메뉴 건너뛰기




Volumn 20, Issue 11, 2011, Pages 1891-1906

Determination of the amino acid sequence requirements for catalysis by the highly proficient orotidine monophosphate decarboxylase

Author keywords

Active site residue stringency; High proficiency; Information content; Orotidine decarboxylase

Indexed keywords

ASPARTIC ACID; CYSTEINE; OROTIDINE 5' PHOSPHATE DECARBOXYLASE;

EID: 80054720806     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.728     Document Type: Article
Times cited : (5)

References (48)
  • 1
  • 2
    • 0035543093 scopus 로고    scopus 로고
    • The depth of chemical time and the power of enzymes as catalysts
    • Wolfenden R, Snider MJ (2001) The depth of chemical time and the power of enzymes as catalysts. Acc Chem Res 34:938-945.
    • (2001) Acc Chem Res , vol.34 , pp. 938-945
    • Wolfenden, R.1    Snider, M.J.2
  • 4
    • 0035997393 scopus 로고    scopus 로고
    • Catalytic proficiency: The unusual case of OMP decarboxylase
    • DOI 10.1146/annurev.biochem.71.110601.135446
    • Miller BG, Wolfenden R (2002) Catalytic proficiency: the unusual case of OMP decarboxylase. Ann Rev Biochem 71:847-885. (Pubitemid 34800237)
    • (2002) Annual Review of Biochemistry , vol.71 , pp. 847-885
    • Miller, B.G.1    Wolfenden, R.2
  • 5
    • 0035900982 scopus 로고    scopus 로고
    • Metal ion inhibition of nonenzymatic pyridoxal phosphate catalyzed decarboxylation and transamination
    • DOI 10.1021/ja0026354
    • Zabinski RF, Toney MD (2001) Metal ion inhibition of nonenzymatic pyridoxal phosphate catalyzed decarboxylation and transamination. J Am Chem Soc 123:193-198. (Pubitemid 32062162)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.2 , pp. 193-198
    • Zabinski, R.F.1    Toney, M.D.2
  • 6
    • 0035997936 scopus 로고    scopus 로고
    • Identification of active antiviral compounds against a New York isolate of West Nile virus
    • DOI 10.1016/S0166-3542(02)00013-X, PII S016635420200013X
    • Morrey JD, Smee DF, Sidwell RW, Tseng C (2002) Identification of active antiviral compounds against a New York isolate of West Nile virus. Antiviral Res 55:107-116. (Pubitemid 34655646)
    • (2002) Antiviral Research , vol.55 , Issue.1 , pp. 107-116
    • Morrey, J.D.1    Smee, D.F.2    Sidwell, R.W.3    Tseng, C.4
  • 7
    • 0023639937 scopus 로고
    • Novel pyrazolo[3,4-d]pyrimidine nucleoside analog with broad-spectrum antiviral activity
    • Smee DF, McKernan PA, Nord LD, Willis RC, Petrie CR, Riley TM, Revankar GR, Robins RK, Smith RA (1987) Novel pyrazolo[3,4-d]pyrimidine nucleoside analog with broad-spectrum antiviral activity. Antimicrob Agents Chemother 31:1535-1541. (Pubitemid 17140807)
    • (1987) Antimicrobial Agents and Chemotherapy , vol.31 , Issue.10 , pp. 1535-1541
    • Smee, D.F.1    McKernan, P.A.2    Nord, L.D.3
  • 9
    • 13444273194 scopus 로고    scopus 로고
    • A novel enzyme complex of orotate phosphoribosyltransferase and orotidine 5′-monophosphate decarboxylase in human malaria parasite Plasmodium falciparum: Physical association, kinetics, and inhibition characterization
    • DOI 10.1021/bi048439h
    • Krungkrai SR, DelFraino BJ, Smiley JA, Prapunwattana P, Mitamura T, Horii T, Krungkrai J (2005) A novel enzyme complex of orotate phosphoribosyltransferase and orotidine 5′-monophosphate decarboxylase in human malaria parasite Plasmodium falciparum: physical association, kinetics, and inhibition characterization. Biochemistry 44:1643-1652. (Pubitemid 40204405)
    • (2005) Biochemistry , vol.44 , Issue.5 , pp. 1643-1652
    • Krungkrai, S.R.1    DelFraino, B.J.2    Smiley, J.A.3    Prapunwattana, P.4    Mitamura, T.5    Horii, T.6    Krungkrai, J.7
  • 11
    • 0034681950 scopus 로고    scopus 로고
    • Structural basis for the catalytic mechanism of a proficient enzyme: Orotidine 5'-monophosphate decarboxylase
    • DOI 10.1021/bi992952r
    • Harris P, Navarro Poulsen JC, Jensen KF, Larsen S (2000) Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5′-monophosphate decarboxylase. Biochemistry 39:4217-4224. (Pubitemid 30212635)
    • (2000) Biochemistry , vol.39 , Issue.15 , pp. 4217-4224
    • Harris, P.1    Poulsen, J.-C.N.2    Jensen, K.F.3    Larsen, S.4
  • 12
    • 35448960396 scopus 로고    scopus 로고
    • OMP decarboxylase - An enigma persists
    • Callahan BP, Miller BG (2007) OMP decarboxylase - an enigma persists. Bioorg Chem 35:465-469.
