Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases
Received date: 27 Sep 2014
Accepted date: 08 Oct 2014
Published date: 22 Jan 2015
Copyright
The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production. Cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne, is a key enzyme in that pathway. Due to its low activity, alk(a/e)ne production by cADO is an inefficient process. Previous biochemical and structural investigations of cADO have provided some information on its catalytic reaction. However, the details of its catalytic processes remain unclear. Here we report five crystal structures of cADO from the Synechococcus elongates strain PCC7942 in both its iron-free and iron-bound forms, representing different states during its catalytic process. Structural comparisons and functional enzyme assays indicate that Glu144, one of the iron-coordinating residues, plays a vital role in the catalytic reaction of cADO. Moreover, the helix where Glu144 resides exhibits two distinct conformations that correlates with the different binding states of the di-iron center in cADO structures. Therefore, our results provide a structural explanation for the highly labile feature of cADO di-iron center, which we proposed to be related to its low enzymatic activity. On the basis of our structural and biochemical data, a possible catalytic process of cADO was proposed, which could aid the design of cADO with improved activity.
Chenjun Jia , Mei Li , Jianjun Li , Jingjing Zhang , Hongmei Zhang , Peng Cao , Xiaowei Pan , Xuefeng Lu , Wenrui Chang . Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases[J]. Protein & Cell, 2015 , 6(1) : 55 -67 . DOI: 10.1007/s13238-014-0108-2
| 1 |
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW
|
| 2 |
Andre C, Kim SW, Yu XH, Shanklin J (2013) Fusing catalase to an alkane-producing enzyme maintains enzymatic activity by converting the inhibitory byproduct H2O2 to the cosubstrate O2. Proc Natl Acad Sci USA110: 3191-3196
|
| 3 |
Aukema KG, Makris TM, Stoian SA, Richman JE, Munck E, Lipscomb JD, Wackett LP (2013) Cyanobacterial aldehyde deformylase oxygenation of aldehydes yields n-1 aldehydes and alcohols in addition to alkanes. ACS Catal3: 2228-2238
|
| 4 |
Das D, Eser BE, Han J, Sciore A, Marsh EN (2011) Oxygenindependent decarbonylation of aldehydes by cyanobacterial aldehyde decarbonylase: a new reaction of diiron enzymes. Angew Chem50: 7148-7152
|
| 5 |
Das D, Ellington B, Paul B, Marsh EN (2014) Mechanistic insights from reaction of alpha-oxiranyl-aldehydes with cyanobacterial aldehyde deformylating oxygenase. ACS Chem Biol9: 570-577
|
| 6 |
Du Bois J, Mizoguchi TJ, Lippard SJ (2000) Understanding the dioxygen reaction chemistry of diiron proteins through synthetic modeling studies. Coord Chem Rev200: 443-485
|
| 7 |
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D66: 486-501
|
| 8 |
Eriksson M, Jordan A, Eklund H (1998) Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms. Biochemistry37: 13359-13369
|
| 9 |
Eser BE, Das D, Han J, Jones PR, Marsh EN (2012) Correction to oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor. Biochemistry51: 5703
|
| 10 |
Hogbom M, Huque Y, Sjoberg BM, Nordlund P (2002) Crystal structure of the di-iron/radical protein of ribonucleotide reductase from corynebacterium ammoniagenes. Biochemistry41: 1381-1389
|
| 11 |
Khara B, Menon N, Levy C, Mansell D, Das D, Marsh EN, Leys D, Scrutton NS (2013) Production of propane and other short-chain alkanes by structure-based engineering of ligand specificity in aldehyde-deformylating oxygenase. ChemBioChem14: 1204-1208
|
| 12 |
Kolberg M, Strand KR, Graff P, Andersson KK (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim Biophys Acta1699: 1-34
|
| 13 |
Krebs C, Bollinger JM, Booker SJ (2011) Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritinlike ‘di-iron-carboxylate’ proteins. Curr Opin Chem Biol15: 291-303
|
| 14 |
