Coordination geometry for cadmium in the catalytic zinc site of horse liver alcohol dehydrogenase: studies by PAC spectroscopy

Bauer, Rogert; Adolph, Hans-Werner; Andersson, Inger; Danielsen, Eva; Formicka, Grazyna; Zeppezauer, Michael

doi:10.1007/bf00183458

Cited by 21 publications

(63 citation statements)

References 16 publications

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“…Spectroscopic studies of cadmium, copper, or cobalt substituted alcohol dehydrogenase in several instances have been taken to provide evidence for the presence of a fivecoordinated catalytic metal site [18][19][20]. The present results indicate that, to the extent that five-coordinate complexes do form with metal-substituted enzyme, this is likely to reflect the disparity in coordination preferences of different metal ions and cannot be taken to suggest that the catalytic metal site in native enzyme is five-coordinate.…”

Section: Comparison With Experimentsmentioning

confidence: 60%

“…On the other hand, there is also strong crystallographic and spectroscopic evidence showing that binding to zinc of certain bidentate inhibitors is fivecoordinate [18][19][20]. Furthermore, spectroscopic studies of metal-substituted alcohol dehydrogenase have indicated that several binary and ternary complexes may be fivecoordinate [11][12][13][20][21][22].…”

Section: Introductionmentioning

confidence: 99%

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The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

Ryde¹

1994

Int J of Quantum Chemistry

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The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal

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Section: Comparison With Experimentsmentioning

confidence: 60%

Section: Introductionmentioning

confidence: 99%

The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

Ryde¹

1994

Int J of Quantum Chemistry

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“…Yet, all experimental evidence (crystallographic and spectroscopic) agrees on that the free enzyme in the open conformation is four-coordinate [2][3]10,16,[19][20][21][22]44 . Further, it is widely assumed that the dehydration of the active site that occurs when the enzyme closes is important for the catalytic mechanism 1,2 .…”

Section: The Relative Stability Of Four-and Five-coordinate Zinc Compmentioning

confidence: 99%

“…Crystallographic and spectroscopic data showing that binding to zinc of certain bidentate inhibitors is fivecoordinate 14,15 have been taken as evidence in favor of these suggestions. Furthermore, spectroscopic studies of metal-substituted alcohol dehydrogenase have indicated that several binary and ternary complexes may be five-coordinate [6][7][8][15][16][17][18][19][20] , although other spectroscopic investigations contradict these results [21][22][23][24][25] . The kinetic evidence is also scattered and has been taken to favor fourcoordination 1,26 , as well as five-coordination 6,7,9,11,27 , of zinc in the catalytically productive ternary complexes.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion

1995

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A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force‐field reproduces excellently the geometry of quantum chemically optimized zinc complexes as well as the crystallographic geometry of the active site of alcohol dehydrogenase and small organic structures. The parameterization is used in molecular dynamics simulations and molecular mechanical energy minimizations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion. The active‐site zinc ion seems to prefer four‐coordination over five‐coordination by at least 36 kJ/mol. The only stable binding site of a fifth ligand at the active‐site zinc ion is opposite to the normal substrate site, in a narrow cavity behind the zinc ion. Only molecules of the size of water or smaller may occupy this site. There are large fluctuations in the geometry of the zinc coordination sphere. A four‐coordinate water molecule alternates frequently (every 7 ps) between the substrate site and the fifth binding site and even two five coordinate water molecules may interchange ligation sites without prior dissociation. Ligand exchange at the zinc ion probably proceeds by a dissociative mechanism. The results show that it is essential to allow for bond stretching degrees of freedom in molecular dynamics simulations to get a correct description of the dynamics of the metal coordination sphere; bond length constraints may restrict the accessible part of the phase space and therefore lead to qualitatively erroneous results. © 1995 Wiley‐Liss, Inc.

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“…This residue has been suggested to be involved in catalysis, either as a structural residue to stabilize the geometry of the active site (12), as a moderator of the electrostatic potential near the substrate (13), or, alternatively, as a possible zinc ligand during the enzyme's catalytic cycle (14)(15)(16). A recent atomic resolution structure of LADH in complex with NADH and Zn provides some evidence for different positions of the zinc-bound water and alternative conformations for Glu-68, indicating its potential as a zinc ligand (17).…”

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confidence: 99%

Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily

Baker

Britton

Fisher

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Despite being the subject of intensive investigations, many aspects of the mechanism of the zinc-dependent medium chain alcohol dehydrogenase (MDR) superfamily remain contentious. We have determined the high-resolution structures of a series of binary and ternary complexes of glucose dehydrogenase, an MDR enzyme from Haloferax mediterranei. In stark contrast to the textbook MDR mechanism in which the zinc ion is proposed to remain stationary and attached to a common set of protein ligands, analysis of these structures reveals that in each complex, there are dramatic differences in the nature of the zinc ligation. These changes arise as a direct consequence of linked movements of the zinc ion, a zinc-bound bound water molecule, and the substrate during progression through the reaction. These results provide evidence for the molecular basis of proton traffic during catalysis, a structural explanation for pentacoordinate zinc ion intermediates, a unifying view for the observed patterns of metal ligation in the MDR family, and highlight the importance of dynamic fluctuations at the metal center in changing the electrostatic potential in the active site, thereby influencing the proton traffic and hydride transfer events.MDR family ͉ structure ͉ zinc metalloenzyme ͉ reaction mechanism Z inc-dependent enzymes catalyze many important cellular processes (1); yet, despite this, the role played by the zinc ion in catalysis is not completely understood, partly because zinc is silent in a range of useful spectroscopic techniques, such as EPR and optical spectroscopy. One of the best characterized zinccontaining enzyme families is the Zn-dependent medium chain alcohol dehydrogenase superfamily (MDR), which catalyzes the oxidation of primary or secondary alcohols to the corresponding aldehydes or ketones using NAD(P) ϩ as a cofactor (2).The structures of many MDR family members have been determined with that of liver alcohol dehydrogenase (LADH) as the prototypical member (3). These studies have shown that the subunit of these enzymes is constructed from two domains, a nucleotide binding domain and a catalytic domain (4), with the essential zinc ion located deep in the cleft between them. The ligands to the zinc are provided by residues from the catalytic domain and, in the absence of substrate, the zinc is coordinated to the side chains of three well conserved residues, which in LADH are Cys-46, His-67, and Cys-174 (2). The tetrahedral coordination shell of the zinc is completed by a water molecule (2).In the classical text book mechanism for this enzyme family (5), this zinc-bound water molecule is suggested to be displaced by the incoming hydroxyl group of the alcohol on substrate binding, to leave the zinc ion coordinated to the substrate and the same three protein ligands as in the apo enzyme. The redox reaction requires the net removal of two hydrogen atoms from the substrate and is thought to proceed via proton loss from the substrate hydroxyl to bulk solvent by using a proton relay system to form an alkoxide intermedia...

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Coordination geometry for cadmium in the catalytic zinc site of horse liver alcohol dehydrogenase: studies by PAC spectroscopy

Cited by 21 publications

References 16 publications

The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion

Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily

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