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PDBsum entry 1qds

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Isomerase PDB id
1qds
Jmol
Contents
Protein chain
250 a.a. *
Ligands
PGA
Waters ×125
* Residue conservation analysis
PDB id:
1qds
Name: Isomerase
Title: Superstable e65q mutant of leishmania mexicana triosephospha isomerase (tim)
Structure: Triosephosphate isomerase. Chain: a. Engineered: yes. Mutation: yes
Source: Leishmania mexicana. Organism_taxid: 5665. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.153     R-free:   0.195
Authors: A.M.Lambeir,J.Backmann,J.Ruiz-Sanz,V.Filimonov,J.E.Nielsen,G I.Kursula,B.V.Norledge,R.K.Wierenga
Key ref:
A.M.Lambeir et al. (2000). The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Eur J Biochem, 267, 2516-2524. PubMed id: 10785370 DOI: 10.1046/j.1432-1327.2000.01254.x
Date:
10-Jul-99     Release date:   13-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P48499  (TPIS_LEIME) -  Triosephosphate isomerase
Seq:
Struc:
251 a.a.
250 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.5.3.1.1  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = PGA)
matches with 72.73% similarity
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1046/j.1432-1327.2000.01254.x Eur J Biochem 267:2516-2524 (2000)
PubMed id: 10785370  
 
 
The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.
A.M.Lambeir, J.Backmann, J.Ruiz-Sanz, V.Filimonov, J.E.Nielsen, I.Kursula, B.V.Norledge, R.K.Wierenga.
 
  ABSTRACT  
 
The amino acid sequence of Leishmania mexicana triose phosphate isomerase is unique in having at position 65 a glutamic acid instead of a glutamine. The stability properties of LmTIM and the E65Q mutant were investigated by pH and guanidinium chloride-induced unfolding. The crystal structure of E65Q was determined. Three important observations were made: (a) there are no structural rearrangements as the result of the substitution; (b) the mutant is more stable than the wild-type; and (c) the stability of the wild-type enzyme shows strong pH dependence, which can be attributed to the ionization of Glu65. Burying of the Glu65 side chain in the uncharged environment of the dimer interface results in a shift in pKa of more than 3 units. The pH-dependent decrease in overall stability is due to weakening of the monomer-monomer interactions (in the dimer). The E65Q substitution causes an increase in stability as the result of the formation of an additional hydrogen bond in each subunit (DeltaDeltaG degrees of 2 kcal.mol-1 per monomer) and the elimination of a charged group in the dimer interface (DeltaDeltaG degrees of at least 9 kcal.mol-1 per dimer). The computated shift in pKa and the stability of the dimer calculated from the charge distribution in the protein structure agree closely with the experimental results. The guanidinium chloride dependence of the unfolding constant was smaller than expected from studies involving monomeric model proteins. No intermediates could be identified in the unfolding equilibrium by combining fluorescence and CD measurements. Study of a stable monomeric triose phosphate isomerase variant confirmed that the phenomenon persists in the monomer.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Schematic diagram of the polar interactions of Gln65 (E65Q). The numbers in bold are the distances (in Å) between the specified atoms of the Gln65 side chain as they occur in the crystal structure of E65Q (PDB entry 1QDS). The equivalent contacts in LmTIM (PDB entry 1AMK) are listed below the E65Q distances in italics. The labels Glu65 and OE2 refer to LmTIM. The asterisk indicates the residue from the partner subunit.
Figure 5.
Fig. 5. Near-UV (upper panel) and far-UV (lower panel) CD spectra of LmTIM (closed symbols) and E65Q (open symbols) at pH 9.0 (squares) and pH 1.8 (circles).
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2000, 267, 2516-2524) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
17189477 B.M.Tynan-Connolly, and J.E.Nielsen (2007).
Redesigning protein pKa values.
  Protein Sci, 16, 239-249.  
17763928 E.Mixcoha-Hernández, L.M.Moreno-Vargas, A.Rojo-Domínguez, and C.G.Benítez-Cardoza (2007).
Thermal-unfolding reaction of triosephosphate isomerase from Trypanosoma cruzi.
  Protein J, 26, 491-498.  
16845054 B.M.Tynan-Connolly, and J.E.Nielsen (2006).
pKD: re-designing protein pKa values.
  Nucleic Acids Res, 34, W48-W51.  
16381845 C.P.Toseland, H.McSparron, M.N.Davies, and D.R.Flower (2006).
PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values.
  Nucleic Acids Res, 34, D199-D203.  
16447255 M.A.Porter, J.R.Hall, J.C.Locke, J.H.Jensen, and P.A.Molina (2006).
Hydrogen bonding is the prime determinant of carboxyl pKa values at the N-termini of alpha-helices.
  Proteins, 63, 621-635.  
15103631 H.Li, A.D.Robertson, and J.H.Jensen (2004).
The determinants of carboxyl pKa values in turkey ovomucoid third domain.
  Proteins, 55, 689-704.  
15175111 S.Mahato, D.De, D.Dutta, M.Kundu, S.Bhattacharya, M.T.Schiavone, and S.K.Bhattacharya (2004).
Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate.
  Microb Cell Fact, 3, 7.  
12522213 I.Kursula, and R.K.Wierenga (2003).
Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution.
  J Biol Chem, 278, 9544-9551.
PDB code: 1n55
12538895 J.E.Nielsen, and J.A.McCammon (2003).
On the evaluation and optimization of protein X-ray structures for pKa calculations.
  Protein Sci, 12, 313-326.  
12006590 K.Maithal, G.Ravindra, H.Balaram, and P.Balaram (2002).
Inhibition of plasmodium falciparum triose-phosphate isomerase by chemical modification of an interface cysteine. Electrospray ionization mass spectrometric analysis of differential cysteine reactivities.
  J Biol Chem, 277, 25106-25114.  
11151009 B.V.Norledge, A.M.Lambeir, R.A.Abagyan, A.Rottmann, A.M.Fernandez, V.V.Filimonov, M.G.Peter, and R.K.Wierenga (2001).
Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.
  Proteins, 42, 383-389.
PDB code: 1dkw
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.