Catalysis by AlcoholDehydrogenase
Aris Kaksis  Riga Stradin's University 2023


Contents:
I. Introduction
II.Liver alcohol dehydrogenase IV
III.Flexible loop 1YE3,1HLD
IV. The catalytic zinc Zn2+
V. NAD binding site 1HLD
VI. NAD+ puckering of the nicotinamide ring 1HET
VII. Strained Michaelis complexes1DXH

Peptides and Backbones

I. Introduction reaction
    Alcohol dehydrogenases (ADH) (EC 1.1.1.1) are enzymes that in catalytic domain
oxidize
alcohols to aldehydes -HC=O or ketones >C=O with transfer two electrons and
one hydride as 2e- two reducing electrons from alcohol -CH2-OH to
nicotinamide adenine dinucleotide NAD+ oxidized form NAD+
to form reduced form NADH NADH.
    In humans and many other animals, they serve to oxidize ethanol, because
ethanol slow down the transport of water + oxygen O2 cross membrane through
aquaporins-channels decreasing water and oxygen O2 supply in body.
High concentration of ethanol more as 0.5 promiles and long time abused in body leads to
dehydratation (lose of water) and hypoxia in tissues (deficiency of oxygen O2) sensed in
brain as obscure mind and filling. Deficiency of oxygen O2 molecules make
body physically week and tired.
    Alcohol dehydrogenases as well oxidize other alcohols. As well alcohol dehydrogenase II
molecules located in stomach, intestinal system is specific in vitamin A retinol convertion to
retinal as vision molecule for eyes.
    Retinal molecule is precursor of retinoic acid as important transcription cofactor ligand in
nuclear receptors which switching transcriptional process to activate for body development
as cell proliferation and cell differentiation. High ethanol concentration long time (days and
weeks) in stomach, intestinal system compete with retinol and leads to abnormalities for
body development especially in embryogenesis.
    Coenzyme B3 vitamins (nicotinic acid, niacin, nicotinic acid amide) NAD+ structure:
nicotin adenine dinucleotide.

    Week Eo=0,38373 V oxidizing agent NAD+ but have got transferred two electrons
together in hydride as compact ion H-(2e-+H+) jumping (as two 2e-reducing equivalents)
forms reducing agent NADH in one attempt from substrate alcohol -CH2-OH to
coenzyme B3 vitamin forming NADH and converting to aldehyde -HC=O or ketone
>C=O molecule from the alcohol:
NAD++H-(2e-+H+)<=>NADH ; Eo= 0,38373 V standard potential 298,15 K (25.̊ C)
Instantly Substrate alcohol -CH2-O-H hydrogen H dissociates and participiate in
a proton H+ relay system via Ser-48, His-51, which transfere proton H+ to water from
the substrate alcohol bound group -CH2-O-H, where Ser-48, His-51 functions as
protolysis to jump H+ at water molecule H2O . By catalytic zinc Zn2+ site coordinated
alcohol group -CH2-O-H protonatie =>H+ the Ser-48, His-51, H2O.
Reduction-Oxidation reactions of BioChemistry page 8: OxRed Biothermodynamics   
Two half ractions from standard potential RedOx tables thermodynamic and classic:
Red H3C-CH2-OH+H2O=H3C-HC=O+H-(2e-+H+)+H3O+; E°H2O= -0,02923 V reaticon
Ox NAD++H-(2e-+H+=NADH ; E°=0,38373 V;standard potential classic 298.15 K;
ΔE°=E°RedH2O-E°Ox=-0,02923+0,38373= 0,3545 V, n electrons are 2;
ΔGeqAerobicOx=ΔE°•F•n=-R•T•ln(Keq)=68,4 kJ/mol Homeostasis joined

=KeqAerobicOx=EXP(-ΔGeq/R/T)=10-12;