    • (2007) Bioorg Chem , vol.35 , pp. 465-469
    • Callahan, B.P.1    Miller, B.G.2
  • 13
    • 38949172353 scopus 로고    scopus 로고
    • a of the C-6 proton of enzyme-bound UMP
    • DOI 10.1021/ja710384t
    • Amyes TL, Wood BM, Chan K, Gerlt JA, Richard JP (2008) Formation and stability of a vinyl carbanion at the active site of orotidine 5′-monophosphate decarboxylase: pKa of the C-6 proton of enzyme-bound UMP. J Am Chem Soc 130:1574-1575. (Pubitemid 351214072)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.5 , pp. 1574-1575
    • Amyes, T.L.1    Wood, B.M.2    Chan, K.3    Gerlt, J.A.4    Richard, J.P.5
  • 14
    • 77952556805 scopus 로고    scopus 로고
    • (YEAR)Product deuterium isotope effects for orotidine 5′-monophosphate decarboxylase: Effect of changing substrate and enzyme structure on the partitioning of the vinyl carbanion reaction intermediate
    • Toth K, Amyes TL, Wood BM, Chan K, Gerlt JA, Richard JP(YEAR)Product deuterium isotope effects for orotidine 5′-monophosphate decarboxylase: effect of changing substrate and enzyme structure on the partitioning of the vinyl carbanion reaction intermediate. J Am Chem Soc 132:7018-7024.
    • J Am Chem Soc , vol.132 , pp. 7018-7024
    • Toth, K.1    Amyes, T.L.2    Wood, B.M.3    Chan, K.4    Gerlt, J.A.5    Richard, J.P.6
  • 15
    • 38849119713 scopus 로고    scopus 로고
    • Carbon isotope effect study on orotidine 5′-monophosphate decarboxylase: Support for an anionic intermediate
    • DOI 10.1021/bi701664n
    • Van Vleet JL, Reinhardt LA, Miller BG, Sievers A, Cleland WW (2008) Carbon isotope effect study on orotidine 5′-monophosphate decarboxylase: support for an anionic intermediate. Biochemistry 47:798-803. (Pubitemid 351195451)
    • (2008) Biochemistry , vol.47 , Issue.2 , pp. 798-803
    • Van Vleet, J.L.1    Reinhardt, L.A.2    Miller, B.G.3    Sievers, A.4    Cleland, W.W.5
  • 17
    • 0036040211 scopus 로고    scopus 로고
    • Substrate binding induces domain movements in orotidine 5′-monophosphate decarboxylase
    • DOI 10.1016/S0022-2836(02)00200-0
    • Harris P, Poulsen JC, Jensen KF, Larsen S (2002) Substrate binding induces domain movements in orotidine 5′-monophosphate decarboxylase. J Mol Biol 318:1019-1029. (Pubitemid 35007365)
    • (2002) Journal of Molecular Biology , vol.318 , Issue.4 , pp. 1019-1029
    • Harris, P.1    Poulsen, J.-C.N.2    Jensen, K.F.3    Larsen, S.4
  • 18
    • 0034682613 scopus 로고    scopus 로고
    • Contribution of enzyme-phosphoribosyl contacts to catalysis by orotidine 5'-phosphate decarboxylase
    • DOI 10.1021/bi000818x
    • Miller BG, Snider MJ, Short SA, Wolfenden R (2000) Contribution of enzyme-phosphoribosyl contacts to catalysis by orotidine 5′-phosphate decarboxylase. Biochemistry 39:8113-8118. (Pubitemid 30460959)
    • (2000) Biochemistry , vol.39 , Issue.28 , pp. 8113-8118
    • Miller, B.G.1    Snider, M.J.2    Short, S.A.3    Wolfenden, R.4
  • 20
    • 27844574242 scopus 로고    scopus 로고
    • Activation of orotidine 5′-monophosphate decarboxylase by phosphite dianion: The whole substrate is the sum of two parts
