Alcohol dehydrogenase
From Proteopedia
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<Structure load='1htb' size='400' frame='true' align='right' caption='human alcohol dehydrogenase β3 dimer ternary complex with NAD, iodopyrazole and chloride (green) and Zn+2 (grey) ions, [[1htb]]'/> | <Structure load='1htb' size='400' frame='true' align='right' caption='human alcohol dehydrogenase β3 dimer ternary complex with NAD, iodopyrazole and chloride (green) and Zn+2 (grey) ions, [[1htb]]'/> | ||
[[Image:1htb2.png|thumb|left|250px|Structure of Alcohol Dehydrogenase]]'''Alcohol dehydrogenase''' (ADH, EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1]) is an 80kDa enzyme that catalyzes the 4th step in the metabolism of fructose before [[glycolysis]]. In the 4th step, glyceraldehyde is converted to the glycolytic intermediate DHAP by the NADH-dependent, ADH catalyzed reduction to glycerol.<ref>Voet, et. al. ''Fundamentals of Biochemistry: 3rd Edition''. Hoboken: Wiley & Sons, Inc, 2008.</ref> ADH catalyzes the oxidation of primary and secondary alcohols to their corresponding aldehydes and ketones through a mechanism that involves the removal of a hydrogen. For detailed discussion of horse liver alcohol dehydrogenase see [[Horse Liver Alcohol Dehydrogenase]]. More detailed discussions in<br /> | [[Image:1htb2.png|thumb|left|250px|Structure of Alcohol Dehydrogenase]]'''Alcohol dehydrogenase''' (ADH, EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1]) is an 80kDa enzyme that catalyzes the 4th step in the metabolism of fructose before [[glycolysis]]. In the 4th step, glyceraldehyde is converted to the glycolytic intermediate DHAP by the NADH-dependent, ADH catalyzed reduction to glycerol.<ref>Voet, et. al. ''Fundamentals of Biochemistry: 3rd Edition''. Hoboken: Wiley & Sons, Inc, 2008.</ref> ADH catalyzes the oxidation of primary and secondary alcohols to their corresponding aldehydes and ketones through a mechanism that involves the removal of a hydrogen. For detailed discussion of horse liver alcohol dehydrogenase see [[Horse Liver Alcohol Dehydrogenase]]. More detailed discussions in<br /> | ||
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*[[Tetrameric alcohol dehydrogenases]]<br /> | *[[Tetrameric alcohol dehydrogenases]]<br /> |
Revision as of 13:00, 16 January 2013
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- Tetrameric alcohol dehydrogenases
- Alcohol dehydrogenase from Clostridium beijerinckii
- Alcohol dehydrogenase from Entamoeba histolytica
- D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica
- Contribution of Pro275 to the Thermostability of the Alcohol Dehydrogenases.
Hydroxyacyl-CoA dehydrogenase (HADH) catalyzes the conversion of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. NAD is the cofactor of HADH activity. HADH oxidates straight-chain 3-hydroxyacyl-CoAs in the β-oxidation pathway of fatty acid metabolism. HADH is classified according to its substrate ads short chain (SHCDH) and long chain HADH. HADH deficiency is a genetic disorder.
For chimeras of alcohol dehydrogenase see
- Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH
- Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH
- Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH
- Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH
The of overall Cα backbone of all these chimeras (rmsd 0.45-0.65 Å) with those of the parent enzymes, did not reveal significant structural changes. So, the differences in the thermal stability of the chimeras and the parent enzymes could be caused by relatively small specific changes located at the important points of the NADP+-dependent alcohol dehydrogenases. For example see Cα superposition for the X23(TET) chimera (red) (3fpc) and its parent ADHs (TbADH, colored blue (1ped), and EhADH1, colored lime (1y9a). The RMSDs of the TbADH−EhADH1, TbADH−Χ23(TET), and EhADH1−Χ23(TET) were 0.68, 0.56, and 0.48 Å, respectively.
