Methanol dehydrogenase (cytochrome c)

 

Methanol dehydrogenase (MEDH) is a periplasmic quinoprotein. It catalyses the oxidation of methanol and other small alcohols to the corresponding aldehyde with the release of two protons and two electrons. The enzyme uses the pyrroloquinolinequinone (PQQ) cofactor.

MEDH is an H2L2 heterotetramer, made of two heavy (H) chains and two light (L) chains. Each H subunit contains one molecule of the prosthetic group PQQ, which is non-covalently bound to the polypeptide chain, as well as one calcium ion which is catalytically essential. There is no interaction between the L chains which fold around the surface of the H chains.

 

Reference Protein and Structure

Sequences
P38539 UniProt (1.1.2.7)
P38540 UniProt (1.1.2.7) IPR017512 (Sequence Homologues) (PDB Homologues)
Biological species
Methylophilus methylotrophus (Bacteria) Uniprot
PDB
1g72 - CATALYTIC MECHANISM OF QUINOPROTEIN METHANOL DEHYDROGENASE: A THEORETICAL AND X-RAY CRYSTALLOGRAPHIC INVESTIGATION (1.9 Å) PDBe PDBsum 1g72
Catalytic CATH Domains
2.140.10.10 CATHdb (see all for 1g72)
Cofactors
Calcium(2+) (1), Pyrroloquinoline quinone(3-) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.1.2.7)

primary alcohol
CHEBI:15734ChEBI
+
iron(3+)
CHEBI:29034ChEBI
→
aldehyde
CHEBI:17478ChEBI
+
hydron
CHEBI:15378ChEBI
+
iron(2+)
CHEBI:29033ChEBI
Alternative enzyme names: Methanol dehydrogenase, MDH,

Enzyme Mechanism

Introduction

In this computationally proposed mechanism, the reaction is initiated by the abstraction of a proton from the alcohol substrate by the general base Glu117. Simultaneously, a hydride is transferred to C'5 of PQQ, forming PQQH-. The aldehyde product then leaves the active site via an unknown pathway. The proton from Glu171 is transferred to Asp297, where it is positioned correctly to be abstracted by the alkoxide of PQQH-, forming PQQH. Quantum mechanical modelling then suggests Glu171 acts as a general base through a water molecule to initiate enolisation of PQQH to PQQH2. The presence of a calcium divalent cation within the active site polarises the PQQ carbonyl towards accepting a hydride.

The exact route that the electrons and protons take out of the active site to the heme of the bound cytochrome cL during the reduction of PQQ is unknown (due to lack of crystal structure with the cytochrome bound). It is assumed that the electrons will take the shortest route and may be the conserved disulfide ring, Asp105 and Asn52 and water molecules. The protons from the quinol are thought to be released to the periplasm through a hydrogen bonded network of proton donor and acceptor groups. This is thought to involve Asp303, Arg331. Glu177 and a channel of water molecules leading out of the active site [PMID:12686102].

Catalytic Residues Roles

UniProt PDB* (1g72)
Asp299 Asp297(299)A In the hydride mechanism, Asp297 is thought to act as a general acid to the PQQH- alkoxide anion, donating a proton relayed from Glu171. Modelling studies have ruled out Asp297 as the general base to initiate hydride transfer, although this has been suggested by structural data. metal ligand, proton acceptor, proton donor
Asn257 Asn255(257)A Forms part of the calcium binding site. metal ligand
Glu173 Glu171(173)A The residue is correctly positioned within the active site to act as a general base towards the alcohol substrate, initiating hydride transfer. It is thought to relay its attained proton to Asp297 which is positioned to act as a general acid to the alkoxide of PQQH-. The carboxylate anion of Glu171 is then thought to initiate enolisation of the PQQH prosthetic group to PQQH2 through a water molecule. metal ligand, proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

hydride transfer, proton transfer, proton relay, electron transfer, native state of cofactor regenerated, inferred reaction step, native state of enzyme regenerated

References

  1. Reddy SY et al. (2004), Protein Sci, 13, 1965-1978. Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. DOI:10.1110/ps.04673404. PMID:15273299.
  2. Rozeboom HJ et al. (2015), Protein Sci, 24, 2044-2054. Crystal structure of quinone-dependent alcohol dehydrogenase fromPseudogluconobacter saccharoketogenes. A versatile dehydrogenase oxidizing alcohols and carbohydrates. DOI:10.1002/pro.2818. PMID:26440996.
  3. Reddy SY et al. (2004), Proc Natl Acad Sci U S A, 101, 15887-15892. Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: A computational approach. DOI:10.1073/pnas.0407209101. PMID:15520392.
  4. Anthony C et al. (2003), Biochim Biophys Acta, 1647, 18-23. The structure and mechanism of methanol dehydrogenase. DOI:10.1016/s1570-9639(03)00042-6. PMID:12686102.
  5. Xia ZX et al. (1999), Biochemistry, 38, 1214-1220. Detailed Active Site Configuration of a New Crystal Form of Methanol Dehydrogenase fromMethylophilusW3A1 at 1.9 Å Resolution†,‡. DOI:10.1021/bi9822574. PMID:9930981.
  6. Anthony C et al. (1994), Biochem J, 304, 665-674. The structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone. DOI:10.1042/bj3040665. PMID:7818466.

Step 1. Glu171 as the catalytic base, abstracting the alcohol hydroxyl proton and initiating hydride transfer to the C5 carbonyl of PQQ. The aldehyde product then leaves the active site via an unknown pathway.