ΔGHess=ΔG°H3O++ΔG°H3CHCO+ΔG°NADH-ΔG°H3CCH2OH-ΔG°H2O-ΔG°NAD+=

ΔGHess=1120,09+24,06-213,275-(1059,11-181,64-237,191)=290,6 kJ/mol

endoergic Hess unfavored, but homeostasis conditions at O2aqua ratio

[NADH]/[NAD+]=10-6 with pH=7,36 favored free energy change negative:

ΔGAerobicOx=68,4+8,3144*298,15*ln(1/10^6*1/1*10^(-7,36)/55,3)=-17,85 kJ/mol;


NAD++H3C-CH2-OH+H2O=>NADH+H3C-HC=O+H3O++;

II. Human ADH7  1AGNNAD , Horse Liver alcohol dehydrogenase IV

    Binding of the complete coenzymeNAD+ is critical for producing the
conformational
change in alcoholdehydrogenase.
left 1JU9zn apoenzyme with ADP
right 1HLDznNAD holoenzyme with NAD+
left 1HLDznNAD holoenzyme with NAD+
    Primary structure 1̊ .
    Amino acids on polypeptide chain start from N-terminus Ser1 to finish C-terminus
amino acid Phe374.
    Quaternary 4̊ structures 1JU9,1HLD.
    The dimeric liver apoenzyme and holoenzyme has two identical proteinsubunits.
left 1JU9zn apoenzymedimer with ADP
right 1HLDznNAD holoenzymedimer with NAD+
    Tertiary structure 3̊ .
    Each identical proteinsubunit has two domains. The conformational change can be
described as a rigid body rotation of about 10° around an axis between the catalytic and
coenzymebinding domains, which "closes" up the "open" activesite.
left "open" conformation 1JU9zn apoenzymemonomer with ADP
left "closed" up conformation 1HLDznNAD holoenzymemonomer with NAD+.
     Secondary structure 2̊ units in monomer.
< >. 16 Alpha-helices H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15,H
on N-terminus domain 4 beta strand-sheet , 6 beta strand-sheet , on coenzyme
binding domain 6 beta strand-sheet
with anti-parallel strands and one single strand.

III. Flexible loop 1YE3,1HLD

    Residues 291 to 300 from the loop of the coenzyme binding domain
apoenzyme 1YE3,1HLD holoenzyme with bound NAD+
1YE3 red < >1HLD blue < >
rearranges so that the catalytic domain move, and this results in the isopropyl group of
Val-294
flipping from a position buried< >in the interface between the
coenzyme binding domains to a position< >in the active site under the
nicotin amide ribose. The rearrangement flips the position of Val-294, which
forms a floor under the nicotin amide ribose< >and protrudes into the
substrate binding site.
   Binding of 2,3,4,5,6-pentafluorobenzyl alcohol< >in the active site of
alcohol dehydrogenase. This complex has an orientation that resembles the
presumed Michaelis Substrate Enzyme complex SE.
Water
HOH463< >is excluded from the active site for hydride H- transfer between
carbon C7< >from benzyl alcohol -CH2-OH and to carbon C4 of the
nicotin amide ring< >. 2,3,4,5,6-pentafluorobenzyl alcoholis a good analog of
benzyl alcohol, a good substrate that has been used extensively for kinetic studies and
evaluation of quantum mechanical tunneling are center piece for understanding the requirements
for hydrogen hydride H- transfertunneling between carbon C7< >from
benzyl alcohol -CH2-OH and to carbon C4 of the nicotin amide ring< >.
   The proton relay system from alcohol oxygen O bound to the
catalyti czinc< >
involving Ser-48< >, the 2'-hydroxyl group< >-OH of the
coenzyme nicotin amide ribose and His-51< >is also installed, which can function to
relay a proton to water< >from the alcohol bound to the catalyticzinc.
    Some amino acid residues from the catalytic domain move about 4.6 Å closer to the
coenzyme binding domain with substrate alcohol bound in the activesite.
   The complex 1HLD,1P1R with the formamide was the first example of a
puckered, reduced nicotin amide ringNADH in a dehydrogenase.
The ring puckering may be relevant for catalysis as it decreases the distance
from 4.6 Å to 3.6 Å between C4 of the nicotin amide ring and the reacting C of the
substrate alcohol
group -CH2-OH. Puckereing decrease the distance
from 4.6 Å to 3.6 Å and facilitate one hydride ion H- tunneling two 2e- electrons
from substrate alcohol group -CHH-O-H to rduce nicotin amide ringin NAD+ and
converts substrate alcohol group to aldehyde -HC=O .
     1HLD The protonH+ relay system from alcohol oxygen bound hydrogen-O-H to the
catalytic zinc< >
involving
Ser-48< >, the 2'-hydroxyl group< >-OH of the coenzyme nicotin amide ribose and
His-51< >is also installed, which can function to relay a
proton
to water< >from the alcohol bound to the catalytic zinc.
See reaction mechanism scheme.
     1P1R The protonH+ relay system from alcohol oxygen O bound hydrogen -O-H to the
catalytic zinc< >involving
Ser-48< >, the 2'-hydroxyl group< >-OH of the coenzyme nicotin amide ribose and
His-51< >
is also installed, which can function to relay
a proton to water< >from the alcohol bound to the catalytic zinc.