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Structure
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The initial scene () shows an overview of the molecule, allowing for a general look at the tertiary structure of alcohol dehydrogenase (it is complexed with Cl, Pyz, NAD, and Zn). A second scene () shows a close view of the ligand within each subunit. Labels have been placed on NAD, CL, and Zn to clearly establish the structure.
Within alcohol dehydrogenase, site of alcohol dehydrogenase has three important residues, Phe 93, Leu 57, and Leu 116. These three residues work together to bind to the alcohol substrate.[2]
Zn plays an important role in the catalysis. It funtions by electrostatically stabilizing the oxygen in alcohol during the reaction, which causes the alcohol to be more acidic. At the , Zinc coordinates with Cys 146, Cys 174, and His 67.[3]
NAD functions as a cosubstrate in the dehydration. NAD binds to numerous residues in a series of beta-alpha-beta folds. shows the domain where NAD binds, and many of the residues with which it interacts are selected.
[4]
Alcohol dehydrogenase exists as a dimer with a zinc molecule complexed in each of the subunits. It has a SCOP catagory of an alpha and beta protein. At the N-terminal, there is a domain that is all beta; however, the C-Terminal domain is alpha and beta, so the catagory is alpha and beta. The C-Terminal core has 3 layers of alpha/beta/alpha and parallel beta sheets of 6 strands.[5]
Reaction and Mechanism
In the oxidation mechanism, ADH is momentarily associated with nicontinamide adenine dinucleotide (NAD+), which functions as a cosubstrate. In its reaction, alcohol dehydrogenase uses zinc and NAD to facilitate the reaction. The function of zinc is to position the –OH group on the ethanol in a conformation that allows for the oxidation to occur. NAD then acts as a cosubstrate and performs the oxidation.
[6] The of alcohol dehydrogenase reaction is as follows: CH3CH2OH + NAD+ -> CH3COH (acetaldehyde) + NADH + H+ (Note: The reaction is actually reversible although the arrow does not show it) [7] The step-wise reduction mechanism for ADH is shown on the left. In the mechanism, His 51 is deprotonated and activated by a base catalyst. This allows histidine to accept a proton from NAD, which also draws a proton Thr 48. As a result of the proton transfer, the Thr is prepared to accept a proton from the alcohol substrate. While Thr accepts the proton, there is also a hydride transfer to NAD. The whole process can be summarized as the oxidation of an alcohol to an aldehyde in concert with the transfer of a hydride to NAD.[8]
The Mechanism for alcohol dehydrogenase follows an random bisubstrate mechanism.[9] In the mechanism, the NAD+ and alcohol bind to the enzyme, so that the enzyme is now attached to the two subtrates. While attached, the hydrogen is formally transferred from the alcohol to NAD, resulting in the products NADH and a ketone or aldehyde. The two products are then released, and the enzyme has catalyzed the reaction.
