A standard numbering scheme for thiamine diphosphate-dependent decarboxylases

BMC Biochemistry

Volumn 13, Issue 1, 2012, Pages

  Vogel, Constantin ^a   Widmann, Michael ^a   Pohl, Martina ^b   Pleiss, Jürgen ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BENZALDEHYDE; CARBOXYLYASE; COCARBOXYLASE; MAGNESIUM ION; PHENYLGLYOXYLIC ACID; PYRUVIC ACID;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CRYSTAL STRUCTURE; DATA BASE; ENZYME ENGINEERING; MUTATION; NONHUMAN; PROTEIN FAMILY; RELIABILITY; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; MARKOV CHAINS; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN STRUCTURE, TERTIARY; PYRUVATE DECARBOXYLASE; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT;

EID: 84869078734     PISSN: None     EISSN: 14712091     Source Type: Journal    
DOI: 10.1186/1471-2091-13-24     Document Type: Article

References (56)

1. The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations. Widmann M, Radloff R, Pleiss J, BMC Biochem 2010 11 9 10.1186/1471-2091-11-9 20122171
2. Domain relationships in thiamine diphosphate-dependent enzymes. Duggleby RG, Acc Chem Res 2006 39 550 557 10.1021/ar068022z 16906751
3. Evolutionary analysis of the TPP-dependent enzyme family. Costelloe SJ, Ward JM, Dalby PA, J Mol Evol 2008 66 36 49 10.1007/s00239-007-9056-2 18043855
4. New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli. Werther T, Zimmer A, Wille G, Golbik R, Weiss MS, König S, FEBS J 2010 277 2628 2640 10.1111/j.1742-4658.2010. 07673.x 20553497
5. Thiamin Diphosphate Dependent Enzymes-Transketolase, Pyruvate Oxidase and Pyruvate Decarboxylase. Lindqvist Y, Schneider G, Curr Opin Biotechnol 1993 3 896 901 (Pubitemid 24001503)
6. Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation. Kutter S, Weiss MS, Wille G, Golbik R, Spinka M, König S, J Biol Chem 2009 284 12136 12144 10.1074/jbc.M806228200 19246454
7. A new perspective on thiamine catalysis. Pohl M, Sprenger GA, Müller M, Curr Opin Biotechnol 2004 15 335 342 10.1016/j.copbio.2004.06.002 15296931 (Pubitemid 39024695)
8. Thiamin-diphosphate-dependent enzymes: new aspects of asymmetric C-C bond formation. Pohl M, Lingen B, Müller M, Chemistry 2002 8 5288 5295 10.1002/1521-3765(20021202)8:23<5288::AID-CHEM5288>3.0.CO;2-F 12432496 (Pubitemid 35453332)
9. Thiamin diphosphate in biological chemistry: exploitation of diverse thiamin diphosphate-dependent enzymes for asymmetric chemoenzymatic synthesis. Müller M, Gocke D, Pohl M, FEBS J 2009 276 2894 2904 10.1111/j.1742-4658. 2009.07017.x 19490096
10. Thiamin diphosphate catalysis: enzymic and nonenzymic covalent intermediates. Kluger R, Tittmann K, Chem Rev 2008 108 1797 1833 10.1021/cr068444m 18491870
11. Enzymatic Acyloin and Benzoin Condensations. Pohl M, Dresen C, Beigi M, Müller M, Enzyme Catalysis in Organic Synthesis Weinheim: Wiley-VCH, Drauz K, Gröger H, May O, 2012 919 945
12. Thiamine-Based Enzymes for Biotransformations. Pohl M, Gocke D, Müller M, Handbook of Green Chemistry. Volume 3 Biocatalysis Weinheim: Wiley-VCH, Anastas PT, 2008 75 114
13. MenD as a versatile catalyst for asymmetric synthesis. Müller M, Kurutsch A, Richter M, Brecht V, Sprenger GA, Journal of Molecular Catalysis B-Enzymatic 2009 61 56 66 10.1016/j.molcatb.2009.03.011