IV. The catalytic zinc Zn2+

     The catalytic zinc Zn2+ 1YE3,1HLD,1P1R is tightly bound to the protein by the
sulfhydryl groups of Cys-46 and Cys-174 and the imidazole of His-67, in a
distorted tetrahedralligand number n=4 where the exogenous ligand
(water, substrate-alcohol, inhibitor-amide) occupies the fourth position.
1YE3 < >Cys-46 and Cys-174 and His-67 water O
1HLD < >Cys-46 and Cys-174 and His-67 alcohol C-O-H
1P1R< >Cys-46 and Cys-174 and His-67 amide carbonyl >C=O
The catalytic zinc Zn2+ on right frame> klick 1YE3zn,1HLDzn,1P1Rzn is
coordinative complexmaker ion with coordination number n=4. image
having four ligans coordinated.

V. NAD+ binding site 1HLD

     1HLDznNAD amino acid residues that affect coenzyme NAD+ binding and the
conformational states as Lys-228 with hydrogen bondings three water molecules
(depicted oxygens OOO) in the
adenosine phosphate-ribose binding site < >.
Lys-228 hydrogen bonds interacts with the 3′-hydroxyl group of the adenosine ribose and
via a water molecules with a phosphate oxygen. Isoleucine residues 224 and 269 make
a sandwich of the adenine ring. Ile224,Ile269 sandwich walls for
adenine rings
and Val292 forms a floor under the nicotinamide ribose flipping out from the
loop
residues 291 to 300 blue chain of amino acids.
Backbone thin off
     Hydride H- transfer became rate-limiting for alcohol oxidation. ADH enzyme
rate
-limiting step for the oxidation of ethanol is hydride H- transfer. Lys-228 in the
adenosine ribose phosphate binding site was responsible for the change in activity.
The lysine in the active site interfere with binding of the coenzyme NAD+.
Binding
of NAD+ is coupled to the isomerization, but the binding may not affect the
position of the isomerization as long as the complete coenzyme with the
nicotinamide
ring is binding. Saturation of the enzyme with coenzyme and motions of the
domains are relevant for catalysis. On the atomic level, these motions could also result in the
puckering of the nicotinamide ring, which would bring the reacting carbons between
C4
of the nicotinamidering and the reacting C of the substrate alcohol group -CH2-OH
together from 4.6 Å to 3.6 Å as well will lead predominantly to shifted
isomerization state E*-NAD+ puckering:
4.6 Å E-NAD+ 3.6 Å E*-NAD+
with puckered nicotinamide ring shorten distance from 4.6 Å to 3.6 Å.

