High-throughput structural biology of metabolic enzymes and its impact on human diseases

Journal of Inherited Metabolic Disease

Volumn 34, Issue 3, 2011, Pages 575-581

  Yue, Wyatt W ^a   Oppermann, Udo ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NIHR OXFORD BIOMEDICAL RESEARCH CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONATE DEHYDRATASE; CYANOCOBALAMIN; GERANYLTRANSFERASE; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; METHYLMALONYL COENZYME A MUTASE; OXIDOREDUCTASE; RISEDRONIC ACID; ZOLEDRONIC ACID;

ARTICLE; DRUG METABOLISM; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG TARGETING; ENZYME ACTIVE SITE; ENZYME INHIBITION; ENZYME MECHANISM; ENZYME STRUCTURE; GENE MUTATION; HIGH THROUGHPUT SCREENING; HUMAN; METHYLMALONIC ACIDURIA; NONHUMAN; PROTEIN FUNCTION; STEROID METABOLISM; STRUCTURE ACTIVITY RELATION;

COBAMIDES; DISEASE; DRUG DISCOVERY; ENZYMES; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; METABOLISM; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION;

EID: 79959799596     PISSN: 01418955     EISSN: 15732665     Source Type: Journal    
DOI: 10.1007/s10545-011-9296-6     Document Type: Article

References (35)

1. Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, Marsden BD (2006) Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci 31:76-78 (Pubitemid 43221839)
2. Banerjee R, Gherasim C, Padovani D (2009) The tinker, tailor, soldier in intracellular B12 trafficking. Curr Opin Chem Biol 13:484-491
3. Bayley JP, Launonen V, Tomlinson IP (2008) The FH mutation database: an online database of fumarate hydratase mutations involved in the MCUL (HLRCC) tumor syndrome and congenital fumarase deficiency. BMC Med Genet 9:20
4. Buhaescu I, Izzedine H (2007) Mevalonate pathway: a review of clinical and therapeutical implications. Clin Biochem 40:575-584 (Pubitemid 46829082)
5. Capriotti E, Fariselli P, Casadio R (2004) A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics 20(Suppl 1):i63-i68 (Pubitemid 41296672)
6. Cottingham K (2008) The structural genomics consortium makes its presence known. J Proteome Res 7:5073
7. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C (2009) PSI-2: structural genomics to cover protein domain family space. Structure 17:869-881
8. Dunford JE, Kwaasi AA, Rogers MJ, Barnett BL, Ebetino FH, Russell RG, Oppermann U, Kavanagh KL (2008) Structure-activity relationships among the nitrogen containing bisphosphonates in clinical use and other analogues: time-dependent inhibition of human farnesyl pyrophosphate synthase. J Med Chem 51:2187-2195 (Pubitemid 351503274)
9. Edwards A (2009) Large-scale structural biology of the human proteome. Annu Rev Biochem 78:541-568
10. Froese DS, Gravel RA (2010) Genetic disorders of vitamin B12 metabolism: eight complementation groups - eight genes. Expert Rev Mol Med 12:e37
11. Froese DS, Kochan G, Muniz JR, Wu X, Gileadi C, Ugochukwu E, Krysztofinska E, Gravel RA, Oppermann U, Yue WW (2010) Structures of the human GTPase MMAA and vitamin B12- dependent methylmalonyl-CoA mutase and insight into their complex formation. J Biol Chem 285:38204-38213
12. Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W (2009) Benefits of structural genomics for drug discovery research. Infect Disord Drug Targets 9:459-474
13. Joachimiak A (2009) High-throughput crystallography for structural genomics. Curr Opin Struct Biol 19:573-584
14. Johansson C, Roos AK, Montano SJ, Sengupta R, Filippakopoulos P, Guo K, von Delft F, Holmgren A, Oppermann U, Kavanagh KL (2010) The crystal structure of human GLRX5: iron-sulfur cluster co-ordination, tetrameric assembly and monomer activity. Biochem J 433(2):303-311
15. Kang TS, Stevens RC (2009) Structural aspects of therapeutic enzymes to treat metabolic disorders. Hum Mutat 30:1591-1610
16. Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U (2006) The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc Natl Acad Sci USA 103:7829-7834
17. Kavanagh KL, Jornvall H, Persson B, Oppermann U (2008) The SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell Mol Life Sci 65:3895-3906
18. Kochan G, Pilka ES, von Delft F, Oppermann U, Yue WW (2009) Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A. J Mol Biol 388:997-1008
19. Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD (2009) SGC-structural biology and human health: a new approach to publishing structural biology results. PLoS ONE 4:e7675
20. Lukacik P, Kavanagh KL, Oppermann U (2006) Structure and function of human 17beta-hydroxysteroid dehydrogenases. Mol Cell Endocrinol 248:61-71
21. Muller S, Weigelt J (2010) Open-access public-private partnerships to enable drug discovery - new approaches. IDrugs 13:175-180
22. Ng PC, Henikoff S (2006) Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7:61-80 (Pubitemid 44627922)
23. Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BM, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature 448:87-91 (Pubitemid 47037008)
24. Oppermann U (2007) Carbonyl reductases: the complex relationships of mammalian carbonyl- and quinone-reducing enzymes and their role in physiology. Annu Rev Pharmacol Toxicol 47:293-322
25. Page R, Stevens RC (2004) Crystallization data mining in structural genomics: using positive and negative results to optimize protein crystallization screens. Methods 34:373-389 (Pubitemid 39127455)
26. Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jornvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U (2009) The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chem Biol Interact 178:94-98
27. Picaud SS, Muniz JR, Kramm A, Pilka ES, Kochan G, Oppermann U, Yue WW (2009) Crystal structure of human carbonic anhydrase-related protein VIII reveals the basis for catalytic silencing. Proteins 76:507-511
28. Pojer F, Ferrer JL, Richard SB, Nagegowda DA, Chye ML, Bach TJ, Noel JP (2006) Structural basis for the design of potent and species-specific inhibitors of 3-hydroxy-3-methylglutaryl CoA synthases. Proc Natl Acad Sci USA 103:11491-11496 (Pubitemid 44182479)
29. Savitsky P, Bray J, Cooper CD, Marsden BD, Mahajan P, Burgess-Brown NA, Gileadi O (2010) High-throughput production of human proteins for crystallization: the SGC experience. J Struct Biol 172:3-13
30. Shafqat N, Turnbull A, Zschocke J, Oppermann U, Yue WW (2010) Crystal structures of human HMG-CoA synthase isoforms provide insights into inherited ketogenesis disorders and inhibitor design. J Mol Biol 398:497-506
31. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, Cooper DN (2009) The human gene mutation database: 2008 update. Genome Med 1:13
32. Steward RE, MacArthur MW, Laskowski RA, Thornton JM (2003) Molecular basis of inherited diseases: a structural perspective. Trends Genet 19:505-513 (Pubitemid 37101091)
33. Thusberg J, Vihinen M (2009) Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bio-informatics methods. Hum Mutat 30:703-714
34. Weigelt J (2010) Structural genomics-impact on biomedicine and drug discovery. Exp Cell Res 316:1332-1338
35. Wu X, Lukacik P, Kavanagh KL, Oppermann U (2007) SDR-type human hydroxysteroid dehydrogenases involved in steroid hormone activation. Mol Cell Endocrinol 265-266:71-76 (Pubitemid 46273953)