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PDBsum entry 1w0m

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1w0m
Jmol
Contents
Protein chains
(+ 2 more) 226 a.a. *
Ligands
PO4 ×8
Waters ×705
* Residue conservation analysis
PDB id:
1w0m
Name: Isomerase
Title: Triosephosphate isomerase from thermoproteus tenax
Structure: Triosephosphate isomerase. Chain: a, b, c, d, e, f, g, h. Synonym: tim. Engineered: yes
Source: Thermoproteus tenax. Organism_taxid: 2271. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.5Å     R-factor:   0.197     R-free:   0.225
Authors: H.Walden,G.Taylor,E.Lorentzen,E.Pohl,H.Lilie,A.Schramm, T.Knura,K.Stubbe,B.Tjaden,R.Hensel
Key ref:
H.Walden et al. (2004). Structure and function of a regulated archaeal triosephosphate isomerase adapted to high temperature. J Mol Biol, 342, 861-875. PubMed id: 15342242 DOI: 10.1016/j.jmb.2004.07.067
Date:
08-Jun-04     Release date:   09-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8NKN9  (TPIS_THETK) -  Triosephosphate isomerase
Seq:
Struc:
226 a.a.
226 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
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: 10.1016/j.jmb.2004.07.067 J Mol Biol 342:861-875 (2004)
PubMed id: 15342242  
 
 
Structure and function of a regulated archaeal triosephosphate isomerase adapted to high temperature.
H.Walden, G.L.Taylor, E.Lorentzen, E.Pohl, H.Lilie, A.Schramm, T.Knura, K.Stubbe, B.Tjaden, R.Hensel.
 
  ABSTRACT  
 
Triosephophate isomerase (TIM) is a dimeric enzyme in eucarya, bacteria and mesophilic archaea. In hyperthermophilic archaea, however, TIM exists as a tetramer composed of monomers that are about 10% shorter than other eucaryal and bacterial TIM monomers. We report here the crystal structure of TIM from Thermoproteus tenax, a hyperthermophilic archaeon that has an optimum growth temperature of 86 degrees C. The structure was determined from both a hexagonal and an orthorhombic crystal form to resolutions of 2.5A and 2.3A, and refined to R-factors of 19.7% and 21.5%, respectively. In both crystal forms, T.tenax TIM exists as a tetramer of the familiar (betaalpha)(8)-barrel. In solution, however, and unlike other hyperthermophilic TIMs, the T.tenax enzyme exhibits an equilibrium between inactive dimers and active tetramers, which is shifted to the tetramer state through a specific interaction with glycerol-1-phosphate dehydrogenase of T.tenax. This observation is interpreted in physiological terms as a need to reduce the build-up of thermolabile metabolic intermediates that would be susceptible to destruction by heat. A detailed structural comparison with TIMs from organisms with growth optima ranging from 15 degrees C to 100 degrees C emphasizes the importance in hyperthermophilic proteins of the specific location of ionic interactions for thermal stability rather than their numbers, and shows a clear correlation between the reduction of heat-labile, surface-exposed Asn and Gln residues with thermoadaptation. The comparison confirms the increase in charged surface-exposed residues at the expense of polar residues.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Superposition of the TtxTIM (purple) and PwTIM (red). (a) Superposition of the monomers with the a-helices and dimer interface loop labeled. (b) Superposition of the classical TIM dimer, each as an C^a trace. (c) A stereo diagram of the TtxTIM and PwTIM tetramers superimposed, showing the twist in the TtxTIM tetramer interface.
Figure 3.
Figure 3. The graph shows the nature of the exposed surface area in each classical TIM dimer.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 861-875) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19247785 P.Del Vecchio, M.Elias, L.Merone, G.Graziano, J.Dupuy, L.Mandrich, P.Carullo, B.Fournier, D.Rochu, M.Rossi, P.Masson, E.Chabriere, and G.Manco (2009).
Structural determinants of the high thermal stability of SsoPox from the hyperthermophilic archaeon Sulfolobus solfataricus.
  Extremophiles, 13, 461-470.  
18186475 A.Pauluhn, H.Ahmed, E.Lorentzen, S.Buchinger, D.Schomburg, B.Siebers, and E.Pohl (2008).
Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax.
  Proteins, 72, 35-43.
PDB codes: 2r91 2r94
18025086 B.Bae, S.Ohene-Adjei, S.Kocherginskaya, R.I.Mackie, M.A.Spies, I.K.Cann, and S.K.Nair (2008).
Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA.
  J Biol Chem, 283, 12415-12425.
PDB codes: 2zew 2zex 2zey 2zez
18824174 E.J.Drake, and A.M.Gulick (2008).
Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin.
  J Mol Biol, 384, 193-205.
PDB codes: 3e59 3eat
18491075 M.Zaparty, B.Tjaden, R.Hensel, and B.Siebers (2008).
The central carbohydrate metabolism of the hyperthermophilic crenarchaeote Thermoproteus tenax: pathways and insights into their regulation.
  Arch Microbiol, 190, 231-245.  
17551578 C.Rodríguez-Almazán, F.J.Torner, M.Costas, R.Pérez-Montfort, M.T.de Gómez-Puyou, and A.G.Puyou (2007).
The stability and formation of native proteins from unfolded monomers is increased through interactions with unrelated proteins.
  PLoS ONE, 2, e497.  
17697123 M.C.Giuliani, P.Tron, G.Leroy, C.Aubert, P.Tauc, and M.T.Giudici-Orticoni (2007).
A new sulfurtransferase from the hyperthermophilic bacterium Aquifex aeolicus. Being single is not so simple when temperature gets high.
  FEBS J, 274, 4572-4587.  
17242514 P.Gayathri, M.Banerjee, A.Vijayalakshmi, S.Azeez, H.Balaram, P.Balaram, and M.R.Murthy (2007).
Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 63, 206-220.
PDB code: 2h6r
16978361 D.Mathur, G.Malik, and L.C.Garg (2006).
Biochemical and functional characterization of triosephosphate isomerase from Mycobacterium tuberculosis H37Rv.
  FEMS Microbiol Lett, 263, 229-235.  
16823036 K.Manikandan, A.Bhardwaj, N.Gupta, N.K.Lokanath, A.Ghosh, V.S.Reddy, and S.Ramakumar (2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
  Protein Sci, 15, 1951-1960.
PDB codes: 2f8q 2fgl
16256419 B.Siebers, and P.Schönheit (2005).
Unusual pathways and enzymes of central carbohydrate metabolism in Archaea.
  Curr Opin Microbiol, 8, 695-705.  
15911615 J.Zhu, J.W.Burgner, E.Harms, B.R.Belitsky, and J.L.Smith (2005).
A new arrangement of (beta/alpha)8 barrels in the synthase subunit of PLP synthase.
  J Biol Chem, 280, 27914-27923.
PDB code: 1znn
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.

 

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