VI. NAD+ puckering of the nicotinamide ring 1HET

     1HETznNAD amino acid residues that affect coenzyme NAD+ binding and the
conformational states as Lys-228 with hydrogen bondings four water molecules
(depicted oxygens OOOO) in the adenosine phosphate-ribose binding site < >.
Lys-228 hydrogen bonds interacts with the 3′-hydroxyl group of the adenosine ribose and
via a water molecules with a phosphate oxygen. Isoleucine residues 224 and 269 make
a sandwich of the adenine ring. Ile224,Ile269 sandwich walls for adenine rings and
Val292 forms a floor under the nicotinamide ribose flipping out from the
loop
residues 291 to 300 blue chain of amino acids.
Backbone thin off
   The catalytic zinc Zn2+ is tightly bound to the protein by the sulfhydryl groups of
Cys-46
and Cys-174 and the imidazole of His-67, in a distorted
tetrahedral ligand number n=4
where the exogenous ligand
(water, substrate-alcohol, inhibitor-amide) occupies the fourth position.
1HETznNAD puckering amino acid residues that affect coenzyme NAD+ binding and
the conformational states puckering < > of the nicotinamide ring< > carbon C4.

Va. NAD+ binding site 1AGN

     1AGNznNADaNAD amino acid residues that affect coenzyme NAD+ binding and
the conformational states as Lys-228 with hydrogen bondings three water molecules
(depicted oxygens O) in the adenosine phosphate-ribose binding site < >.
Lys-228 hydrogen bonds interacts with the 3′-hydroxyl group of the adenosine ribose and
via a water molecules with a phosphate oxygen. Isoleucine residues 222 and 269 make
a sandwich of the adenine ring. Ile222,Ile269 sandwich walls for adenine rings and
Val292, Val268 forms a floor under the nicotinamide ribose flipping out from the
loop
residues 291 to 300 blue chain of amino acids.
Backbone thin off
     Hydride H- transfer became rate-limiting for alcohol oxidation.
ADH enzyme rate-limiting step for the oxidation of ethanol is hydride H- transfer.
Lys-228 in the adenosine ribose phosphate binding site was responsible for the
change in activity. The lysine in the active site interfere with binding of the coenzyme
NAD+
. Binding of NAD+ is coupled to the isomerization, but the binding may
not affect the position of the isomerization as long as the complete coenzyme with the
nicotinamide ring is binding. Saturation of the enzyme with coenzyme and motions of the
domains are relevant for catalysis. On the atomic level, these motions could also result in the
puckering of the nicotinamide ring, which would bring the reacting carbons between
C4
of the nicotinamidering and the reacting C of the substrate alcohol group -CH2-OH
together from 4.6 Å to 3.6 Å as well will lead predominantly to shifted isomerization state
=> E*-NAD+ :
4.6 Å E-NAD+ 3.6 Å E*-NAD+
with puckered nicotinamide ring in E*-NAD+.

VIa. NAD+ puckering of the nicotinamide ring 1AGN

     1AGNznNADaNAD amino acid residues that affect coenzyme NAD+ binding and
the conformational states as Lys-228 with hydrogen bondings four water molecules
(depicted oxygens O) in the adenosine phosphate-ribose binding site < >.
Lys-228 hydrogen bonds interacts with the 3′-hydroxyl group of the adenosine ribose and
via a water molecules with a phosphate oxygen. Residues I222 and I269 make
a sandwich of the adenine ring. Ile222,Ile269 sandwich walls for adenine rings and
Val292,Val268 forms a floor under the nicotinamide ribose flipping out from the
loop
residues 291 to 300 blue chain of amino acids.
Backbone thin off
   The catalytic zinc Zn2+ is tightly bound to the protein by the sulfhydryl groups of
Cys-46
and Cys-174 and the imidazole of His-67, in a distorted
tetrahedralligand number n=4 where the exogenous ligand
(water, substrate-alcohol, acetate, inhibitor-amide) occupies the fourth position.
 1AGNznNADaNAD puckering amino acid residues that affect coenzyme NAD+
binding and the conformational states puckering < > of the
nicotinamide ring< > carbon C4.

