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PDBsum entry 1btm

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1btm
Jmol
Contents
Protein chains
251 a.a. *
Ligands
PGA ×2
* Residue conservation analysis
PDB id:
1btm
Name: Isomerase
Title: Triosephosphate isomerase (tim) complexed with 2- phosphoglycolic acid
Structure: Triosephosphate isomerase. Chain: a, b. Synonym: tim. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: potential. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.80Å     R-factor:   0.176    
Authors: L.F.Delboni,S.C.Mande,W.G.J.Hol
Key ref: L.F.Delboni et al. (1995). Crystal structure of recombinant triosephosphate isomerase from Bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three-dimensional structures points to the importance of hydrophobic interactions. Protein Sci, 4, 2594-2604. PubMed id: 8580851 DOI: 10.1002/pro.5560041217
Date:
11-Nov-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00943  (TPIS_GEOSE) -  Triosephosphate isomerase
Seq:
Struc:
253 a.a.
251 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 = PGA)
matches with 72.00% 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/pro.5560041217 Protein Sci 4:2594-2604 (1995)
PubMed id: 8580851  
 
 
Crystal structure of recombinant triosephosphate isomerase from Bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three-dimensional structures points to the importance of hydrophobic interactions.
L.F.Delboni, S.C.Mande, F.Rentier-Delrue, V.Mainfroid, S.Turley, F.M.Vellieux, J.A.Martial, W.G.Hol.
 
  ABSTRACT  
 
The structure of the thermostable triosephosphate isomerase (TIM) from Bacillus stearothermophilus complexed with the competitive inhibitor 2-phosphoglycolate was determined by X-ray crystallography to a resolution of 2.8 A. The structure was solved by molecular replacement using XPLOR. Twofold averaging and solvent flattening was applied to improve the quality of the map. Active sites in both the subunits are occupied by the inhibitor and the flexible loop adopts the "closed" conformation in either subunit. The crystallographic R-factor is 17.6% with good geometry. The two subunits have an RMS deviation of 0.29 A for 248 C alpha atoms and have average temperature factors of 18.9 and 15.9 A2, respectively. In both subunits, the active site Lys 10 adopts an unusual phi, psi combination. A comparison between the six known thermophilic and mesophilic TIM structures was conducted in order to understand the higher stability of B. stearothermophilus TIM. Although the ratio Arg/(Arg+Lys) is higher in B. stearothermophilus TIM, the structure comparisons do not directly correlate this higher ratio to the better stability of the B. stearothermophilus enzyme. A higher number of prolines contributes to the higher stability of B. stearothermophilus TIM. Analysis of the known TIM sequences points out that the replacement of a structurally crucial asparagine by a histidine at the interface of monomers, thus avoiding the risk of deamidation and thereby introducing a negative charge at the interface, may be one of the factors for adaptability at higher temperatures in the TIM family. Analysis of buried cavities and the areas lining these cavities also contributes to the greater thermal stability of the B. stearothermophilus enzyme. However, the most outstanding result of the structure comparisons appears to point to the hydrophobic stabilization of dimer formation by burying the largest amount of hydrophobic surface area in B. stearothermophilus TIM compared to all five other known TIM structures.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
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.  
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
16759231 M.Karlström, I.H.Steen, D.Madern, A.E.Fedöy, N.K.Birkeland, and R.Ladenstein (2006).
The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima.
  FEBS J, 273, 2851-2868.
PDB code: 1zor
15688447 H.K.Liang, C.M.Huang, M.T.Ko, and J.K.Hwang (2005).
Amino acid coupling patterns in thermophilic proteins.
  Proteins, 59, 58-63.  
15858262 Y.Eisenberg-Domovich, V.P.Hytönen, M.Wilchek, E.A.Bayer, M.S.Kulomaa, and O.Livnah (2005).
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
  Acta Crystallogr D Biol Crystallogr, 61, 528-538.
PDB codes: 1y52 1y53 1y55
15532068 C.H.Chan, H.K.Liang, N.W.Hsiao, M.T.Ko, P.C.Lyu, and J.K.Hwang (2004).
Relationship between local structural entropy and protein thermostability.
  Proteins, 57, 684-691.  
14674757 V.H.Moreau, A.W.Rietveld, and S.T.Ferreira (2003).
Persistent conformational heterogeneity of triosephosphate isomerase: separation and characterization of conformational isomers in solution.
  Biochemistry, 42, 14831-14837.  
12009903 A.Hierro, J.M.Arizmendi, S.Bañuelos, A.Prado, and A.Muga (2002).
Electrostatic interactions at the C-terminal domain of nucleoplasmin modulate its chromatin decondensation activity.
