The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 å

Ghosh, Minakshi; Anthony, Christopher; Harlos, K.; Goodwin, Matthew G; Blake, C. C. F.

doi:10.1016/s0969-2126(01)00148-4

Cited by 198 publications

(210 citation statements)

References 42 publications

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“…The Nand C-terminal ␤-strands of each blade are located on the inner and outer side, respectively, of the ␤-propeller, and the Cterminal strand is connected to the N-terminal strand of the neighboring blade. The ␤-propeller fold has also been observed in galactose oxidase (25) and in quinoproteins such as TTQcontaining methylamine dehydrogenase (27) and PQQ-dependent glucose (28), methanol (29) and ethanol (30) dehydrogenases. A structure similarity search (31) showed that the large ␤-propeller subunit of methylamine dehydrogenase is quite similar to the ␤-subunit of QH-AmDH.…”

Section: Resultsmentioning

confidence: 92%

Crystal Structure of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida

Satoh¹,

Kim²,

Miyahara³

et al. 2002

Journal of Biological Chemistry

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The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-Å resolution. The enzyme comprises three non-identical subunits: a four-domain ␣-subunit that harbors a di-heme cytochrome c, a seven-bladed ␤-propeller ␤-subunit that provides part of the active site, and a small ␥-subunit that contains a novel crosslinked, proteinous quinone cofactor, cysteine tryptophylquinone. More surprisingly, the catalytic ␥-subunit contains three additional chemical cross-links that encage the cysteine tryptophylquinone cofactor, involving a cysteine side chain bridged to either an Asp or Glu residue all in a hitherto unknown thioether bonding with a methylene carbon atom of acidic amino acid side chains. Thus, the structure of the 79-residue ␥-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure.Recently, a number of modified amino acids have been identified in proteins that are generated by post-translational oxidation or non-oxidation processes (1, 2). Such a controlled modification of a specific amino acid residue forming part of the active site provides catalytic power to the protein. In the case of a certain class of amine-oxidizing enzymes, depending on the enzyme concerned, oxidation of a specific tyrosine or tryptophan residue leads to the generation of a redox-active quinone cofactor: 2,4,5-trihydroxyphenylalanine quinone (topaquinone) (3), lysine tyrosylquinone (4), or tryptophan tryptophylquinone (TTQ) 1 (5). Together with several enzymes containing the first identified, non-proteinous quinone cofactor, pyrroloquinoline quinone (PQQ), the enzymes containing those cofactors constitute a quinoprotein family of enzymes (6).Quinohemoprotein amine dehydrogenases (QH-AmDH) from Gram-negative bacteria represent a new type in the quinoprotein class of amine-oxidizing enzymes because they contain not only a quinone but also one or two hemes as a redox active group (7, 8) providing an opportunity for intramolecular electron transfer. Intermolecular electron transfer from QHAmDH has been demonstrated with the natural electron acceptors azurin for the enzyme from Pseudomonas putida (7) and cytochrome c-550 for the enzyme from Paracoccus denitrificans (9). The structure of the presumed quinone cofactor in QH-AmDH remain to be settled, although biochemical and spectroscopic analyses have suggested the presence of a quinone group similar to, but not identical, with TTQ (7, 8).To identify the quinone cofactor and its position in the protein, we (10) have recently determined the primary structure of the quinone-containing small subunit of QH-AmDH from P. putida using a combination of automated Edman degradation and mass spectrometry, and we have also cloned the genes coding for the three subunits of the heterotrimeric enzyme. Although we initially encountered difficulties in the interpretation of the chemical and mass data, the progress in elucidating the crystal struct...

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Section: Resultsmentioning

confidence: 92%

Crystal Structure of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida

Satoh¹,

Kim²,

Miyahara³

et al. 2002

Journal of Biological Chemistry

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“…Such an atypical disulfide bridge, connecting residues that are adjacent in sequence, is rare in available protein structures. Two of these proteins are members of the alcohol dehydrogenase family, specifically methanol dehydrogenase from Methylobacterium extorquens (48,49) and ethanol dehydrogenase from Pseudomonas aeruginosa (50). The atypical disulfide bridge may stabilize the non-planar semiquinone form of the enzyme's prosthetic group pyrroloquinoline quinone (49).…”

Section: Zinc Is a Competitive Active Site Inhibitor That Binds To Thementioning

confidence: 99%

“…Two of these proteins are members of the alcohol dehydrogenase family, specifically methanol dehydrogenase from Methylobacterium extorquens (48,49) and ethanol dehydrogenase from Pseudomonas aeruginosa (50). The atypical disulfide bridge may stabilize the non-planar semiquinone form of the enzyme's prosthetic group pyrroloquinoline quinone (49). We speculate that, under the specific living conditions of P. woesei at high temperatures, rigidification of the active site area by additional conformational constraints imposed by the presence of such a disulfide bridge may be required for in vivo catalytic activity.…”

Section: Zinc Is a Competitive Active Site Inhibitor That Binds To Thementioning

confidence: 99%

Differential Regulation of a Hyperthermophilic α-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc

Lindén

Mayans

Meyer‐Klaucke

et al. 2003

Journal of Biological Chemistry

100

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The crystal structure of the ␣-amylase from the hyperthermophilic archaeon Pyrococcus woesei was solved in the presence of three inhibitors: acarbose, Tris, and zinc. In the absence of exogenous metals, this ␣-amylase bound 1 and 4 molar eq of zinc and calcium, respectively. The structure reveals a novel, activating, twometal (Ca,Zn)-binding site and a second inhibitory zincbinding site that is found in the ؊1 sugar-binding pocket within the active site. The data resolve the apparent paradox between the zinc requirement for catalytic activity and its strong inhibitory effect when added in molar excess. They provide a rationale as to why this ␣-amylase, in contrast to commercially available ␣-amylases, does not require the addition of metal ions for full catalytic activity, suggesting it as an ideal target to maximize the efficiency of industrial processes like liquefaction of starch.

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“…10) of the reduced PQQ bound to MDH presents Wat1 hydrogen bonding to the -CO 2 Ϫ group of Asp-297 (Asp-297-CO 2 Ϫ ) and ϪCO 2 Ϫ group of Glu-171 (Glu-171-CO 2 Ϫ ) associated with Ca 2ϩ . Attempts to crystallize MDH with MeOH substrate at the active site have not yet been successful (10,12,13). The hydride transfer mechanism was shown to be correct by x-ray crystallography (10).…”

mentioning

confidence: 99%

Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase

Zhang

Reddy

Bruice

2007

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

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hydride transfer ͉ molecular dynamics ͉ pyrroloquinoline quinone W e have had a long standing interest in the mechanism of o-quinone cofactor and model reactions (for examples, see refs. 1-4). More recently, our attention has been directed to the employment of computational methods, particularly in the mechanism of the oxidation of methanol and glucose by the appropriate quinoprotein enzymes (5-11).The present study concerns bacterial quinoprotein methanol dehydrogenase (MDH) catalysis of the oxidation of CH 3 OH 3 CH 2 O by the pyrroloquinoline quinone (PQQ) cofactor. MDH is a hetrotetramer with two heavy and two light subunits. The catalytic chemistry is located in the heavy subunits. The crystal structure (PDB code 1G72; ref. 10) of the reduced PQQ bound to MDH presents Wat1 hydrogen bonding to the -CO 2

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The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 å

Cited by 198 publications

References 42 publications

Crystal Structure of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida

Crystal Structure of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida

Differential Regulation of a Hyperthermophilic α-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc

Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase

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