1tph › Citations

Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution.

Zhang Z, Sugio S, Komives EA, Liu KD, Knowles JR, Petsko GA, Ringe D
Biochemistry 33 2830-7 (1994)
Cited: 72 times
EuropePMC logo PMID: 8130195

Abstract

The crystal structure of recombinant chicken triosephosphate isomerase (TIM, E.C. 5.3.1.1) complexed with the intermediate analogue phosphoglycolohydroxamate (PGH) has been solved by the method of molecular replacement and refined to an R-factor of 18.5% at 1.8-A resolution. The structure is essentially identical to that of the yeast TIM-PGH complex [Davenport, R. C., et al. (1991) Biochemistry 30, 5821-5826] determined earlier and refined at comparable resolution. This identity extends to the high-energy conformations of the active-site residues Lys13 and Ser211, as well as the positions of several bound water molecules that are retained in the active site when PGH is bound. Comparison with the structure of uncomplexed chicken TIM shows that the catalytic base, Glu165, moves several angstroms when PGH binds. This movement may provide a trigger for a larger conformational change, one of 7 A, in a loop near the active site, which folds down like a lid to shield the bound inhibitor and catalytic residues from contact with bulk solvent. These same conformational changes were seen in crystalline yeast TIM upon binding of PGH; their occurrence here in a different crystal form of TIM eliminates the possibility that they are an artifact of crystal packing.

Reviews - 1tph mentioned but not cited (2)

  1. A role for flexible loops in enzyme catalysis. Malabanan MM, Amyes TL, Richard JP. Curr Opin Struct Biol 20 702-710 (2010)
  2. Enzyme activation through the utilization of intrinsic dianion binding energy. Amyes TL, Malabanan MM, Zhai X, Reyes AC, Richard JP. Protein Eng Des Sel 30 157-165 (2017)

Articles - 1tph mentioned but not cited (23)

  1. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Huang B, Schroeder M. BMC Struct Biol 6 19 (2006)
  2. THEMATICS: a simple computational predictor of enzyme function from structure. Ondrechen MJ, Clifton JG, Ringe D. Proc Natl Acad Sci U S A 98 12473-12478 (2001)
  3. Dynamic requirements for a functional protein hinge. Kempf JG, Jung JY, Ragain C, Sampson NS, Loria JP. J Mol Biol 368 131-149 (2007)
  4. Prediction of functional sites based on the fuzzy oil drop model. Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I. PLoS Comput Biol 3 e94 (2007)
  5. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase. Zhai X, Amyes TL, Richard JP. J Am Chem Soc 137 15185-15197 (2015)
  6. Coupling between catalytic loop motions and enzyme global dynamics. Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P. PLoS Comput Biol 8 e1002705 (2012)
  7. Structural mutations that probe the interactions between the catalytic and dianion activation sites of triosephosphate isomerase. Zhai X, Amyes TL, Wierenga RK, Loria JP, Richard JP. Biochemistry 52 5928-5940 (2013)
  8. Reflections on the catalytic power of a TIM-barrel. Richard JP, Zhai X, Malabanan MM. Bioorg Chem 57 206-212 (2014)
  9. Evidence of a triosephosphate isomerase non-catalytic function crucial to behavior and longevity. Roland BP, Stuchul KA, Larsen SB, Amrich CG, Vandemark AP, Celotto AM, Palladino MJ. J Cell Sci 126 3151-3158 (2013)
  10. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. Stovgaard K, Andreetta C, Ferkinghoff-Borg J, Hamelryck T. BMC Bioinformatics 11 429 (2010)
  11. Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase. Zhai X, Go MK, O'Donoghue AC, Amyes TL, Pegan SD, Wang Y, Loria JP, Mesecar AD, Richard JP. Biochemistry 53 3486-3501 (2014)
  12. Wildtype and engineered monomeric triosephosphate isomerase from Trypanosoma brucei: partitioning of reaction intermediates in D2O and activation by phosphite dianion. Malabanan MM, Go MK, Amyes TL, Richard JP. Biochemistry 50 5767-5779 (2011)
  13. A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. Martínez-Castilla LP, Rodríguez-Sotres R. PLoS One 5 e12483 (2010)
  14. ResBoost: characterizing and predicting catalytic residues in enzymes. Alterovitz R, Arvey A, Sankararaman S, Dallett C, Freund Y, Sjölander K. BMC Bioinformatics 10 197 (2009)
  15. Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. Li Z, He Y, Liu Q, Zhao L, Wong L, Kwoh CK, Nguyen H, Li J. BMC Bioinformatics 14 Suppl 16 S11 (2013)
  16. Altered dynamics upon oligomerization corresponds to key functional sites. Mishra SK, Sankar K, Jernigan RL. Proteins 85 1422-1434 (2017)
  17. Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei. Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, López-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Biochim Biophys Acta 1864 1696-1706 (2016)
  18. Protein Conformational Transitions from All-Atom Adaptively Biased Path Optimization. Wu H, Post CB. J Chem Theory Comput 14 5372-5382 (2018)
  19. Prediction of four kinds of simple supersecondary structures in protein by using chemical shifts. Yonge F. ScientificWorldJournal 2014 978503 (2014)
  20. Structural Analysis of an Epitope Candidate of Triosephosphate Isomerase in Opisthorchis viverrini. Son J, Kim S, Kim SE, Lee H, Lee MR, Hwang KY. Sci Rep 8 15075 (2018)
  21. Models to Approximate the Motions of Protein Loops. Skliros A, Jernigan RL, Kloczkowski A. J Chem Theory Comput 6 3249-3258 (2010)
  22. Evolution of Enzyme Function and the Development of Catalytic Efficiency: Triosephosphate Isomerase, Jeremy R. Knowles, and W. John Albery. Gerlt JA. Biochemistry 60 3529-3538 (2021)
  23. Exploring the landscape of protein-ligand interaction energy using probabilistic approach. Pacholczyk M, Kimmel M. J Comput Biol 18 843-850 (2011)


