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PDBsum entry 1i45

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protein Protein-protein interface(s) links
Isomerase PDB id
1i45
Jmol
Contents
Protein chains
247 a.a. *
Waters ×629
* Residue conservation analysis
PDB id:
1i45
Name: Isomerase
Title: Yeast triosephosphate isomerase (mutant)
Structure: Triosephosphate isomerase. Chain: a, b. Synonym: triosephosphate isomerase, tim, tpi1p. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.175     R-free:   0.208
Authors: S.Rozovsky,G.Jogl,L.Tong,A.E.Mcdermott
Key ref:
S.Rozovsky et al. (2001). Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics. J Mol Biol, 310, 271-280. PubMed id: 11419952 DOI: 10.1006/jmbi.2001.4673
Date:
19-Feb-01     Release date:   30-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00942  (TPIS_YEAST) -  Triosephosphate isomerase
Seq:
Struc:
248 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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     mitochondrion   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.2001.4673 J Mol Biol 310:271-280 (2001)
PubMed id: 11419952  
 
 
Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics.
S.Rozovsky, G.Jogl, L.Tong, A.E.McDermott.
 
  ABSTRACT  
 
Product release is partially rate determining in the isomerization reaction catalyzed by Triosephosphate Isomerase, the conversion of dihydroxyacetone phosphate to D-glyceraldehyde 3-phosphate, probably because an active-site loop movement is necessary to free the product from confinement in the active-site. The timescale of the catalytic loop motion and of ligand release were studied using 19F and 31P solution-state NMR. A 5'-fluorotryptophan was incorporated in the loop N-terminal hinge as a reporter of loop motion timescale. Crystallographic studies confirmed that the structure of the fluorinated enzyme is indistinguishable from the wild-type; the fluorine accepts a hydrogen bond from water and not from a protein residue, with minimal perturbation to the flexible loop stability. Two distinct loop conformations were observed by 19F NMR. Both for unligated (empty) and ligated enzyme samples a single species was detected, but the chemical shifts of these two distinct species differed by 1.2 ppm. For samples in the presence of subsaturating amounts of a substrate analogue, glycerol 3-phosphate, both NMR peaks were present, with broadened lineshapes at 0 degrees C. In contrast, a single NMR peak representing a rapid average of the two species was observed at 30 degrees C. We conclude that the rate of loop motion is less than 1400 s(-1) at 0 degrees C and more than 1400 s(-1) at 30 degrees C. Ligand release was studied under similar sample conditions, using 31P NMR of the phosphate group of the substrate analogue. The rate of ligand release is less than 1000 s(-1) at 0 degrees C and more than 1000 s(-1) at 30 degrees C. Therefore, loop motion and product release are probably concerted and likely to represent a rate limiting step for chemistry.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) The superposition of loop 6 from both the wild-type yeast TIM structure (PDB entry 1YPI [Lolis et al 1990]) and the Trp90Tyr Trp157Phe with 5'-fluorotryptophan incorporated at position 168 are shown. Loop 6 backbone is identical in both structures. A slight variation is found in Ile170 side-chain, which is not unusual for a solvent exposed side-chain. (b) The electron density of the 5'-fluorotryptophan incorporated into a single location on TIM's flexible loop is shown. The presence of the fluorine atom does not modify the hydrophobic packing and hydrogen bonding interactions observed for the unmodified tryptophan in the wild-type yeast TIM [Lolis et al 1990]. A water molecule is within hydrogen bond distance from the fluorine atom in both subunits. Graphical representations were prepared with the program MOLSCRIPT [Kraulis 1991] and RASTER3D [Merritt and Bacon 1997].
Figure 4.
Figure 4. Lineshape simulations for the flexible loop 5'-fluorotryptophan 19F resonance (at 9.4 T, Figure 2 right panel, reproduced for convenience on the left). The unligated state can be simulated with two sites corresponding to the open and closed loop's conformation, at any arbitrary skewed populations, assuming that the unligated enzyme is not likely to close on an unligated active-site. Loop motion in the present of G3P was simulated using a three site model and constraint from kinetic data. Loop opening rate is 1000 s -1 at 0°C and 5000 s -1 at 30°C. Line broadening used in the simulation is 10 Hz. The T[2]-induced linewidth is certainly borader, but has not been considered here. Populations of the loop conformations were selected based on sample conditions; the encounter complex occupancy is assumed to be 1 % of the closed loop enzyme occupancy. Simulations are scaled in a manner analogous to the experimental data.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 271-280) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20730847 G.F.Wang, C.Li, and G.J.Pielak (2010).