VII. Strained Michaelis complexes 4DXH

    4DXHznNAD Alternative dimeric subunits conformations for amino acid side chains
were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 in
click black adopt different conformations to accommodate the different alcohols at the
active site instantly 2,2,2-trifluoroethanol (ETF) in red click< > Lys-228
hydrogen bonds interacts with the 3′-hydroxyl group of the adenosine ribose
in red click< > and via a water molecule HOH664 with a phosphate oxygen.
    Isoleucine residues 224 and 269 make a sandwich of the adenine ring. Ile224,Ile269
sandwich walls for adenine rings and Val292 forms a floor under the
nicotinamide ribose
flipping out from the loop residues 291 to 300
blue chain
of amino acids< >.
  4DXHznNAD Michaelis complexes with the pro-R hydrogens of the
methylene carbons of the alcohols directed toward the re face of C4N of the
nicotinamide ring < >with a C-C distance 3.43 Å< >.
    Use mouse right button on MDL screen in menu choose "selec" than
choose "Mouse Click Action" than choose "Distance" start with click on
C4N < > of the nicotinamide ring atom and folowing second click on
methylene carbons
of the alcohol -CH2-OH directed toward the re face of C4N so
can see on status bar appeares the distance C-C mesure in angstrems 3.43 Å between
C4N and alcohol -CH2-OH.
    The oxygens of the alcohols are ligated to the catalytic zinc Zn2+at a distance
expected for a zinc Zn2+ alkoxide < >1.953 Å and substrate alcohol bound
oxygen O
atom -CH2-O-H hydrogenparticipate in a low-barrier
hydrogen bond
2.52 Å H...O-H with Ser-48 < > hydroxyl group -O-H oxygen.
    Substrate alcohol -CH2-O-H bound to oxygen O atom hydrogen H dissociates and
participiate in a proton H+ relay system via His-51< > is also installed, which
can function to relay a proton to water< >from the substrate
alcohol bound
group -CH2-O-H proton H+, which dissociates and
jump to His-51< > installed water molecule in water medium driven by
catalytic zinc Zn2+ site moiety.
    Proton sticks to water molecule H+ +H2OarowsTwoH3O+ (H2O:=>H+) by
oxygen O:=> electron pair donor acceptor bonds with H+ forming hydroxonium ion H3O+.
   The catalytic zinc Zn2+ is tightly bound< >to the protein by the sulfhydryl groups of
Cys-46 and Cys-174 and the imidazole of His-67, in a distorted
tetrahedral ligand number n=4
where the exogenous ligand
(water, substrate-alcohol, inhibitor-amide) occupies the fourth position
at a distance 1.953 Å< >. Use mouse right button on MDL screen in menu
choose "select" than choose "Mouse Click Action" than choose "Distance" start with click on
zinc Zn2+ atom < >and folowing second click on 2,2,2-trifluoroethanol (ETF)
substrate alcohol bound oxygen O atom -CH2-OH so can see on status bar appeares the
distance mesure in angstrems 1.953 Å between zinc Zn2+ and oxygen O.
   As determined by X-ray refinement with no restraints on bond distances and planarity, the
nicotin amide rings in the two complexes are slightly puckered-savilkt-čokurī -lūpas
(quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to
the plane of the other atoms) and have bond distances that are somewhat different compared
to those found for NAD(P)(+). It appears that the nicotin amide ring is strained toward the
transition state on the path to alcohol oxidation.
4DXHznNAJ puckering amino acid residues that affect coenzyme NAD+(NAJ) binding and
the conformational states puckering < > with torsion angles of
5.9°
for C4N and 4.8° for N1N relative to the plane of the other atoms of the
nicotin amide ring carbon C4.
   Binding of 2,2,2-trifluoro ethanol (ETF) alcohol< >in the active site of
alcohol dehydrogenase. This complex has an orientation that resembles the presumed
Michaelis Substrate Enzyme complex SE. Alcohol in active site transfere-tunneling
hydride H- ion between carbon C2 from alcohol -CH2-OH and to carbon C4 of the
nicotin amide ring< >. 2,2,2-trifluoroethanol (ETF) alcohol is a good analog of
alcohol, a good substrate that has been used extensively for kinetic studies and evaluation
of quantum mechanical tunneling are central piece for understanding the requirements for
hydrogen
hydride H- transfer tunneling between
carbon C2< > from 2,2,2-trifluoroethanol (ETF) alcohol -CH2-OH and
to carbon C4 of the nicotin amide ring< >.