14. Using Substrate Analogues To Probe the Kinetic Mechanism and Active Site of Escherichia coli MenD. Fang M, Macova A, Hanson KL, Kos J, Palmer DRJ, Biochemistry 2011 50 8712 8721 10.1021/bi201202n 21928762
15. Benzaldehyde lyase-catalyzed enantioselective carboligation of aromatic aldehydes with mono- and dimethoxy acetaldehyde. Demir AS, Sesenoglu O, Dünkelmann P, Müller M, Org Lett 2003 5 2047 2050 10.1021/ol034415b 12790525 (Pubitemid 37140923)
16. Development of a donor-acceptor concept for enzymatic cross-coupling reactions of aldehydes: the first asymmetric cross-benzoin condensation. Dünkelmann P, Kolter-Jung D, Nitsche A, Demir AS, Siegert P, Lingen B, Baumann M, Pohl M, Müller M, J Am Chem Soc 2002 124 12084 12085 10.1021/ja0271476 12371834 (Pubitemid 35154862)
17. Stereoselective formation of bis(alpha-hydroxy ketones) via enzymatic carboligation. Dünnwald T, Müller M, J Org Chem 2000 65 8608 8612 10.1021/jo0010274 11112581
18. Enantioselective synthesis of hydroxy ketones through cleavage and formation of acyloin linkage. Enzymatic kinetic resolution via C-C bond cleavage. Demir AS, Pohl M, Janzen E, Müller M, J Chem Soc Perkin Trans 2001 1 633 635
19. Menaquinone Biosynthesis in Escherichia coli: Identification of 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a Novel Intermediate and Re-Evaluation of MenD Activity. Jiang M, Cao Y, Guo Z-F, Chen M, Chen X, Guo Z, Biochemistry 2007 46 10979 10989 10.1021/bi700810x 17760421 (Pubitemid 47463049)
20. Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases. Jordan F, Li H, Brown A, Biochemistry 1999 38 6369 6373 10.1021/bi990373g 10350453 (Pubitemid 29242028)
21. Role of glutamate 91 in information transfer during substrate activation of yeast pyruvate decarboxylase. Li H, Furey W, Jordan F, Biochemistry 1999 38 9992 10003 10.1021/bi9902438 10433706 (Pubitemid 29374952)
22. Active site mutants of pyruvate decarboxylase from Zymomonas mobilis-A site-directed mutagenesis study of L112, I472, I476, E473 and N482. Pohl M, Siegert P, Mesch K, Bruhn H, Grötzinger J, Eur J Biochem 1998 257 538 546 10.1046/j.1432-1327.1998.2570538.x 9839941 (Pubitemid 28512120)
23. Catalytic acid-base groups in yeast pyruvate decarboxylase. 1. Site-directed mutagenesis and steady-state kinetic studies on the enzyme with the D28A, H114F, H115F, and E477Q substitutions. Liu M, Sergienko EA, Guo F, Wang J, Tittmann K, Hübner G, Furey W, Jordan F, Biochemistry 2001 40 7355 7368 10.1021/bi002855u 11412090 (Pubitemid 32578001)
24. Catalytic acid-base groups in yeast pyruvate decarboxylase. 3. A steady-state kinetic model consistent with the behavior of both wild-type and variant enzymes at all relevant pH values. Sergienko EA, Jordan F, Biochemistry 2001 40 7382 7403 10.1021/bi002857e 11412092 (Pubitemid 32578003)
25. Catalytic acid-base groups in yeast pyruvate decarboxylase. 2. Insights into the specific roles of D28 and E477 from the rates and stereospecificity of formation of carboligase side products. Sergienko EA, Jordan F, Biochemistry 2001 40 7369 7381 10.1021/bi002856m 11412091 (Pubitemid 32578002)