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Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand
Glu171(173)A proton acceptor

Chemical Components

hydride transfer, proton transfer

Step 2. Glu171 donates a proton to Asp297.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand
Asp297(299)A proton acceptor
Glu171(173)A proton donor

Chemical Components

proton transfer

Step 3. Asp297, which is thought to be correctly positioned to act as a general acid towards the alkoxide anion of PQQH-, forming PQQH.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand
Asp297(299)A proton donor

Chemical Components

proton transfer

Step 4. Computer modelling studies, which support the alternative hydride mechanism suggest that Glu171 acts as a general base through a water molecule to initiate enolisation of PQQH to PQQH2.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand, proton acceptor

Chemical Components

proton relay

Step 5. In the first step of the reduction of PQQ, a single electron and single proton are lost from the cofactor.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand

Chemical Components

electron transfer

Step 6. In the final step of the reduction of PQQ, a single electron is lost from the cofactor.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand

Chemical Components

electron transfer, native state of cofactor regenerated

Step 7. In an inferred return step, Glu171 is deprotonated by a water molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand, proton donor

Chemical Components

inferred reaction step, native state of enzyme regenerated, proton transfer
Download: Image, Marvin File

Step 1. Glu171 as the catalytic base, abstracting the alcohol hydroxyl proton and initiating hydride transfer to the C5 carbonyl of PQQ. The aldehyde product then leaves the active site via an unknown pathway.

Step 2. Glu171 donates a proton to Asp297.

Step 3. Asp297, which is thought to be correctly positioned to act as a general acid towards the alkoxide anion of PQQH-, forming PQQH.

Step 4. Computer modelling studies, which support the alternative hydride mechanism suggest that Glu171 acts as a general base through a water molecule to initiate enolisation of PQQH to PQQH2.

Step 5. In the first step of the reduction of PQQ, a single electron and single proton are lost from the cofactor.

Step 6. In the final step of the reduction of PQQ, a single electron is lost from the cofactor.

Step 7. In an inferred return step, Glu171 is deprotonated by a water molecule.

Products.

Introduction

In this original addition/elimination mechanism proposal, Asp297 is the only general acid/base. In this mechanism Asp297 abstracts a proton from the alcohol substrate, which initiates a nucleophilic attack on the PQQ cofcator. The cofactor then undergoes an intramolecular elimination to produce the formic acid product. PQQ is then regenerated through two successive single electron transfers from PQQ to cytochrome cL. However, the exact route that the electrons and protons take out of the active site to the heme of the bound cytochrome cL during the reduction of PQQ is unknown (due to lack of crystal structure with the cytochrome bound). It is assumed that the electrons will take the shortest route and may be the conserved disulfide ring, Asp105 and Asn52 and water molecules. The protons from the quinol are thought to be released to the periplasm through a hydrogen bonded network of proton donor and acceptor groups. This is thought to involve Asp303, Arg331. Glu177 and a channel of water molecules leading out of the active site [PMID:12686102].

Catalytic Residues Roles

UniProt PDB* (1g72)
Asp299 Asp297(299)A Acts as a general acid/base. metal ligand, proton acceptor, proton donor
Asn257, Glu173 Asn255(257)A, Glu171(173)A Forms part of the calcium binding site. metal ligand
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

cofactor used, intermediate formation, overall reactant used, bimolecular nucleophilic addition, proton transfer, intramolecular elimination, electron transfer

References

  1. Xia ZX et al. (1999), Biochemistry, 38, 1214-1220. Detailed Active Site Configuration of a New Crystal Form of Methanol Dehydrogenase fromMethylophilusW3A1 at 1.9 Å Resolution†,‡. DOI:10.1021/bi9822574. PMID:9930981.
  2. Zhang X et al. (2007), Proc Natl Acad Sci U S A, 104, 745-749. Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase. DOI:10.1073/pnas.0610126104. PMID:17215371.
  3. Anthony C et al. (1994), Biochem J, 304, 665-674. The structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone. DOI:10.1042/bj3040665. PMID:7818466.

Step 1. Asp297 deprotonates the alcohol group of the primary alcohol, which initiates a nucleophilic attack on the C5 of PQQ.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand
Asp297(299)A proton acceptor

Chemical Components

cofactor used, intermediate formation, overall reactant used, ingold: bimolecular nucleophilic addition, proton transfer

Step 2. The oxyanion of PQQ deprotonates Asp297.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand
Asp297(299)A proton donor

Chemical Components

proton transfer

Step 3. The oxygen of the PQQ C6 carbonyl group abstracts a proton from the bound primary alcohol, eliminating the reduced PQQ and forming the aldehyde product.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand

Chemical Components

ingold: intramolecular elimination, proton transfer

Step 4. In the first step of the reduction of PQQ, a single electron and single proton are lost from the cofactor.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand

Chemical Components

electron transfer

Step 5. In the final step of the reduction of PQQ, a single electron and single proton are lost from the cofactor.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn255(257)A metal ligand
Asp297(299)A metal ligand
Glu171(173)A metal ligand

Chemical Components

electron transfer
Download: Image, Marvin File

Step 1. Asp297 deprotonates the alcohol group of the primary alcohol, which initiates a nucleophilic attack on the C5 of PQQ.

Step 2. The oxyanion of PQQ deprotonates Asp297.

Step 3. The oxygen of the PQQ C6 carbonyl group abstracts a proton from the bound primary alcohol, eliminating the reduced PQQ and forming the aldehyde product.

Step 4. In the first step of the reduction of PQQ, a single electron and single proton are lost from the cofactor.

Step 5. In the final step of the reduction of PQQ, a single electron and single proton are lost from the cofactor.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Sophie T. Williams, James W. Murray, Craig Porter