    • DOI 10.1021/ja055493s
    • Amyes TL, Richard JP, Tait JJ (2005) Activation of orotidine 5′-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts. J Am Chem Soc 127:15708-15709. (Pubitemid 41643272)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.45 , pp. 15708-15709
    • Amyes, T.L.1    Richard, J.P.2    Tait, J.J.3
  • 21
    • 79955438648 scopus 로고    scopus 로고
    • OMP decarboxylase: Phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate
    • Goryanova B, Amyes TL, Gerlt JA, Richard JP (2011) OMP decarboxylase: phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate. J Am Chem Soc 133:6545-6548.
    • (2011) J Am Chem Soc , vol.133 , pp. 6545-6548
    • Goryanova, B.1    Amyes, T.L.2    Gerlt, J.A.3    Richard, J.P.4
  • 22
    • 40849097646 scopus 로고    scopus 로고
    • Free-energy landscape of enzyme catalysis
    • DOI 10.1021/bi800049z
    • Benkovic SJ, Hammes GG, Hammes-Schiffer S (2008) Free-energy landscape of enzyme catalysis. Biochemistry 47:3317-3321. (Pubitemid 351399220)
    • (2008) Biochemistry , vol.47 , Issue.11 , pp. 3317-3321
    • Benkovic, S.J.1    Hammes, G.G.2    Hammes-Schiffer, S.3
  • 24
  • 25
    • 7944238165 scopus 로고    scopus 로고
    • Analysis of the context dependent sequence requirements of active site residues in the metallo-beta-lactamase IMP-1
    • DOI 10.1016/j.jmb.2004.09.074, PII S0022283604012318
    • Materon IC, Beharry Z, Huang W, Perez C, Palzkill T (2004) Analysis of the context dependent sequence requirements of active site residues in the metallobeta- lactamase IMP-1. J Mol Biol 344:653-663. (Pubitemid 39469210)
    • (2004) Journal of Molecular Biology , vol.344 , Issue.3 , pp. 653-663
    • Materon, I.C.1    Beharry, Z.2    Huang, W.3    Perez, C.4    Palzkill, T.5
  • 26
    • 0025363984 scopus 로고
    • Deciphering the message in protein sequences: Tolerance to amino acid substitutions
    • Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT (1990) Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247:1306-1310.
    • (1990) Science , vol.247 , pp. 1306-1310
    • Bowie, J.U.1    Reidhaar-Olson, J.F.2    Lim, W.A.3    Sauer, R.T.4
  • 27
    • 0018408037 scopus 로고
    • Evidence for transcriptional regulation of orotidine-5'-phosphate decarboxylase in yeast by hybridization of mRNA to the yeast structural gene cloned in Escherichia coli
    • Bach ML, Lacroute F, Botstein D (1979) Evidence for transcriptional regulation of orotidine-5′-phosphate decarboxylase in yeast by hybridization of mRNA to the yeast structural gene cloned in Escherichia coli. Proc Natl Acad Sci USA 76:386-390. (Pubitemid 9110201)
    • (1979) Proceedings of the National Academy of Sciences of the United States of America , vol.76 , Issue.1 , pp. 386-390
    • Bach, M.L.1    Lacroute, F.2    Botstein, D.3
  • 28
    • 0028180877 scopus 로고
    • PKSS - A second-generation general purpose cloning vector for efficient positive selection of recombinant clones
    • Kast P (1994) pKSS - a second-generation general purpose cloning vector for efficient positive selection of recombinant clones. Gene 138:109-114.
