PDBsum entry 2jgq

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Isomerase PDB id
Protein chains
232 a.a. *
PO4 ×2
Waters ×312
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Kinetics and structural properties of triosephosphate isomerase from helicobacter pylori
Structure: Triosephosphate isomerase. Chain: a, b. Fragment: residues 2-234. Synonym: tim, triose-phosphate isomerase. Engineered: yes. Other_details: missing residues, lys 167 and lys 168
Source: Helicobacter pylori. Organism_taxid: 85962. Strain: 26695. Atcc: 700392d. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.200     R-free:   0.249
Authors: C.-H.Chu,Y.-J.Lai,Y.-J.Sun
Key ref:
C.H.Chu et al. (2008). Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori. Proteins, 71, 396-406. PubMed id: 17957775 DOI: 10.1002/prot.21709
14-Feb-07     Release date:   26-Feb-08    
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Protein chains
Pfam   ArchSchema ?
P56076  (TPIS_HELPY) -  Triosephosphate isomerase
234 a.a.
232 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = PO4)
matches with 50.00% 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   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  


    Added reference    
DOI no: 10.1002/prot.21709 Proteins 71:396-406 (2008)
PubMed id: 17957775  
Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori.
C.H.Chu, Y.J.Lai, H.Huang, Y.J.Sun.
Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate in the glycolysis-gluconeogenesis metabolism pathway. The Helicobacter pylori TIM gene (HpTIM) was cloned, and HpTIM was expressed and purified. The enzymatic activity of HpTIM for the substrate GAP was determined (K(m) = 3.46 +/- 0.23 mM and k(cat) = 8.8 x 10(4) min(-1)). The crystal structure of HpTIM was determined by molecular replacement at 2.3 A resolution. The overall structure of HpTIM was (beta/alpha)beta(beta/alpha)(6), which resembles the common TIM barrel fold, (beta/alpha)(8); however, a helix is missing after the second beta-strand. The conformation of loop 6 and binding of phosphate ion suggest that the determined structure of HpTIM was in the "closed" state. A highly conserved Arg-Asp salt bridge in the "DX(D/N)G" motif of most TIMs is absent in HpTIM because the sequence of this motif is "(211)SVDG(214)." To determine the significance of this salt bridge to HpTIM, four mutants, including K183S, K183A, D213Q, and D213A, were constructed and characterized. The results suggest that this conserved salt bridge is not essential for the enzymatic activity of HpTIM; however, it might contribute to the conformational stability of HpTIM.
  Selected figure(s)  
Figure 2.
Figure 2. HpTIM. (a) A ribbon representation of the HpTIM monomer. Twelve -helices are colored in pink and labeled 1 to 12 and eight -strands are colored in blue and labeled A to H. The loops from strand to helix are labeled as L1 to L8. The phosphate ion and the C-HEGA-9 detergent molecules are shown as ball-and-stick models. (b) A ribbon representation of the HpTIM dimer. The four loops (L1 to L4) involving in dimerization interactions of each monomer are colored in magenta and cyan for two monomers, respectively. L1 to L4 loops of one monomer are labeled. Furthermore, the active site of HpTIM is labeled with an asterisk and three key residues Lys10, His90, and Glu159 are represented as ball-and-stick and labeled. (c) Closed and open conformational TIM structures. The essential L6 loop for the conformation was colored in different colors: closed conformation: HpTIM (red), TbTIM (1AG1: yellow), and CeTIM (1MO0: green) and open conformation: SeTIM (1YPI: blue) and TbTIM (3TIM: cyan). The structures are in the same orientations and generated using MOLSCRIPT[29] and rendered using Raster3D.[30] (d) The active site of HpTIM with bound phosphate ion. The electron-density omit map (F[o] - F[c]) of phosphate is shown at 3.0 . The image was generated using PyMOL (DeLano Scientific, San Carlos, CA, (e) Direct hydrogen bond interactions between phosphate ion and HpTIM are indicated. (f) The water-mediated hydrogen bond interactions between phosphate ion and HpTIM are indicated. The interactions of (e) and (f) are represented as dashed lines and labeled with distance.
Figure 3.
Figure 3. Structural comparison of TIMs. (a) Superimposition of seven closed TIM structures: HpTIM (red), CeTIM (1MO0: purple), ScTIM (2YPI: cyan), EcTIM (1TMH: green), LmTIM (1AMK: yellow), TbTIM (1AG1: blue), and PfTIM (1LYX: magenta). Four structural differences among HpTIM and the other six TIMs are labeled as I (loop 2- B), II (L2), III (loop 7- F), and IV (loop 9- G). The image was generated using MOLSCRIPT[29] and rendered using Raster3D.[30] (b) Superimposition of binding pockets of TbTIM (1AG1: cyan) and HpTIM (magenta). Several residues, phosphate ion, and water molecules surrounding the binding pocket of HpTIM are labeled.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 396-406) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21289039 M.Banerjee, H.Balaram, N.V.Joshi, and P.Balaram (2011).
Engineered dimer interface mutants of triosephosphate isomerase: the role of inter-subunit interactions in enzyme function and stability.
  Protein Eng Des Sel, 24, 463-472.  
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