Probing the micelle-bound aggregation-prone state of α-synuclein with (19)F NMR spectroscopy.
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20734112 J.L.Kitevski-LeBlanc, F.Evanics, and R.Scott Prosser (2010).
Optimizing ¹⁹F NMR protein spectroscopy by fractional biosynthetic labeling.
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20160956 F.Jordan, P.Arjunan, S.Kale, N.S.Nemeria, and W.Furey (2009).
Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis.
  J Mol Catal B Enzym, 61, 14-22.  
19391777 H.Berthoumieux, C.Antoine, L.Jullien, and A.Lemarchand (2009).
Resonant response to temperature modulation for enzymatic dynamics characterization.
  Phys Rev E Stat Nonlin Soft Matter Phys, 79, 021906.  
19339520 J.I.Friedman, A.Majumdar, and J.T.Stivers (2009).
Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage.
  Nucleic Acids Res, 37, 3493-3500.  
19337664 J.Kubelka (2009).
Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics.
  Photochem Photobiol Sci, 8, 499-512.  
19267450 L.J.Juszczak, and R.Z.Desamero (2009).
Extension of the tryptophan chi2,1 dihedral angle-W3 band frequency relationship to a full rotation: correlations and caveats.
  Biochemistry, 48, 2777-2787.  
19588901 N.Doucet, E.D.Watt, and J.P.Loria (2009).
The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.
  Biochemistry, 48, 7160-7168.  
19836335 O.Davulcu, P.F.Flynn, M.S.Chapman, and J.J.Skalicky (2009).
Intrinsic domain and loop dynamics commensurate with catalytic turnover in an induced-fit enzyme.
  Structure, 17, 1356-1367.  
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
19745816 S.M.Elvington, C.W.Liu, and M.C.Maduke (2009).
Substrate-driven conformational changes in ClC-ec1 observed by fluorine NMR.
  EMBO J, 28, 3090-3102.  
19348462 Y.Wang, R.B.Berlow, and J.P.Loria (2009).
Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase.
  Biochemistry, 48, 4548-4556.  
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.  
17957775 C.H.Chu, Y.J.Lai, H.Huang, and Y.J.Sun (2008).
Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori.
  Proteins, 71, 396-406.
PDB code: 2jgq
18219118 M.Alahuhta, M.G.Casteleijn, P.Neubauer, and R.K.Wierenga (2008).
Structural studies show that the A178L mutation in the C-terminal hinge of the catalytic loop-6 of triosephosphate isomerase (TIM) induces a closed-like conformation in dimeric and monomeric TIM.
  Acta Crystallogr D Biol Crystallogr, 64, 178-188.
PDB codes: 2v0t 2v2c 2v2d 2v2h
18216265 S.Kale, G.Ulas, J.Song, G.W.Brudvig, W.Furey, and F.Jordan (2008).
Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex.
  Proc Natl Acad Sci U S A, 105, 1158-1163.  
18053245 D.M.Lemaster, J.S.Anderson, L.Wang, Y.Guo, H.Li, and G.Hernandez (2007).
NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin.
  BMC Struct Biol, 7, 81.
PDB codes: 2pve 2pvx
17915350 G.Cornilescu, E.B.Hadley, M.G.Woll, J.L.Markley, S.H.Gellman, and C.C.Cornilescu (2007).
Solution structure of a small protein containing a fluorinated side chain in the core.
  Protein Sci, 16, 2089.  
17336327 J.G.Kempf, J.Y.Jung, C.Ragain, N.S.Sampson, and J.P.Loria (2007).
Dynamic requirements for a functional protein hinge.
  J Mol Biol, 368, 131-149.  
17696453 M.Gulotta, L.Qiu, R.Desamero, J.Rösgen, D.W.Bolen, and R.Callender (2007).
Effects of cell volume regulating osmolytes on glycerol 3-phosphate binding to triosephosphate isomerase.
  Biochemistry, 46, 10055-10062.  
17287353 S.Rozovsky, and A.E.McDermott (2007).
Substrate product equilibrium on a reversible enzyme, triosephosphate isomerase.
  Proc Natl Acad Sci U S A, 104, 2080-2085.  
17444661 T.L.Amyes, and J.P.Richard (2007).
Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion.
