Vriend, and V.Eijsink (1993).
Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases.
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Mutations in the codon for a conserved arginine-1563 in the COL4A5 collagen gene in Alport syndrome.
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8479962 M.Michael, and G.Folkers (1993).
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8389296 R.Bogumil, R.Kappl, J.Hüttermann, C.Sudfeldt, and H.Witzel (1993).
X- and Q-band EPR studies on the two Mn(2+)-substituted metal-binding sites of D-xylose isomerase.
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18609636 S.H.Brown, C.Sjøholm, and R.M.Kelly (1993).
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.