Kinetics
The alcohol dehydrogenase catalyzed aldehyde-NADH reaction show kinetics consistent with a random-order mechanism, and the rate-limiting step is the dissociation of the product enzyme-NAD+ complex. [10] Alcohol dehydrogenase is more effective for smaller alcohol substrates, and it becomes less effective as substrate size increases. It is also more effective for primary than secondary alcohols.[11] In a study where ADH was immobilized in tresyl-chloride-activate agarose, it was shown that the Michaelis-Menten model could not take into consideration all the constraints induced by the immobilization on the enzyme properties but that the Theorell-Chance model was more appropriate.[12]
Regulation
Substrate size is a regulator, where larger substrates inhibit alcohol dehydrogenase. Further, alcohol dehydrogenase is somewhat inhibited if the substrate is a secondary alcohol, as opposed to a primary alcohol. [13] Pyrazoles have also been shown to be inhibitors of ADH. [14] Other inhibitors include heavy metals, thiourea, purine and pyrimidine derivatives, and both chloroethanol and flouroethanol. [15] Activators include sulfhydryl activating reagents, mercaptoethanol, dithiothreitol, and cysteine.[16]
Tetrameric alcohol dehydrogenases
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Additional Resources
For additional information, see: Carbohydrate Metabolism
3D Structures of Alcohol dehydrogenase
Update May 2012
ADH I
3jv7 – RrADH I – Rhodococcus rubber
2vna - hADH I catalytic domain - human
2hcy – yADH I – yeast
ADH I binary complex
1u3t – hADH I α chain + inhibitor
1hsz, 1hdz, 3hud - hADH I β chain + NAD
1u3w - hADH I γ chain + inhibitor
1ht0 - hADH I γ chain (mutant) + NAD
ADH I ternary complex
2xaa – RrADH I + NAD + alcohol
3fx4 – pADH I + NADP + inhibitor – pig
2w98, 2w4q – hADH I catalytic domain + NADP + inhibitor
1hso - hADH I α chain + NAD + pyrazole derivative
1hdx - hADH I β chain + NAD + alcohol
1u3u, 1u3v - hADH I β chain + inhibitor
1deh, 1hdy - hADH I β chain + NAD + pyrazole derivative
1htb - hADH I β3 chain + NAD + pyrazole derivative
ADH II
3owo – ZmADH II iron-dependent – Zymomonas mobilis
ADH II binary complex
3ox4 - ZmADH II iron-dependent + NAD
3cos - hADH II + NAD + Zn
1e3e – mADH II + NADH – mouse
1e3l - mADH II (mutant) + NADH
1e3i - mADH II + NADH + inhibitor
ADH III
1m6h, 1m6w, 1teh - hADH III χ chain
2fze - hADH III χ chain + ADP-ribose
2fzw - hADH III χ chain + NAD
1mc5 – hADH III χ chain + glutathione + NADH
1ma0 - hADH III χ chain + dodecanoic acid + NAD
3qj5 - hADH III χ chain + inhibitor + NAD
ADH IV
1ye3, 8adh, 5adh - hoADH IV e chain – horse
1qlj - hoADH IV e chain (mutant)
3iv7 – ADH IV – Corynebacterium glutamicum
ADH IV binary complex
2jhf, 2jhg, 1het, 1heu, 1hf3, 1ee2, 2oxi, 2ohx, 6adh - hoADH IV e chain + NAD
1adb, 1adc, 1adf, 1adg, 7adh - hoADH IV e chain + NAD derivative
1mgo, 1ju9, 1qlh, 1a72 - hoADH IV e chain (mutant) + NAD
1d1s, 1agn – hADH IV σ chain + NAD
1d1t - hADH IV σ chain (mutant) + NAD
ADH IV ternary complex
3oq6, 1qv6, 1qv7, 1a71, 1axe, 1axg – hoADH IV e chain (mutant) + NAD + alcohol
4dwv, 4dxh - hoADH IV e chain + NAD + alcohol
1p1r, 1ldy, 1lde - hoADH IV e chain + NADH + formamide derivative
1n92 - hoADH IV e chain + NAD + pyrazole derivative