  Biochemistry, 46, 5841-5854.  
17989778 V.Olivares-Illana, A.Rodríguez-Romero, I.Becker, M.Berzunza, J.García, R.Pérez-Montfort, N.Cabrera, F.López-Calahorra, M.T.de Gómez-Puyou, and A.Gómez-Puyou (2007).
Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi.
  PLoS Negl Trop Dis, 1, e1.
PDB code: 2oma
17221869 V.Zomosa-Signoret, B.Aguirre-López, G.Hernández-Alcántara, R.Pérez-Montfort, M.T.de Gómez-Puyou, and A.Gómez-Puyou (2007).
Crosstalk between the subunits of the homodimeric enzyme triosephosphate isomerase.
  Proteins, 67, 75-83.  
17316687 W.Labeikovsky, E.Z.Eisenmesser, D.A.Bosco, and D.Kern (2007).
Structure and dynamics of pin1 during catalysis by NMR.
  J Mol Biol, 367, 1370-1381.  
17068837 D.M.LeMaster, and G.Hernández (2006).
Additivity of differential conformational dynamics in hyperthermophile/mesophile rubredoxin chimeras as monitored by hydrogen exchange.
  Chembiochem, 7, 1886-1889.  
16323206 F.A.Konuklar, V.Aviyente, and T.Haliloğlu (2006).
Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model.
  Proteins, 62, 715-727.  
15890082 D.La, and D.R.Livesay (2005).
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets.
  BMC Bioinformatics, 6, 116.  
15795383 D.McElheny, J.R.Schnell, J.C.Lansing, H.J.Dyson, and P.E.Wright (2005).
Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis.
  Proc Natl Acad Sci U S A, 102, 5032-5037.  
15840824 D.R.Livesay, and D.La (2005).
The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.
  Protein Sci, 14, 1158-1170.  
16267559 E.Z.Eisenmesser, O.Millet, W.Labeikovsky, D.M.Korzhnev, M.Wolf-Watz, D.A.Bosco, J.J.Skalicky, L.E.Kay, and D.Kern (2005).
Intrinsic dynamics of an enzyme underlies catalysis.
  Nature, 438, 117-121.  
15796706 R.A.Friesner, and V.Guallar (2005).
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.
  Annu Rev Phys Chem, 56, 389-427.  
14993670 D.Maes, L.A.Gonzalez-Ramirez, J.Lopez-Jaramillo, B.Yu, H.De Bondt, I.Zegers, E.Afonina, J.M.Garcia-Ruiz, and S.Gulnik (2004).
Structural study of the type II 3-dehydroquinate dehydratase from Actinobacillus pleuropneumoniae.
  Acta Crystallogr D Biol Crystallogr, 60, 463-471.
PDB code: 1uqr
15334070 M.Wolf-Watz, V.Thai, K.Henzler-Wildman, G.Hadjipavlou, E.Z.Eisenmesser, and D.Kern (2004).
Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair.
  Nat Struct Mol Biol, 11, 945-949.  
12509510 G.Jogl, S.Rozovsky, A.E.McDermott, and L.Tong (2003).
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.
  Proc Natl Acad Sci U S A, 100, 50-55.
PDB codes: 1ney 1nf0
12522213 I.Kursula, and R.K.Wierenga (2003).
Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution.
  J Biol Chem, 278, 9544-9551.
PDB code: 1n55
12581214 P.Pattanaik, G.Ravindra, C.Sengupta, K.Maithal, P.Balaram, and H.Balaram (2003).
Unusual fluorescence of W168 in Plasmodium falciparum triosephosphate isomerase, probed by single-tryptophan mutants.
  Eur J Biochem, 270, 745-756.  
14563846 S.Parthasarathy, K.Eaazhisai, H.Balaram, P.Balaram, and M.R.Murthy (2003).
Structure of Plasmodium falciparum triose-phosphate isomerase-2-phosphoglycerate complex at 1.1-A resolution.
  J Biol Chem, 278, 52461-52470.
PDB code: 1o5x
11859194 E.Z.Eisenmesser, D.A.Bosco, M.Akke, and D.Kern (2002).
Enzyme dynamics during catalysis.
  Science, 295, 1520-1523.  
12069788 L.Columbus, and W.L.Hubbell (2002).
A new spin on protein dynamics.
  Trends Biochem Sci, 27, 288-295.  
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.