VII. Strained Michaelis complexes 3OQ6

    3OQ6znNAJ Alternative dimeric subunits conformations for amino acid side chains were
identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 in
click black adopt different conformations to accommodate the different alcohols at the
active site instantly 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) in
red click< > Lys-228 hydrogen bonds interacts with the 3′-hydroxyl group of the
adenosine ribose in red click< > and via a water molecule HOH664 with
a phosphate oxygen.
    Isoleucine residues 224 and 269 make a sandwich of the adenine ring.
Ile224,Ile269 sandwich walls for adenine rings and Val292 forms a floor under the
nicotinamide ribose flipping out from the loop residues 291 to 300 blue chain of
amino acids< >.
  3OQ6znNAJ Michaelis complexes with the pro-R hydrogens of the
methylene carbons of the alcohols directed toward the re face of C4N of the
nicotinamide ring < >with a C-C distance 3.23 Å< >.
Use mouse right button on MDL screen in menu choose "selec" than
choose "Mouse Click Action" than choose "Distance" start with click on C4N< >of the
nicotinamide ring atom and folowing second click on methylene carbons of the
alcohol -CH2-OH directed toward the re face of C4N so can see on status bar appeares the
distance C-C mesure in angstrems 3.23 Å between C4N and alcohol -CH2-OH.
    The oxygens of the alcohols are ligated to the catalytic zinc Zn2+at a distance expected
for a zinc Zn2+ alkoxide < >1.894 Å and substrate alcohol bound oxygen O atom
-CH2-O-H hydrogen participate in a low-barrier hydrogen bond 2.52 Å H...O-H with
Ser-48 < > hydroxyl group -O-H oxygen. Substrate alcohol -CH2-O-H bound to
oxygen O atom hydrogen H dissociates and participiate in a proton H+ relay system
via His-51< >is also installed, which can function to relay a proton to water< >
from the substrate alcohol bound group -CH2-O-H proton H+, which dissociates and
jump to His-51< > installed water molecule in water medium driven by
catalytic zinc Zn2+ site
moiety. Proton sticks to water molecule
H+
+H2OarowsTwoH3O+ (H2O:=>H+) by oxygen O:=> electron pair donor acceptor bons with
H+
forming hydroxonium ion H3O+.
   The catalytic zinc Zn2+ is tightly bound< >to the protein by the sulfhydryl groups of
Cys-46 and Cys-174 and the imidazole of His-67, in a distorted tetrahedral ligand
number n=4
where the exogenous ligand (water, substrate-alcohol, inhibitor-amide)
occupies the fourth position at a distance 1.894 Å< >. Use mouse right button on MDL
screen in menu choose "select" than choose "Mouse Click Action" than
choose "Distance" start with click on zinc Zn2+ atom< > and folowing second click on
2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) substrate alcohol bound oxygen O atom
-CH2-OH so can see on status bar appeares the distance mesure in angstrems 1.894 Å
between zinc Zn2+ and oxygen O.
   As determined by X-ray refinement with no restraints on bond distances and planarity, the
nicotin amide rings in the two complexes are slightly puckered-savilkt-čokurī -lūpas
(quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to
the plane of the other atoms) and have bond distances that are somewhat different compared
to those found for NAD(P)(+). It appears that the nicotin amide ring is strained toward the
transition state on the path to alcohol oxidation.
3OQ6znNAJ puckering amino acid residues that affect coenzyme NAD+(NAJ) binding and
the conformational states puckering < > with torsion angles of 5.9° for C4N and
4.8° for N1N relative to the plane of the other atoms of the nicotin amide ring carbon C4.
   Binding of 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) < >in the active site of
alcohol dehydrogenase. This complex has an orientation that resembles the presumed
Michaelis Substrate Enzyme complex SE. Alcohol in active site transfere-tunneling
hydride H- ion between carbon C2 from alcohol -CH2-OH and to carbon C4 of the
nicotin amide ring< >
. 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) is a good analog of
alcohol, a good substrate that has been used extensively for kinetic studies and
evaluation of quantum mechanical tunneling are central piece for understanding the
requirements for hydrogen hydride H- transfer tunneling between
carbon C2< > from 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) -CH2-OH and
to carbon C4 of the nicotin amide ring< >.