26. Exchanging the substrate specificities of pyruvate decarboxylase from Zymomonas mobilis and benzoylformate decarboxylase from Pseudomonas putida. Siegert P, McLeish MJ, Baumann M, Iding H, Kneen MM, Kenyon GL, Pohl M, Protein Eng Des Sel 2005 18 345 357 10.1093/protein/gzi035 15930043 (Pubitemid 41399429)
27. Alteration of the substrate specificity of benzoylformate decarboxylase from Pseudomonas putida by directed evolution. Lingen B, Kolter-Jung D, Dünkelmann P, Feldmann R, Grötzinger J, Pohl M, Müller M, ChemBioChem 2003 4 721 726 10.1002/cbic.200200475 12898622 (Pubitemid 37020875)
28. Substrate specificity in thiamin diphosphate-dependent decarboxylases. Andrews FH, McLeish MJ, Bioorg Chem 2012 43 26 36 22245019
29. Berthold Siöberg CL, Gauchenova E, Knoll M, Pleiss J, Müller M, Schneider G, Pohl M: (S)-Selective mixed benzoin condensation by structure-based design of the pyruvate decarboxylase from Acetobacter pasteurianus. Rother D, Kolter G, Gerhards T, ChemCatChem 2011 3 1587 1596 10.1002/cctc.201100054
30. Factors mediating activity, selectivity, and substrate specificity for the thiamin diphosphate-dependent enzymes benzaldehyde lyase and benzoylformate decarboxylase. Knoll M, Müller M, Pleiss J, Pohl M, ChemBioChem 2006 7 1928 1934 10.1002/cbic.200600277 17051662 (Pubitemid 44893528)
31. Rational protein design of ThDP-dependent enzymes-engineering stereoselectivity. Gocke D, Walter L, Gauchenova E, Kolter G, Knoll M, Berthold CL, Schneider G, Pleiss J, Müller M, Pohl M, ChemBioChem 2008 9 406 412 10.1002/cbic.200700598 18224647
32. Standard numbering scheme for class B beta-lactamases. Galleni M, Lamotte-Brasseur J, Rossolini GM, Spencer J, Dideberg O, Frere JM, Antimicrob Agents Chemother 2001 45 660 663 10.1128/AAC.45.3.660-663.2001 11181339 (Pubitemid 32182004)
33. The structure of beta-lactamases. Ambler RP, Philos Trans R Soc Lond B Biol Sci 1980 289 321 331 10.1098/rstb.1980.0049 6109327
34. Update of the standard numbering scheme for class B beta-lactamases. Garau G, Garcia-Saez I, Bebrone C, Anne C, Mercuri P, Galleni M, Frere JM, Dideberg O, Antimicrob Agents Chemother 2004 48 2347 2349 10.1128/AAC.48.7.2347- 2349.2004 15215079 (Pubitemid 38823395)
35. Standard conformations for the canonical structures of immunoglobulins. Al-Lazikani B, Lesk AM, Chothia C, J Mol Biol 1997 273 927 948 10.1006/jmbi.1997.1354 9367782 (Pubitemid 27493729)
36. Kabat EA, Wu TT, Perry H, Sequences of Proteins of Immunological Interest Bethesda, MD: NIH Publication Fifth Edition edn 1991
37. The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis. Takenaka A, Juan ECM, Hoque MM, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Sekiguchi T, Acta Crystallogr Sect F Struct Biol Cryst Commun 2007 63 900 907 10.1107/S1744309107041012 18007037 (Pubitemid 350134955)
38. Pyruvate decarboxylase: A molecular modeling study of pyruvate decarboxylation and acyloin formation. Lobell M, Crout DHG, J Am Chem Soc 1996 118 1867 1873 10.1021/ja951830t (Pubitemid 26100199)
39. Current mechanistic understanding of thiamin diphosphatedependent enzymatic reactions. Jordan F, Nat Prod Rep 2003 20 184 201 10.1039/b111348h 12735696 (Pubitemid 36453606)