Reviews citing this publication (3)

  1. Triosephosphate isomerase: a highly evolved biocatalyst. Wierenga RK, Kapetaniou EG, Venkatesan R. Cell Mol Life Sci 67 3961-3982 (2010)
  2. Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism. Stengl B, Reuter K, Klebe G. Chembiochem 6 1926-1939 (2005)
  3. A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer. Reyes AC, Amyes TL, Richard JP. Org Biomol Chem 15 8856-8866 (2017)

Articles citing this publication (44)

  1. Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. Copley RR, Bork P. J Mol Biol 303 627-641 (2000)
  2. Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion. Amyes TL, Richard JP. Biochemistry 46 5841-5854 (2007)
  3. Local motions in a benchmark of allosteric proteins. Daily MD, Gray JJ. Proteins 67 385-399 (2007)
  4. The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. Hall DR, Leonard GA, Reed CD, Watt CI, Berry A, Hunter WN. J Mol Biol 287 383-394 (1999)
  5. A substrate in pieces: allosteric activation of glycerol 3-phosphate dehydrogenase (NAD+) by phosphite dianion. Tsang WY, Amyes TL, Richard JP. Biochemistry 47 4575-4582 (2008)
  6. A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase. Richard JP. Biochemistry 51 2652-2661 (2012)
  7. Loop motions of triosephosphate isomerase observed with elastic networks. Kurkcuoglu O, Jernigan RL, Doruker P. Biochemistry 45 1173-1182 (2006)
  8. Mechanism for activation of triosephosphate isomerase by phosphite dianion: the role of a hydrophobic clamp. Malabanan MM, Koudelka AP, Amyes TL, Richard JP. J Am Chem Soc 134 10286-10298 (2012)
  9. Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase. Wang Y, Berlow RB, Loria JP. Biochemistry 48 4548-4556 (2009)
  10. Synthetic peptides as inactivators of multimeric enzymes: inhibition of Plasmodium falciparum triosephosphate isomerase by interface peptides. Singh SK, Maithal K, Balaram H, Balaram P. FEBS Lett 501 19-23 (2001)
  11. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Biophys J 97 1178-1187 (2009)
  12. Molecular wear and tear leads to terminal marking and the unstable isoforms of aging. Gracy RW, Talent JM, Zvaigzne AI. J Exp Zool 282 18-27 (1998)
  13. The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid. Arsenieva D, Hardre R, Salmon L, Jeffery CJ. Proc Natl Acad Sci U S A 99 5872-5877 (2002)
  14. A functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli. Zgiby S, Plater AR, Bates MA, Thomson GJ, Berry A. J Mol Biol 315 131-140 (2002)
  15. Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity. Aparicio R, Ferreira ST, Polikarpov I. J Mol Biol 334 1023-1041 (2003)
  16. Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. Kopp J, Kopriva S, Süss KH, Schulz GE. J Mol Biol 287 761-771 (1999)
  17. Structural determinants for ligand binding and catalysis of triosephosphate isomerase. Kursula I, Partanen S, Lambeir AM, Antonov DM, Augustyns K, Wierenga RK. Eur J Biochem 268 5189-5196 (2001)
  18. Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase. Sun J, Sampson NS. Protein Sci 7 1495-1505 (1998)
  19. Synthesis and biochemical evaluation of selective inhibitors of class II fructose bisphosphate aldolases: towards new synthetic antibiotics. Fonvielle M, Coinçon M, Daher R, Desbenoit N, Kosieradzka K, Barilone N, Gicquel B, Sygusch J, Jackson M, Therisod M. Chemistry 14 8521-8529 (2008)
  20. The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase. Xiang J, Sun J, Sampson NS. J Mol Biol 307 1103-1112 (2001)
  21. Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics. Roland BP, Zeccola AM, Larsen SB, Amrich CG, Talsma AD, Stuchul KA, Heroux A, Levitan ES, VanDemark AP, Palladino MJ. PLoS Genet 12 e1005941 (2016)
  22. Subunit interface mutation disrupting an aromatic cluster in Plasmodium falciparum triosephosphate isomerase: effect on dimer stability. Maithal K, Ravindra G, Nagaraj G, Singh SK, Balaram H, Balaram P. Protein Eng 15 575-584 (2002)
  23. Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency. Roland BP, Amrich CG, Kammerer CJ, Stuchul KA, Larsen SB, Rode S, Aslam AA, Heroux A, Wetzel R, VanDemark AP, Palladino MJ. Biochim Biophys Acta 1852 61-69 (2015)