    • (1994) Gene , vol.138 , pp. 109-114
    • Kast, P.1
  • 29
    • 0035805488 scopus 로고    scopus 로고
    • Dissecting a charged network at the active site of orotidine- 5′-phosphate decarboxylase
    • Miller BG, Snider MJ, Wolfenden R, Short SA (2001) Dissecting a charged network at the active site of orotidine- 5′-phosphate decarboxylase. J Biol Chem 276: 15174-15176.
    • (2001) J Biol Chem , vol.276 , pp. 15174-15176
    • Miller, B.G.1    Snider, M.J.2    Wolfenden, R.3    Short, S.A.4
  • 30
    • 0037177230 scopus 로고    scopus 로고
    • Mapping the active site - Ligand interactions of orotidine 5′-monophosphate decarboxylase by crystallography
    • DOI 10.1021/bi015758p
    • Wu N, Gillon W, Pai EF (2002) Mapping the active site-ligand interactions of orotidine 5′-monophosphate decarboxylase by crystallography. Biochemistry 41: 4002-4011. (Pubitemid 34251039)
    • (2002) Biochemistry , vol.41 , Issue.12 , pp. 4002-4011
    • Wu, N.1    Gillon, W.2    Pai, E.F.3
  • 31
    • 0023042283 scopus 로고
    • Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes
    • Studier FW, Moffatt BA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189:113-130.
    • (1986) J Mol Biol , vol.189 , pp. 113-130
    • Studier, F.W.1    Moffatt, B.A.2
  • 32
    • 33746911969 scopus 로고    scopus 로고
    • Design of inhibitors of orotidine monophosphate decarboxylase using bioisosteric replacement and determination of inhibition kinetics
    • DOI 10.1021/jm060202r
    • Poduch E, Bello AM, Tang S, Fujihashi M, Pai EF, Kotra LP (2006) Design of inhibitors of orotidine monophosphate decarboxylase using bioisosteric replacement and determination of inhibition kinetics. J Med Chem 49:4937-4945. (Pubitemid 44201051)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.16 , pp. 4937-4945
    • Poduch, E.1    Bello, A.M.2    Tang, S.3    Fujihashi, M.4    Pai, E.F.5    Kotra, L.P.6
  • 34
    • 0026342532 scopus 로고
    • Information- Theoretical entropy as a measure of sequence variability
    • Shenkin PS, Erman B, Mastrandrea LD (1991) Information- theoretical entropy as a measure of sequence variability. Proteins 11:297-313.
    • (1991) Proteins , vol.11 , pp. 297-313
    • Shenkin, P.S.1    Erman, B.2    Mastrandrea, L.D.3
  • 35
    • 41149088218 scopus 로고    scopus 로고
    • Structure and inhibition of orotidine 5′-monophosphate decarboxylase from Plasmodium falciparum
    • DOI 10.1021/bi702390k
    • Langley DB, Shojaei M, Chan C, Lok HC, Mackay JP, Traut TW, Guss JM, Christopherson RI (2008) Structure and inhibition of orotidine 5′-monophosphate decarboxylase from Plasmodium falciparum. Biochemistry 47:3842-3854. (Pubitemid 351431374)
    • (2008) Biochemistry , vol.47 , Issue.12 , pp. 3842-3854
    • Langley, D.B.1    Shojaei, M.2    Chan, C.3    Hiu, C.L.4    Mackay, J.P.5    Traut, T.W.6    Guss, J.M.7    Christopherson, R.I.8
  • 36
    • 0034665993 scopus 로고    scopus 로고
    • The chemistry of the reaction determines the invariant amino acids during the evolution and divergence of orotidine 5′-monophosphate decarboxylase
    • Traut TW, Temple BR (2000) The chemistry of the reaction determines the invariant amino acids during the evolution and divergence of orotidine 5′-monophosphate decarboxylase. J Biol Chem 275:28675-28681.