40. The role of residues glutamate-50 and phenylalanine-496 in Zymomonas mobilis pyruvate decarboxylase. Candy JM, Koga J, Nixon PF, Duggleby RG, Biochem J 1996 315 745 751 8645153 (Pubitemid 26147598)
41. Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid. Schütz A, Sandalova T, Ricagno S, Hübner G, König S, Schneider G, Eur J Biochem 2003 270 2312 2321 10.1046/j.1432-1033.2003.03601.x 12752451 (Pubitemid 36605580)
42. Role of Glu51 for Cofactor Binding and Catalytic Activity in Pyruvate Decarboxylase from Yeast Studied by Site-Directed Mutagenesis. Killenberg-Jabs M, König S, Eberhardt I, Hohmann S, Hübner G, Biochemistry 1997 36 1900 1905 10.1021/bi961341l 9048576 (Pubitemid 27086288)
43. Reaction mechanisms of thiamin diphosphate enzymes: new insights into the role of a conserved glutamate residue. Shaanan B, Chipman DM, FEBS J 2009 276 2447 2453 10.1111/j.1742-4658.2009.06965.x 19476486
44. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Notredame C, Higgins DG, Heringa J, J Mol Biol 2000 302 205 217 10.1006/jmbi.2000.4042 10964570
45. A common structural motif in thiamin pyrophosphate-binding enzymes. Hawkins CF, Borges A, Perham RN, FEBS Lett 1989 255 77 82 10.1016/0014-5793(89) 81064-6 2792374 (Pubitemid 19224047)
46. Pyruvate decarboxylase is like acetolactate synthase (ILV2) and not like the pyruvate dehydrogenase E1 subunit. Green JB, FEBS Lett 1989 246 1 5 10.1016/0014-5793(89)80241-8 2651151 (Pubitemid 19087759)
47. Molecular cloning of the gene for indolepyruvate decarboxylase from Enterobacter cloacae. Koga J, Adachi T, Hidaka H, Mol Gen Genet 1991 226 10 16 10.1007/BF00273581 2034209
48. Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL, Biochemistry 1990 29 9856 9862 10.1021/bi00494a015 2271624 (Pubitemid 20348519)
49. Systematic Analysis of Metallo-beta-Lactamases Using an Automated Database. Widmann M, Pleiss J, Oelschlaeger P, Antimicrob Agents Chemother 2012 56 3481 3491 10.1128/AAC.00255-12 22547615
50. A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. Thompson JD, Linard B, Lecompte O, Poch O, PLoS One 2011 6 18093 10.1371/journal.pone.0018093 21483869
51. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li WZ, Lopez R, McWilliam H, Remmert M, Soding J, et al. Mol Syst Biol 2011 7 539 21988835
52. Multiple Protein-Sequence Alignment from Tertiary Structure Comparison-Assignment of Global and Residue Confidence Levels. Russell RB, Barton GJ, Proteins 1992 14 309 323 10.1002/prot.340140216 1409577
53. Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes. Kaplun A, Binshtein E, Vyazmensky M, Steinmetz A, Barak Z, Chipman DM, Tittmann K, Shaanan B, Nat Chem Biol 2008 4 113 118 10.1038/nchembio.62 18176558
54. Structural and sequence patterns in the loops of beta-alpha-beta units. Edwards MS, Sternberg MJE, Thornton JM, Protein Eng 1987 1 173 181 10.1093/protein/1.3.173 3507703 (Pubitemid 18025226)
55. HMMER http://hmmer.janelia.org/
56. Role of pyruvate in enhancing pyruvate decarboxylase stability towards benzaldehyde. Rosche B, Breuer M, Hauer B, Rogers PL, J Biotechnol 2005 115 91 99 10.1016/j.jbiotec.2004.08.002 15607228 (Pubitemid 39656436)