  Biochemistry, 41, 6408-6413.  
12112681 H.Reyes-Vivas, E.Martínez-Martínez, G.Mendoza-Hernández, G.López-Velázquez, R.Pérez-Montfort, M.Tuena de Gómez-Puyou, and A.Gómez-Puyou (2002).
Susceptibility to proteolysis of triosephosphate isomerase from two pathogenic parasites: characterization of an enzyme with an intact and a nicked monomer.
  Proteins, 48, 580-590.  
11133966 A.M.Hutchins, J.F.Holden, and M.W.Adams (2001).
Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 183, 709-715.  
11453986 B.Clantin, C.Tricot, T.Lonhienne, V.Stalon, and V.Villeret (2001).
Probing the role of oligomerization in the high thermal stability of Pyrococcus furiosus ornithine carbamoyltransferase by site-specific mutants.
  Eur J Biochem, 268, 3937-3942.  
11258928 H.Reyes-Vivas, G.Hernández-Alcantara, G.López-Velazquez, N.Cabrera, R.Pérez-Montfort, M.T.de Gómez-Puyou, and A.Gómez-Puyou (2001).
Factors that control the reactivity of the interface cysteine of triosephosphate isomerase from Trypanosoma brucei and Trypanosoma cruzi.
  Biochemistry, 40, 3134-3140.  
10957646 J.Wouters, and D.Maes (2000).
Identification of a potential metal cation-pi binding site in the structure of a thermophilic Bacillus stearothermophilus triosephosphate isomerase mutant.
  Acta Crystallogr D Biol Crystallogr, 56, 1201-1203.  
10745009 R.Thoma, M.Hennig, R.Sterner, and K.Kirschner (2000).
Structure and function of mutationally generated monomers of dimeric phosphoribosylanthranilate isomerase from Thermotoga maritima.
  Structure, 8, 265-276.
PDB code: 1dl3
10591103 D.Maes, J.P.Zeelen, N.Thanki, N.Beaucamp, M.Alvarez, M.H.Thi, J.Backmann, J.A.Martial, L.Wyns, R.Jaenicke, and R.K.Wierenga (1999).
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
  Proteins, 37, 441-453.
PDB code: 1b9b
10409823 L.Lo Leggio, S.Kalogiannis, M.K.Bhat, and R.W.Pickersgill (1999).
High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture.
  Proteins, 36, 295-306.
PDB codes: 1tax 1tix
10368293 M.Singleton, M.Isupov, and J.Littlechild (1999).
X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis.
  Structure, 7, 237-244.
PDB code: 1a2z
10194326 R.Pérez-Montfort, G.Garza-Ramos, G.H.Alcántara, H.Reyes-Vivas, X.G.Gao, E.Maldonado, M.T.de Gómez-Puyou, and A.Gómez-Puyou (1999).
Derivatization of the interface cysteine of triosephosphate isomerase from Trypanosoma brucei and Trypanosoma cruzi as probe of the interrelationship between the catalytic sites and the dimer interface.
  Biochemistry, 38, 4114-4120.  
10468562 X.G.Gao, E.Maldonado, R.Pérez-Montfort, G.Garza-Ramos, M.T.de Gómez-Puyou, A.Gómez-Puyou, and A.Rodríguez-Romero (1999).
Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.
  Proc Natl Acad Sci U S A, 96, 10062-10067.
PDB code: 1ci1
  10417229 Y.Korkhin, A.J.Kalb (Gilboa), M.Peretz, O.Bogin, Y.Burstein, and F.Frolow (1999).
Oligomeric integrity--the structural key to thermal stability in bacterial alcohol dehydrogenases.
  Protein Sci, 8, 1241-1249.  
  9828010 E.J.Spek, A.H.Bui, M.Lu, and N.R.Kallenbach (1998).
Surface salt bridges stabilize the GCN4 leucine zipper.
  Protein Sci, 7, 2431-2437.  
10089525 G.S.Bell, R.J.Russell, M.Kohlhoff, R.Hensel, M.J.Danson, D.W.Hough, and G.L.Taylor (1998).
Preliminary crystallographic studies of triosephosphate isomerase (TIM) from the hyperthermophilic Archaeon Pyrococcus woesei.
  Acta Crystallogr D Biol Crystallogr, 54, 1419-1421.  
  9684881 J.Sun, and N.S.Sampson (1998).
Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase.
  Protein Sci, 7, 1495-1505.  
9753433 K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, and C.Kratky (1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
  Biochemistry, 37, 13475-13485.