VII. Strained Michaelis complexes 4DWV

    4DWVznNAD Alternative dimeric subunits conformations for amino acid side chains
were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 in
click black adopt different conformations to accommodate the different alcohols at the
active site instantly 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) in red click< >
Lys-228 hydrogen bonds interacts with the 3′-hydroxyl group of the adenosine ribose
in red click< > and via a water molecule HOH664 with a phosphate oxygen.
    Isoleucine residues 224 and 269 make a sandwich of the adenine ring.
Ile224,Ile269 sandwich walls for adenine rings and Val292 forms a floor under the
nicotinamide ribose flipping out from the loop residues 291 to 300
blue chain of amino acids< >.
  4DWVznNAD Michaelis complexes with the pro-R hydrogens of the
methylene carbons of the alcohols directed toward the re face of C4N of the
nicotinamide ring < >with a C-C distance
3.357 Å< >. Use mouse right button on MDL screen in menu choose "selec" than
choose "Mouse Click Action" than choose "Distance" start with click on C4N< > of the
nicotinamide ring atom and folowing second click on methylene carbons of the alcohol
-CH2-OH directed toward the re face of C4N so can see on status bar appeares the
distance C-C mesure in angstrems 3.357 Å between C4N and alcohol -CH2-OH.
    The oxygens of the alcohols are ligated to the catalytic zinc Zn2+at a distance expected
for a zinc Zn2+ alkoxide < >1.938 Å and substrate alcohol bound oxygen O atom
-CH2-O-H hydrogenparticipate in a low-barrier hydrogen bond 2.52 Å H...O-H with
Ser-48 < > hydroxyl group -O-H oxygen. Substrate alcohol -CH2-O-H bound to
oxygen O atom hydrogen H dissociates and participiate in a proton H+ relay system via
His-51< > is also installed, which can function to relay a proton to water< > from the
substrate alcohol bound group -CH2-O-H proton H+, which dissociates and jump to
His-51< >
installed water molecule in water medium driven by
catalytic zinc Zn2+ site
moiety.
Proton sticks to water molecule H+ +H2OarowsTwoH3O+ (H2O:=>H+) by
oxygen O:
=> electron pair donor acceptor bons with H+ forming hydroxonium ion H3O+.
   The catalytic zinc Zn2+ is tightly bound < > to the protein by the sulfhydryl groups of
Cys-46 and Cys-174 and the imidazole of His-67, in a distorted tetrahedral ligand
number n=4
where the exogenous ligand (water, substrate-alcohol, inhibitor-amide)
occupies the fourth position at a distance 1.938 Å < >. Use mouse right button on MDL
screen in menu choose "select" than choose "Mouse Click Action" than choose "Distance"
start with click on zinc Zn2+ atom< >and folowing second click on
2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) substrate alcohol bound oxygen O atom
-CH2-OH so can see on status bar appeares the distance mesure in angstrems 1.938 Å
between zinc Zn2+ and oxygen O.
   As determined by X-ray refinement with no restraints on bond distances and planarity, the
nicotin amide rings in the two complexes are slightly puckered-savilkt-čokurī -lūpas
(quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to
the plane of the other atoms) and have bond distances that are somewhat different compared
to those found for NAD(P)(+). It appears that the nicotin amide ring is strained toward the
transition state on the path to alcohol oxidation.
4DWVznNAJ puckering amino acid residues that affect coenzyme NAD+(NAJ) binding
and the conformational states puckering < > with torsion angles of 5.9° for C4N and
4.8° for N1N relative to the plane of the other atoms of the nicotin amide ring carbon C4.
   Binding of 2,3,4,5,6-pentafluoro-benzyl alcohol(PFB) alcohol< >in the active site of
alcohol dehydrogenase. This complex has an orientation that resembles the presumed
Michaelis Substrate Enzyme complex SE. Alcohol in active site transfere-tunneling
hydride H- ion between carbon C7 from alcohol -CH2-OH and to carbon C4 of the
nicotin amide ring< >
. 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) alcohol is a good
analog of alcohol, a good substrate that has been used extensively for kinetic studies and
evaluation of quantum mechanical tunneling are central piece for understanding the
requirements for hydrogen hydride H- transfer tunneling between
carbon C7< > from 2,3,4,5,6-pentafluoro-benzyl alcohol (PFB) alcohol -CH2-OH and
to carbon C4 of the nicotin amide ring< >.