1bto, 3bto - hoADH IV e chain + NADH + butylthiolane derivative
1n8k - hoADH IV e chain (mutant) + NAD + pyrazole
1mg0, 1hld - hoADH IV e chain + NAD + alcohol
ADH
1a4u – SlADH – Scaptodrosophila lebanonensis
3my7 – ADH ACDH domain – Vibrio parahaemolyticus
3meq – ADH – Brucella suis
3l4p – ADH – Desulfovibrio gigas
1jvb - SsADH – Sulfolobus solfataricus
3i4c, 1nto, 1nvg – SsADH (mutant)
3goh – ADH – Shewanella oneidensis
3gaz – ADH residues 2-334 – Novosphingobium aromaticivorans
2eih – ADH – Thermus thermophilus
1rjw – GsADH – Geobacillus stearothermophilus
1vj0, 1vhd – TmADH -Thermotoga maritima
2eer – ADH – Sulfolobus tokodaii
ADH binary complex
3l77 – ADH short-chain + NADP – Thermococcus sibiricus
1h2b – ADH + NAD – Aeropyrum pernix
1f8f – Benzyl-ADH + NAD – Acinetobacter calcoaceticus
1o2d - TmADH + NADP
1b16, 1b14, 1b15 - SlADH + NAD derivative
1cdo – ADH + NAD - cod
1rhc – ADH F420-dependent +F420-acetone – Methanoculleus thermophilus
1agn – hADH (sigma) +NAD
3pii – GsADH + butyramide
3rj5, 3rj9 – SlADH (mutant) + NAD
3s1l – ADH + Zn – Ralstonia eutropha
ADH ternary complex
1mg5 – ADH + NADH + acetate – Drosophila melanogaster
1r37 – SsADH + NAD + alcohol
1sby – SlADH + NAD + alcohol
1b2l - SlADH + NAD + cyclohexanone
1llu - ADH + NAD + alcohol – Pseudomonas aeruginosa
3cv7 – pADH + NAD + NAP
3rf7 – SoADH + NAD + Fe + Ni
NADP-dependent ADH
1ped - CbADH – Clostridium beijerinckii
2b83, 1jqb – CbADH (mutant)
2nvb - TbADH (mutant) – Thermoanaerobacter brockii
3ftn, 3fpc, 3fpl, 3fsr – ADH chimera
1y9a - EhADH – Entamoeba histolytica
2oui – EhADH (mutant)
1p0c – RpADH8 – Rana perezi
NADP-dependent ADH binary complex
1kev – CbADH + NADPH
1bxz – CbADH catalytic domain + alcohol
1ykf – TbADH + NADP
3h4g – pADH + NADP
1p0f – RpADH + NADP
R-specific ADH
1nxq - LbRADH – Lactobacillus brevis
1zk2, 1zk3 - LbRADH (mutant)
1zjy, 1zjz, 1zk0, 1zk1 – LbRADH (mutant) + NADH + alcohol
1zk4 - LbRADH (mutant) + NADH + acetophenone
Specific alcohol ADH
2cf5, 2cf6 – Cinnamyl-ADH – Arabidopsis thaliana
1piw, 1q1n, 1ps0 – Cinnamyl-yADH
3two - Cinnamyl-ADH + NADP – Helicobacter pylori
1m2w – Mannitol-ADH – Pseudomonas fluorescens
1w6s – Methanol-ADH – Methylobacterium extorquens
1yqx – Sinapyl-aADH II – aspen
1yqd – Sinapyl-aADH II + NADP
1bdb – Biphenyl dihydrodiol-ADH + NAD - Pseudomonas
Quinohemoprotein ADH
1kv9, 1yiq – PpQADH II + PQQ + heme – Pseudomonas putida
1kb0 - QADH I + PQQ + heme – Comamonas testosteroni
Hydroxyacyl-CoA dehydrogenase
Short chain HADH
1so8 – hSHCDH II – human
3rqs - hSHCDH
1f14 - hSHCDH (mutant)
Short chain HADH binary complex
1f12 - hSHCDH (mutant) + hydroxybutyryl-CoA
1f17, 1lsj, 1lso - hSHCDH (mutant) + NAD
1zbq - hSHCDH IV + NAD
1e3s - rSHCDH + NAD – rat
Short chain HADH ternary complex
1u7t - hSHCDH II + inhibitor + NAD
1f0y - hSHCDH + acetoacetyl-CoA + NAD
1il0, 1m75, 1m76 - hSHCDH (mutant) + acetoacetyl-CoA + NAD
1e3w - rSHCDH + 3-keto-butyrate + NAD
1e6w - rSHCDH + estradiol + NAD
Unspecified HADH
1uay - HADH II – Thermus thermophilus
1zej, 3ctv - HADH – Archaeoglobus fulgidus
1zcj - rHADH
2x58 - rHADH + CoA
2et6 – HADH (mutant) – Candida tropicalis
References
- ↑ Voet, et. al. Fundamentals of Biochemistry: 3rd Edition. Hoboken: Wiley & Sons, Inc, 2008.