  24. Enzyme Architecture: The Role of a Flexible Loop in Activation of Glycerol-3-phosphate Dehydrogenase for Catalysis of Hydride Transfer. He R, Reyes AC, Amyes TL, Richard JP. Biochemistry 57 3227-3236 (2018)
  25. Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction-intermediate analog: new insight in the proton transfer reaction mechanism. Alahuhta M, Wierenga RK. Proteins 78 1878-1888 (2010)
  26. Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase. Kulkarni YS, Amyes TL, Richard JP, Kamerlin SCL. J Am Chem Soc 141 16139-16150 (2019)
  27. Revisiting the mechanism of the triosephosphate isomerase reaction: the role of the fully conserved glutamic acid 97 residue. Samanta M, Murthy MR, Balaram H, Balaram P. Chembiochem 12 1886-1896 (2011)
  28. Structure-based inhibitor screening: a family of sulfonated dye inhibitors for malaria parasite triosephosphate isomerase. Joubert F, Neitz AW, Louw AI. Proteins 45 136-143 (2001)
  29. Active site prediction for comparative model structures with thematics. Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ. J Bioinform Comput Biol 3 127-143 (2005)
  30. Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde. Toteva MM, Silvaggi NR, Allen KN, Richard JP. Biochemistry 50 10170-10181 (2011)
  31. Discrimination between closed and open forms of lipases using electrophoretic techniques. Miled N, Riviere M, Cavalier JF, Buono G, Berti L, Verger R. Anal Biochem 338 171-178 (2005)
  32. Missense variant in TPI1 (Arg189Gln) causes neurologic deficits through structural changes in the triosephosphate isomerase catalytic site and reduced enzyme levels in vivo. Roland BP, Richards KR, Hrizo SL, Eicher S, Barile ZJ, Chang TC, Savon G, Bianchi P, Fermo E, Ricerca BM, Tortorolo L, Vockley J, VanDemark AP, Palladino MJ. Biochim Biophys Acta Mol Basis Dis 1865 2257-2266 (2019)
  33. Molecular modeling of the amyloid-beta-peptide using the homology to a fragment of triosephosphate isomerase that forms amyloid in vitro. Contreras CF, Canales MA, Alvarez A, De Ferrari GV, Inestrosa NC. Protein Eng 12 959-966 (1999)
  34. An efficient method for reconstructing protein backbones from alpha-carbon coordinates. Iwata Y, Kasuya A, Miyamoto S. J Mol Graph Model 21 119-128 (2002)
  35. Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase. Salin M, Kapetaniou EG, Vaismaa M, Lajunen M, Casteleijn MG, Neubauer P, Salmon L, Wierenga RK. Acta Crystallogr D Biol Crystallogr 66 934-944 (2010)
  36. Practical synthesis of 4-hydroxy-3-oxobutylphosphonic acid and its evaluation as a bio-isosteric substrate of DHAP aldolase. Arth HL, Fessner WD. Carbohydr Res 305 313-321 (1997)
  37. Structures of unliganded and inhibitor complexes of W168F, a Loop6 hinge mutant of Plasmodium falciparum triosephosphate isomerase: observation of an intermediate position of loop6. Eaazhisai K, Balaram H, Balaram P, Murthy MR. J Mol Biol 343 671-684 (2004)
  38. Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model. Konuklar FA, Aviyente V, Haliloğlu T. Proteins 62 715-727 (2006)
  39. Tyr74 is essential for the formation, stability and function of Plasmodium falciparum triosephosphate isomerase dimer. Espinoza-Fonseca LM, Wong-Ramírez C, Trujillo-Ferrara JG. Arch Biochem Biophys 494 46-57 (2010)
  40. Itavastatin and resveratrol increase triosephosphate isomerase protein in a newly identified variant of TPI deficiency. VanDemark AP, Hrizo SL, Eicher SL, Kowalski J, Myers TD, Pfeifer MR, Riley KN, Koeberl DD, Palladino MJ. Dis Model Mech 15 dmm049261 (2022)
  41. A computational study of the molecular basis of antibiotic resistance in a DXR mutant. Krebs FS, Esque J, Stote RH. J Comput Aided Mol Des 33 927-940 (2019)
  42. Identifying functional sites based on prediction of charged group behavior. Ondrechen MJ. Curr Protoc Bioinformatics Chapter 8 Unit 8.6 (2004)
  43. Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum. Park SH, Kim HS, Park MS, Moon S, Song MK, Park HS, Hahn H, Kim SJ, Bae E, Kim HJ, Han BW. PLoS One 10 e0145331 (2015)
  44. Triosephosphate Isomerase: The Crippling Effect of the P168A/I172A Substitution at the Heart of an Enzyme Active Site. Hegazy R, Richard JP. Biochemistry 62 2916-2927 (2023)


Quick links