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Structural basis of compound recognition by adenosine deaminase.

Kinoshita T, Nakanishi I, Terasaka T, Kuno M, Seki N, Warizaya M, Matsumura H, Inoue T, Takano K, Adachi H, Mori Y, Fujii T
Biochemistry 44 10562-9 (2005)
Cited: 28 times
EuropePMC logo PMID: 16060665

Abstract

Structural snapshots corresponding to various states enable elucidation of the molecular recognition mechanism of enzymes. Adenosine deaminase has two distinct conformations, an open form and a closed form, although it has so far been unclear what factors influence adaptation of the alternative conformations. Herein, we have determined the first nonligated structure as an initial state, which was the open form, and have thereby rationally deduced the molecular recognition mechanism. Inspection of the active site in the nonligated and ligated states indicated that occupancy at one of the water-binding positions in the nonligated state was highly significant in determining alternate conformations. When this position is empty, subsequent movement of Phe65 toward the space induces the closed form. On the other hand, while occupied, the overall conformation remains in the open form. This structural understanding should greatly assist structure-oriented drug design and enable control of the enzymatic activity.

Articles - 1wxy mentioned but not cited (5)

  1. Sampling protein motion and solvent effect during ligand binding. Limongelli V, Marinelli L, Cosconati S, La Motta C, Sartini S, Mugnaini L, Da Settimo F, Novellino E, Parrinello M. Proc Natl Acad Sci U S A 109 1467-1472 (2012)
  2. Development and validation of an improved algorithm for overlaying flexible molecules. Taylor R, Cole JC, Cosgrove DA, Gardiner EJ, Gillet VJ, Korb O. J Comput Aided Mol Des 26 451-472 (2012)
  3. Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase. Jia Q, Xie W. Nucleic Acids Res 47 3233-3243 (2019)
  4. The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. Xia J, Hsieh JH, Hu H, Wu S, Wang XS. J Chem Inf Model 57 1414-1425 (2017)
  5. Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels. Pan Y, Qi R, Li M, Wang B, Huang H, Han W. RSC Adv 10 43994-44002 (2020)


Reviews citing this publication (2)

  1. Moonlighting adenosine deaminase: a target protein for drug development. Cortés A, Gracia E, Moreno E, Mallol J, Lluís C, Canela EI, Casadó V. Med Res Rev 35 85-125 (2015)
  2. [Application and development of structure-based drug design using X-ray analysis]. Kinoshita T. Nihon Yakurigaku Zasshi 129 186-190 (2007)

Articles citing this publication (21)

  1. Structural basis for the growth factor activity of human adenosine deaminase ADA2. Zavialov AV, Yu X, Spillmann D, Lauvau G, Zavialov AV. J Biol Chem 285 12367-12377 (2010)
  2. Chemical Mutagenesis of an Emissive RNA Alphabet. Rovira AR, Fin A, Tor Y. J Am Chem Soc 137 14602-14605 (2015)
  3. Molecular Evidence of Adenosine Deaminase Linking Adenosine A2A Receptor and CD26 Proteins. Moreno E, Canet J, Gracia E, Lluís C, Mallol J, Canela EI, Cortés A, Casadó V. Front Pharmacol 9 106 (2018)
  4. Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase. Xu S, Li W, Zhu J, Wang R, Li Z, Xu GL, Ding J. Cell Res 23 1296-1309 (2013)
  5. The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors. Gracia E, Farré D, Cortés A, Ferrer-Costa C, Orozco M, Mallol J, Lluís C, Canela EI, McCormick PJ, Franco R, Fanelli F, Casadó V. FASEB J 27 1048-1061 (2013)
  6. Structural insight into human CK2alpha in complex with the potent inhibitor ellagic acid. Sekiguchi Y, Nakaniwa T, Kinoshita T, Nakanishi I, Kitaura K, Hirasawa A, Tsujimoto G, Tada T. Bioorg Med Chem Lett 19 2920-2923 (2009)
  7. Enzymatic interconversion of isomorphic fluorescent nucleosides: adenosine deaminase transforms an adenosine analogue into an inosine analogue. Sinkeldam RW, McCoy LS, Shin D, Tor Y. Angew Chem Int Ed Engl 52 14026-14030 (2013)
  8. Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity. Larson ET, Deng W, Krumm BE, Napuli A, Mueller N, Van Voorhis WC, Buckner FS, Fan E, Lauricella A, DeTitta G, Luft J, Zucker F, Hol WG, Verlinde CL, Merritt EA. J Mol Biol 381 975-988 (2008)
  9. Conformational change of adenosine deaminase during ligand-exchange in a crystal. Kinoshita T, Tada T, Nakanishi I. Biochem Biophys Res Commun 373 53-57 (2008)
  10. Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine. Goble AM, Zhang Z, Sauder JM, Burley SK, Swaminathan S, Raushel FM. Biochemistry 50 6589-6597 (2011)
  11. Mixed inhibition of adenosine deaminase activity by 1,3-dinitrobenzene: a model for understanding cell-selective neurotoxicity in chemically-induced energy deprivation syndromes in brain. Wang Y, Liu X, Schneider B, Zverina EA, Russ K, Wijeyesakere SJ, Fierke CA, Richardson RJ, Philbert MA. Toxicol Sci 125 509-521 (2012)
  12. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Biochemistry 52 6525-6536 (2013)
  13. Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations. Tian X, Liu Y, Zhu J, Yu Z, Han J, Wang Y, Han W. PLoS One 13 e0207234 (2018)
  14. Role of adenosine deaminase 2 gene variants in pediatric deficiency of adenosine deaminase 2: A structural biological approach. Zervou MI, Goulielmos GN, Matalliotakis M, Matalliotaki C, Spandidos DA, Eliopoulos E. Mol Med Rep 21 876-882 (2020)
  15. Exploring the binding modes of cordycepin to human adenosine deaminase 1 (ADA1) compared to adenosine and 2'-deoxyadenosine. Niramitranon J, Pongprayoon P. J Mol Model 26 29 (2020)
  16. Inhibitory activity of hibifolin on adenosine deaminase- experimental and molecular modeling study. Arun KG, Sharanya CS, Sandeep PM, Sadasivan C. Comput Biol Chem 64 353-358 (2016)
  17. Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog. Bucardo MS, Wu Y, Ludford PT, Li Y, Fin A, Tor Y. ACS Chem Biol 16 1208-1214 (2021)
  18. Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation. Ma MT, Jennings MR, Blazeck J, Lieberman RL. Acta Crystallogr D Struct Biol 78 91-103 (2022)
  19. A Quantitative Measure of Conformational Changes in Apo, Holo and Ligand-Bound Forms of Enzymes. Singh S, Singh AK, Wadhwa G, Singh DB, Dwivedi S, Gautam B, Ramteke PW. Interdiscip Sci 8 192-201 (2016)
  20. A quantitative measure of conformational changes in Apo, holo and ligand bound form of enzymes. Singh S, Singh AK, Wadhwa G, Singh DB, Dwivedi S, Gautam B, Ramteke PW. Interdiscip Sci (2015)
  21. Optimized expression and purification of a human adenosine deaminase in E. coli and characterization of its Asp8Asn variant. Jennings MR, Min S, Xu GS, Homayuni K, Suresh B, Haikal YA, Blazeck J. Protein Expr Purif 213 106362 (2024)


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