- ↑ Protein: Alcohol Dehydrogenase. The College of Saint Benedict and Saint John's University. 1 March 2010 < http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/index.htm>
- ↑ Protein: Alcohol Dehydrogenase. The College of Saint Benedict and Saint John's University. 1 March 2010 < http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/index.htm>
- ↑ Protein: Alcohol Dehydrogenase. The College of Saint Benedict and Saint John's University. 1 March 2010 < http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/index.htm>
- ↑ Protein: Alcohol dehydrogenase from Human (Homo sapiens), different isozymes. SCOP. 2009. 1 March 2010 < http://scop.berkeley.edu/data/scop.b.d.c.b.b.c.html>
- ↑ Protein: Alcohol Dehydrogenase. The College of Saint Benedict and Saint John's University. 1 March 2010 < http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/index.htm>
- ↑ Voet, et. al. Fundamentals of Biochemistry: 3rd Edition. Hoboken: Wiley & Sons, Inc, 2008.
- ↑ Protein: Alcohol Dehydrogenase. The College of Saint Benedict and Saint John's University. 1 March 2010 < http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/index.htm>
- ↑ Voet, et. al. Fundamentals of Biochemistry: 3rd Edition. Hoboken: Wiley & Sons, Inc, 2008.
- ↑ Dickinson FM, Monger GP. A study of the kinetics and mechanism of yeast alcohol dehydrogenase with a variety of substrates. Biochem J. 1973 Feb;131(2):261-70. PMID:4352908
- ↑ Dickinson FM, Monger GP. A study of the kinetics and mechanism of yeast alcohol dehydrogenase with a variety of substrates. Biochem J. 1973 Feb;131(2):261-70. PMID:4352908
- ↑ Bille V, Remacle J. Simple-kinetic descriptions of alcohol dehydrogenase after immobilization on tresyl-chloride-activated agarose. Eur J Biochem. 1986 Oct 15;160(2):343-8. PMID:3769934
- ↑ Dickinson FM, Monger GP. A study of the kinetics and mechanism of yeast alcohol dehydrogenase with a variety of substrates. Biochem J. 1973 Feb;131(2):261-70. PMID:4352908
- ↑ Blomstrand R, Ostling-Wintzell H, Lof A, McMartin K, Tolf BR, Hedstrom KG. Pyrazoles as inhibitors of alcohol oxidation and as important tools in alcohol research: an approach to therapy against methanol poisoning. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3499-503. PMID:115004
- ↑ Alcohol Dehydrogenase. Worthington Biochemical Corporation . 31 March 2010 < http://http://www.worthington-biochem.com/ADH/default.html>
- ↑ Alcohol Dehydrogenase.Worthington Biochemical Corporation . 31 March 2010 < http://http://www.worthington-biochem.com/ADH/default.html>
- ↑ Goihberg E, Dym O, Tel-Or S, Levin I, Peretz M, Burstein Y. A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase. Proteins. 2007 Jan 1;66(1):196-204. PMID:17063493 doi:10.1002/prot.21170
- ↑ Goihberg E, Dym O, Tel-Or S, Shimon L, Frolow F, Peretz M, Burstein Y. Thermal stabilization of the protozoan Entamoeba histolytica alcohol dehydrogenase by a single proline substitution. Proteins. 2008 Feb 7;. PMID:18260103 doi:10.1002/prot.21946
- ↑ Goihberg E, Peretz M, Tel-Or S, Dym O, Shimon L, Frolow F, Burstein Y. Biochemical and Structural Properties of Chimeras Constructed by Exchange of Cofactor-Binding Domains in Alcohol Dehydrogenases from Thermophilic and Mesophilic Microorganisms. Biochemistry. 2010 Feb 9. PMID:20102159 doi:10.1021/bi901730x
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