    • (2000) J Biol Chem , vol.275 , pp. 28675-28681
    • Traut, T.W.1    Temple, B.R.2
  • 37
    • 48249090425 scopus 로고    scopus 로고
    • Dissecting the total transition state stabilization provided by amino acid side chains at orotidine 5′- Monophosphate decarboxylase: A two-part substrate approach
    • Barnett SA, Amyes TL, Wood BM, Gerlt JA, Richard JP (2008) Dissecting the total transition state stabilization provided by amino acid side chains at orotidine 5′- monophosphate decarboxylase: a two-part substrate approach. Biochemistry 47:7785-7787.
    • (2008) Biochemistry , vol.47 , pp. 7785-7787
    • Barnett, S.A.1    Amyes, T.L.2    Wood, B.M.3    Gerlt, J.A.4    Richard, J.P.5
  • 38
    • 0031765412 scopus 로고    scopus 로고
    • Chemical reactivity of penicillins and cephalosporins. Intramolecular involvement of the acyl-amido side chain
    • DOI 10.1021/jo981628j
    • Llinas A, Vilanova B, Frau J, Munoz F, Donoso J, Page MI (1998) Chemical reactivity of penicillins and cephalosporins, intramolecular involvement of the acyl-amido side chain. J Org Chem 63:9052-9060. (Pubitemid 28557565)
    • (1998) Journal of Organic Chemistry , vol.63 , Issue.24 , pp. 9052-9060
    • Llinas, A.1    Vilanova, B.2    Frau, J.3    Munoz, F.4    Donoso, J.5    Page, M.I.6
  • 40
    • 0000182975 scopus 로고
    • XL1- Blue: A high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection
    • Bullock WO, Fernandez JM, Short JM (1987) XL1- Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection. BioTechniques 5:376-379.
    • (1987) BioTechniques , vol.5 , pp. 376-379
    • Bullock, W.O.1    Fernandez, J.M.2    Short, J.M.3
  • 41
    • 0036841628 scopus 로고    scopus 로고
    • Creating randomized amino acid libraries with the QuikChange Multi Site-Directed Mutagenesis Kit
    • Hogrefe HH, Cline J, Youngblood GL, Allen RM (2002) Creating randomized amino acid libraries with the QuikChange Multi Site-Directed Mutagenesis Kit. Bio- Techniques 33:1158-1160, 1162, 1164-1165.
    • (2002) Bio- Techniques , vol.33
    • Hogrefe, H.H.1    Cline, J.2    Youngblood, G.L.3    Allen, R.M.4
  • 42
    • 0028828710 scopus 로고
    • New plasmids carrying antibiotic-resistance cassettes
    • Reece KS, Phillips GJ (1995) New plasmids carrying antibiotic-resistance cassettes. Gene 165:141-142.
    • (1995) Gene , vol.165 , pp. 141-142
    • Reece, K.S.1    Phillips, G.J.2
  • 43
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254.
    • (1976) Anal Biochem , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 44
    • 0026677723 scopus 로고
    • Orotidylate decarboxylase: Insights into the catalytic mechanism from substrate specificity studies
    • DOI 10.1021/bi00163a026
    • Shostak K, Jones ME (1992) Orotidylate decarboxylase: insights into the catalytic mechanism from substrate specificity studies. Biochemistry 31:12155-12161. (Pubitemid 23011361)
    • (1992) Biochemistry , vol.31 , Issue.48 , pp. 12155-12161
    • Shostak, K.1    Jones, M.E.2
  • 45
    • 67649173263 scopus 로고    scopus 로고
    • Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Effect of solvent viscosity on kinetic constants
    • Wood BM, Chan KK, Amyes TL, Richard JP, Gerlt JA (2009) Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: effect of solvent viscosity on kinetic constants. Biochemistry 48:5510-5517.
    • (2009) Biochemistry , vol.48 , pp. 5510-5517
    • Wood, B.M.1    Chan, K.K.2    Amyes, T.L.3    Richard, J.P.4    Gerlt, J.A.5
  • 46
  • 48
    • 0003845223 scopus 로고    scopus 로고
    • San Carlos, CA, USA: Delano Scientific. Available at
    • DeLano WL (2002) The PyMOL Molecular Graphics System. San Carlos, CA, USA: Delano Scientific. Available at: www.pymol.org.
    • (2002) The PyMOL Molecular Graphics System
    • DeLano, W.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.