PDB code: 1yna
9715904 M.B.Berry, and G.N.Phillips (1998).
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
  9797305 M.Wyss, L.Pasamontes, R.Rémy, J.Kohler, E.Kusznir, M.Gadient, F.Müller, and van Loon APGM (1998).
Comparison of the thermostability properties of three acid phosphatases from molds: Aspergillus fumigatus phytase, A. niger phytase, and A. niger PH 2.5 acid phosphatase.
  Appl Environ Microbiol, 64, 4446-4451.  
  9836874 O.Bogin, M.Peretz, Y.Hacham, Y.Korkhin, F.Frolow, A.J.Kalb(Gilboa), and Y.Burstein (1998).
Enhanced thermal stability of Clostridium beijerinckii alcohol dehydrogenase after strategic substitution of amino acid residues with prolines from the homologous thermophilic Thermoanaerobacter brockii alcohol dehydrogenase.
  Protein Sci, 7, 1156-1163.  
9893953 R.Scandurra, V.Consalvi, R.Chiaraluce, L.Politi, and P.C.Engel (1998).
Protein thermostability in extremophiles.
  Biochimie, 80, 933-941.  
9692946 W.Zhu, K.Sandman, G.E.Lee, J.N.Reeve, and M.F.Summers (1998).
NMR structure and comparison of the archaeal histone HFoB from the mesophile Methanobacterium formicicum with HMfB from the hyperthermophile Methanothermus fervidus.
  Biochemistry, 37, 10573-10580.  
9249046 A.Landa, A.Rojo-Domínguez, L.Jiménez, and D.A.Fernández-Velasco (1997).
Sequencing, expression and properties of triosephosphate isomerase from Entamoeba histolytica.
  Eur J Biochem, 247, 348-355.  
9265720 B.Lee, and G.Vasmatzis (1997).
Stabilization of protein structures.
  Curr Opin Biotechnol, 8, 423-428.  
9063445 E.Bismuto, G.Irace, S.D'Auria, M.Rossi, and R.Nucci (1997).
Multitryptophan-fluorescence-emission decay of beta-glycosidase from the extremely thermophilic archaeon Sulfolobus solfataricus.
  Eur J Biochem, 244, 53-58.  
9067626 J.A.Boutin (1997).
Myristoylation.
  Cell Signal, 9, 15-35.  
  9165087 L.Prade, P.Hof, and B.Bieseler (1997).
Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
  Biol Chem, 378, 317-320.  
9166771 M.Hennig, R.Sterner, K.Kirschner, and J.N.Jansonius (1997).
Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability.
  Biochemistry, 36, 6009-6016.
PDB code: 1nsj
  9336838 N.Beaucamp, A.Hofmann, B.Kellerer, and R.Jaenicke (1997).
Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase.
  Protein Sci, 6, 2159-2165.  
  9278147 N.Beaucamp, H.Schurig, and R.Jaenicke (1997).
The PGK-TIM fusion protein from Thermotoga maritima and its constituent parts are intrinsically stable and fold independently.
  Biol Chem, 378, 679-685.  
9254593 R.J.Russell, J.M.Ferguson, D.W.Hough, M.J.Danson, and G.L.Taylor (1997).
The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,.
  Biochemistry, 36, 9983-9994.
PDB code: 1aj8
  9352934 S.E.Unkles, J.M.Logsdon, K.Robison, J.R.Kinghorn, and J.M.Duncan (1997).
The tigA gene is a transcriptional fusion of glycolytic genes encoding triose-phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase in oomycota.
  J Bacteriol, 179, 6816-6823.  
9261072 S.S.Velanker, S.S.Ray, R.S.Gokhale, S.Suma, H.Balaram, P.Balaram, and M.R.Murthy (1997).
Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design.
  Structure, 5, 751-761.
PDB code: 1ydv
9195883 U.Ermler, M.Merckel, R.Thauer, and S.Shima (1997).
Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability.
  Structure, 5, 635-646.
PDB code: 1ftr
  8931142 D.H.Shin, H.K.Song, I.S.Seong, C.S.Lee, C.H.Chung, and S.W.Suh (1996).
Crystal structure analyses of uncomplexed ecotin in two crystal forms: implications for its function and stability.
  Protein Sci, 5, 2236-2247.
PDB codes: 1ecy 1ecz
  8762133 T.Salminen, A.Teplyakov, J.Kankare, B.S.Cooperman, R.Lahti, and A.Goldman (1996).
An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases.
  Protein Sci, 5, 1014-1025.  
8672446 V.Mainfroid, S.C.Mande, W.G.Hol, J.A.Martial, and K.Goraj (1996).
Stabilization of human triosephosphate isomerase by improvement of the stability of individual alpha-helices in dimeric as well as monomeric forms of the protein.
  Biochemistry, 35, 4110-4117.  
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.