References
1. Biochemistry, 2017, 56 (28), pp 3632–3646.
5ENV,8ADH,1QLH,4DWV,1N92,1N8K,1P1R,4DXH,1N92,1N8K,1LDE,1LDY,1MGO,5VKR, 1HEU,2JHF,1HET,2JHG,1H2B,1MAO,1PL6,1PL6,1YKF,1YE3,4XD2,5VJ5,5VJG,5VKR,5VL0,5VN1
2. Arch Biochem Biophys. 2018;653:97-106.
3. J Biol Chem. 2000 Mar 23;276(12):9316-21;1HET; 2OHXZn; 1HEU,1HF3,1HET
4. BioChem. 2007, 46 (18), pp 5446–5454. ;1HET; 2OHXZn; 1HEU,1HF3,1HET
5. Biochemistry. 2012 May 15;51(19):4035-484DXHa ZN;dimer4DXH;4DWV;1SBY;3DJJ,1LQU,1YNQ,1HEJ,1KMS,1N92,1N8K,1C1D,1EK6,2J6L 1AXE;1A71,1HET,2JHG,1US0,3BCJ,3OQ6,1PWM,2J8T,1ZK4;3BTO;1HEU;
1P1R;1U3U,1U3V,1U3W;1ZJZ,1SBY,1T2D,3JYO,2O23, 1ZJY
6. Chem Biol Interact. 2011 May 30;191(1-3):42-7.3OQ6 ZN;dimer;1DEH;1DIS;1HLD
7. BioChem. 2012 , 51 (19), pp 4035–4048.
8. BioChem. 2012 , 51 (19), pp 4035–4048.
9. Östberg et al. BMC Biochemistry 2016 1U3W, Protein Sci. 1999;8(12):2639-44. 1D1S, 1AGN,
    J Biol Chem. 1997;272(30):18558-63 1AGN , Zn
http://aris.gusc.lv/ChemFiles/AlhoDeHydrogenase/4DXH5VJ5hOhBioChem1718/5VJ5hOhBioChem17.pdf
Nomenclature for Human Alcohol Dehydrogenase

The Class pdb

System

Protein Gene

Uni-Prot KB

Gene  new

Gene old

Class I 1HSO

α-subunit

ADH1A

ADH1A_HUMAN

ADH1

ADH1A

Class I 1DEH

β-subunit

ADH1B

ADH1B_HUMAN

ADH2

ADH1B

Class I 1HT0

 γ-subunit

ADH1C

ADH1G_HUMAN

ADH3

ADH1C

Class II

π-subunit

ADH2

ADH4_HUMAN

ADH4

ADH4

Class III1MP0

χ-subunit

ADH3

ADHX_HUMAN

ADH5

ADH5

Class IV1AGN

σ-subunit

ADH4

ADH7_HUMAN

ADH7

ADH7

ClassV absent

 

ADH5

ADH6_HUMAN

ADH6

ADH6

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