Kurtz DM (1997) Structural similarity and functional diversity in diiron-oxo proteins. J Biol Inorg Chem2: 159-167
|
| 15 |
Li N, Norgaard H, Warui DM, Booker SJ, Krebs C, Bollinger JM Jr (2011) Conversion of fatty aldehydes to alka(e)nes and formate by a cyanobacterial aldehyde decarbonylase: cryptic redox by an unusual dimetal oxygenase. J Am Chem Soc133: 6158-6161
|
| 16 |
Li N, Chang WC, Warui DM, Booker SJ, Krebs C, Bollinger JM Jr (2012) Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases. Biochemistry51: 7908-7916
|
| 17 |
Lindqvist Y, Huang W, Schneider G, Shanklin J (1996) Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. EMBO J15: 4081-4092
|
| 18 |
Logan DT, Su XD, Aberg A, Regnstrom K, Hajdu J, Eklund H, Nordlund P (1996) Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site. Structure4: 1053-1064
|
| 19 |
Logan DT, deMare F, Persson BO, Slaby A, Sjoberg BM, Nordlund P (1998) Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygeninsertion step of hydroxylation reactions catalyzed by diiron proteins. Biochemistry37: 10798-10807
|
| 20 |
Mccoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr40: 658-674
|
| 21 |
Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Muller J, Lippard SJ (2001) Dioxygen activation and methane hydroxylation by soluble methane monooxygenase: a tale of two irons and three proteins. Angew Chem Int Ed40: 2782-2807
|
| 22 |
Nordlund P, Eklund H (1995) Di-iron-carboxylate proteins. Curr Opin Struct Biol5: 758-766
|
| 23 |
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol276: 307-326
|
| 24 |
Pandelia ME, Li N, Norgaard H, Warui DM, Rajakovich LJ, Chang WC, Booker SJ, Krebs C, Bollinger JM (2013) Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate. J Am Chem Soc135(42): 15801-15812
|
| 25 |
Paul B, Das D, Ellington B, Marsh EN (2013) Probing the mechanism of cyanobacterial aldehyde decarbonylase using a cyclopropyl aldehyde. J Am Chem Soc135: 5234-5237
|
| 26 |
Sazinsky MH, Lippard SJ (2006) Correlating structure with function in bacterial multicomponent monooxygenases and related diiron proteins. Acc Chem Res39: 558-566
|
| 27 |
Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB (2010) Microbial biosynthesis of alkanes. Science329: 559-562
|
| 28 |
Strand KR, Karlsen S, Kolberg M, Rohr AK, Gorbitz CH, Andersson KK (2004) Crystal structural studies of changes in the native dinuclear iron center of ribonucleotide reductase protein R2 from mouse. J Biol Chem279: 46794-46801
|
| 29 |
Wang W, Liu X, Lu X (2013) Engineering cyanobacteria to improve photosynthetic production of alka(e)nes. Biotechnol Biofuels6: 69
|
| 30 |
Wang Q, Huang X, Zhang J, Lu X, Li S, Li JJ (2014) Engineering self-sufficient aldehyde deformylating oxygenases fused to alternative electron transfer systems for efficient conversion of aldehydes into alkanes. Chem Commun50: 4299-4301
|
| 31 |
Warui DM, Li N, Norgaard H, Krebs C, Bollinger JM Jr, Booker SJ (2011) Detection of formate, rather than carbon monoxide, as the stoichiometric coproduct in conversion of fatty aldehydes to alkanes by a cyanobacterial aldehyde decarbonylase. J Am Chem Soc133: 3316-3319
|
| 32 |
Whittington DA, Lippard SJ (2001) Crystal structures of the soluble methane monooxygenase hydroxylase from methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site. J Am Chem Soc123: 827-838
|
| 33 |
Yang YS, Baldwin J, Ley BA, Bollinger JM, Solomon EI (2000) Spectroscopic and electronic structure description of the reduced binuclear non-heme iron active site in ribonucleotide reductase from E. coli: comparison to reduced delta(9) desaturase and electronic structure contributions to differences in O-2 reactivity. J Am Chem Soc122: 8495-8510
|
| 34 |
Zhang J, Lu X, Li JJ (2013) Conversion of fatty aldehydes into alk (a/e)nes by in vitro reconstituted cyanobacterial aldehyde-deformylating oxygenase with the cognate electron transfer system. Biotechnol Biofuels6: 86
|
/
| 〈 |
|
〉 |