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PDBsum entry 2h6r

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protein Protein-protein interface(s) links
Isomerase PDB id
2h6r
Jmol
Contents
Protein chains
(+ 2 more) 203 a.a. *
Waters ×384
* Residue conservation analysis
PDB id:
2h6r
Name: Isomerase
Title: Crystal structure of triosephosphate isomerase (tim) from methanocaldococcus jannaschii
Structure: Triosephosphate isomerase. Chain: a, b, c, d, e, f, g, h. Synonym: tim, triose-phosphate isomerase. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 243232. Strain: dsm 2661. Gene: tpia. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.213     R-free:   0.278
Authors: P.Gayathri,M.Banerjee,A.Vijayalakshmi,H.Balaram,P.Balaram, M.R.N.Murthy
Key ref:
P.Gayathri et al. (2007). Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii. Acta Crystallogr D Biol Crystallogr, 63, 206-220. PubMed id: 17242514 DOI: 10.1107/S0907444906046488
Date:
01-Jun-06     Release date:   06-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58923  (TPIS_METJA) -  Triosephosphate isomerase
Seq:
Struc:
219 a.a.
203 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444906046488 Acta Crystallogr D Biol Crystallogr 63:206-220 (2007)
PubMed id: 17242514  
 
 
Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii.
P.Gayathri, M.Banerjee, A.Vijayalakshmi, S.Azeez, H.Balaram, P.Balaram, M.R.Murthy.
 
  ABSTRACT  
 
The crystal structure of a recombinant triosephosphate isomerase (TIM) from the archaeabacterium Methanocaldococcus jannaschii has been determined at a resolution of 2.3 A using X-ray diffraction data from a tetartohedrally twinned crystal. M. jannaschii TIM (MjTIM) is tetrameric, as suggested by solution studies and from the crystal structure, as is the case for two other structurally characterized archaeal TIMs. The archaeabacterial TIMs are shorter compared with the dimeric TIMs; the insertions in the dimeric TIMs occur in the vicinity of the tetramer interface, resulting in a hindrance to tetramerization in the dimeric TIMs. The charge distribution on the surface of the archaeal TIMs also facilitates tetramerization. Analysis of the barrel interactions in TIMs suggests that these interactions are unlikely to account for the thermal stability of the archaeal TIMs. A novelty of the unliganded structure of MjTIM is the complete absence of electron density for the loop 6 residues. The disorder of this loop could be ascribed to a missing salt bridge between residues at the N- and C-terminal ends of the loop in MjTIM.
 
  Selected figure(s)  
 
Figure 7.
Figure 7 Electrostatic surface-potential representation of dimeric and tetrameric TIMs. (a) MjTIM dimer, (b) PfTIM dimer, (c) MjTIM tetramer. MjTIM and PfTIM dimers are shown in the same orientation, with the tetrameric interface of MjTIM facing towards the viewer. The tetramer is also represented in the same orientation. The figures were generated using GRASP (Nicholls et al., 1991[Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins, 11, 281-296.]). Blue, red and white regions represent positively charged, negatively charged and hydrophobic regions respectively. (d) A section of the structure-based sequence alignment of all TIMs, showing the insertion region in the vicinity of helix 5. Acidic residues are coloured blue, hydrophobic red, basic magenta and polar amino acids with hydroxyl and/or amide groups green.
Figure 10.
Figure 10 Loop 6 residues in PwTIM and PfTIM. (a) Loop 6 in the closed state for PfTIM (PDB code 1m7p ). (b) Loop 6 in the open state for PfTIM (PDB code 1lyx ). The residues interacting with Trp168 are also highlighted. (c) Conformation of loop 6 in the PwTIM structure (PDB code 1hg3 ). The salt bridge formed between Glu147 and Lys159 is highlighted and the residues involved are labelled. (d) Alignment of the loop 6 residues of PwTIM, MjTIM and PfTIM. The residues corresponding to Glu147 and Lys159 of PwTIM are highlighted.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 206-220) copyright 2007.  
  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.  
19583769 M.Banerjee, H.Balaram, and P.Balaram (2009).
Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase. The role of conserved residues and complementary mutations.
  FEBS J, 276, 4169-4183.  
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.  
18562316 C.Rodríguez-Almazán, R.Arreola, D.Rodríguez-Larrea, B.Aguirre-López, M.T.de Gómez-Puyou, R.Pérez-Montfort, M.Costas, A.Gómez-Puyou, and A.Torres-Larios (2008).
Structural basis of human triosephosphate isomerase deficiency: mutation E104D is related to alterations of a conserved water network at the dimer interface.
  J Biol Chem, 283, 23254-23263.
PDB codes: 2jk2 2vom
  18607087 P.Fernández-Millán, D.Kortazar, M.Lucas, M.L.Martínez-Chantar, E.Astigarraga, J.A.Fernández, O.Sabas, A.Albert, J.M.Mato, and L.A.Martínez-Cruz (2008).
Crystallization and preliminary crystallographic analysis of merohedrally twinned crystals of MJ0729, a CBS-domain protein from Methanococcus jannaschii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 605-609.  
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.