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PDBsum entry 1r2t

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protein Protein-protein interface(s) links
Isomerase PDB id
1r2t
Jmol
Contents
Protein chains
246 a.a. *
Waters ×335
* Residue conservation analysis
PDB id:
1r2t
Name: Isomerase
Title: Crystal structure of rabbit muscle triosephosphate isomerase
Structure: Triosephosphate isomerase. Chain: a, b. Synonym: tim. Ec: 5.3.1.1
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: muscle
Biol. unit: Dimer (from PQS)
Resolution:
2.25Å     R-factor:   0.184     R-free:   0.220
Authors: R.Aparicio,S.T.Ferreira,I.Polikarpov
Key ref:
R.Aparicio et al. (2003). Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity. J Mol Biol, 334, 1023-1041. PubMed id: 14643664 DOI: 10.1016/j.jmb.2003.10.022
Date:
29-Sep-03     Release date:   23-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00939  (TPIS_RABIT) -  Triosephosphate isomerase
Seq:
Struc:
248 a.a.
246 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   3 terms 
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2003.10.022 J Mol Biol 334:1023-1041 (2003)
PubMed id: 14643664  
 
 
Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity.
R.Aparicio, S.T.Ferreira, I.Polikarpov.
 
  ABSTRACT  
 
The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo drawings of the electron density map and structural alignment of the active site loop region. Water molecules are omitted for clarity. Labels refer to the A1 structure, subunit 2 (chain B). A single conformation of Lys13 Nz (see Materials and Methods) was adopted to prepare the Figure. (a) The active site loop comprises Pro166-Val167-Trp168-Ala169-Ile170-Gly171-Thr172-Gly173-Lys174-Thr175-Ala176. The residues responsible for catalysis are Lys13, His95 and Glu165. The electron density map (2mF[obs] -DF[calc]) was plotted at 1.25s. Three hydrogen bonds (broken lines in green) characteristic of the closed conformation are shown: Trp168 N epsilon 1-O epsilon 2 Glu129 (distance of 2.88 Å); Ala176 N-OH Tyr208 (distance of 2.96 Å); Gly173 N-Og Ser211 (distance of 3.06 Å). (b) Superposition onto the A1 structure of the same region from subunit 2 of the trypanosomal TIM structure complexed with G3P (PDB entry 6TIM,[10.] carbon atoms colored in gray), in which the loop assumes the closed conformation. The G3P molecule bound to the active site of the TIM-G3P complex is shown with the phosphorous atom colored in brown. Except for the side-chain of Lys174 of rabbit TIM, which points to a solvent region, the residues occupy nearly identical positions in both structures. Drawings were prepared using PyMOL (DeLano Scientific, San Carlos, CA, http://www.pymol.org) and edited using GIMP (http://www.gimp.org) under Linux.
Figure 3.
Figure 3. Stereo views of the active site region in subunit 2 (chain B) of the A1 structure. A single conformation of Lys13 Nz and Ser96 Og (see Materials and Methods) was adopted to prepare the Figure. (a) Electron density map (2mF[obs] -DF[calc]) contoured at 1.25s. The positions of water molecules interacting with residues in the active site region are also shown. The Figure illustrates in detail the well-defined conformation of main- and side-chain residues derived from experimental data. (b) The same region of trypanosomal TIM structure (carbon atoms colored in gray) complexed with G3P (PDB entry 6TIM,[10.] subunit 2) superposed onto the A1 structure. For clarity, water molecules are not labeled. The residues shown are strictly conserved and superpose very well, including the catalytic residue Glu165 side-chain. Note that the position of the G3P molecule is occupied by water molecules in the A1 structure. Three water molecules, W65, W98 and W488, labeled in (a), have nearly identical positions in both structures. Two additional water molecules, W108 and W377, are very close to the carbon hydroxyl groups of G3P (distances of 0.62 Å and 0.88 Å, respectively) and a third molecule, W171, is at a distance of 0.87 Å from the phosphorous atom in G3P. The juxtaposition of the residues shown in this Figure and in the Figure 2(b) unequivocally indicates that the active site loop is in the closed conformation in the A1 structure. (c) Schematic diagram of the hydrogen-bonding network in the active site region of the A1 structure. Hydrogen bonds are represented by broken lines and bond lengths are given in Å. Water oxygen atoms are colored in green. (a) and (b) were prepared using PyMOL (DeLano Scientific, San Carlos, CA, http://www.pymol.org) and edited using GIMP (http://www.gimp.org) under Linux. (c) was produced using LIGPLOT[84.] and edited using GIMP (http://www.gimp.org) under Linux.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 1023-1041) copyright 2003.  
  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.  
19622869 P.Gayathri, M.Banerjee, A.Vijayalakshmi, H.Balaram, P.Balaram, and M.R.Murthy (2009).
Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site.
  Acta Crystallogr D Biol Crystallogr, 65, 847-857.
PDB codes: 2vfd 2vfe 2vff 2vfg 2vfh 2vfi
  19342791 S.Mukherjee, D.Dutta, B.Saha, and A.K.Das (2009).
Expression, purification, crystallization and preliminary X-ray diffraction studies of triosephosphate isomerase from methicillin-resistant Staphylococcus aureus (MRSA252).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 398-401.  
19261703 S.S.Thakur, P.D.Deepalakshmi, P.Gayathri, M.Banerjee, M.R.Murthy, and P.Balaram (2009).
Detection of the protein dimers, multiple monomeric states and hydrated forms of Plasmodium falciparum triosephosphate isomerase in the gas phase.
  Protein Eng Des Sel, 22, 289-304.  
18175010 A.C.O'Donoghue, T.L.Amyes, and J.P.Richard (2008).
Slow proton transfer from the hydrogen-labelled carboxylic acid side chain (Glu-165) of triosephosphate isomerase to imidazole buffer in D(2)O.
  Org Biomol Chem, 6, 391-396.  
17932934 S.Wong, and M.P.Jacobson (2008).
Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins, 71, 153-164.  
16533835 C.E.Chang, T.Shen, J.Trylska, V.Tozzini, and J.A.McCammon (2006).
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.
  Biophys J, 90, 3880-3885.  
16323206 F.A.Konuklar, V.Aviyente, and T.Halilo─člu (2006).
Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model.
  Proteins, 62, 715-727.  
16861278 M.G.Botelho, A.W.Rietveld, and S.T.Ferreira (2006).
Long-lived conformational isomerism of protein dimers: the role of the free energy of subunit association.
  Biophys J, 91, 2826-2832.  
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 codes are shown on the right.