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|PQQ structure as seen by X-ray crystallography of methanol dehydrogenase|
|This shows the 'propeller structure of methanol dehydrogenase. PQQ can be seen in middle of protein.|
|These sequences are what search engines use to find propeller structures;
they were then sometimes wrongly labelled as PQQ binding sites.
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|Wikipedia article on PQQ TOP of PAGE http://en.wikipedia.org/wiki/Pyrroloquinoline_quinone
This article, which concentrates on PQQ as having potential importance in mammalian physiology, has many errors in it. My concern here is about the parts that I know about; I was one of the first discoverers of PQQ and have worked on it for nearly 50 years and published many papers on the subject (Listed here).
The first part of the Wikipedia article is an introduction, flawed by many errors of fact. After discussing these I will propose an alternative. The last section is titled Controversy. This seems to think that science is a matter of weighing up opinions rather that looking at the evidence. It is very misleading. In my discussion below I have put the Wikipedia statements in italics.
Wikipedia IntroductionThe cofactors are not nicotinamide and flavin. They are NAD (nicotinamide adenine dinucleotide) and flavin nucleotides (flavin adenine mononucleotide and flavin adenine dinucleotide). Perhaps it would be simpler to say “ after nicotinamide and flavin derivatives in bacteria”.
We (Anthony & Zatman) did not name it Methoxatin. This was a name proposed (but not now used) by Salisbury et al (reference 3) when they first described its structure.
We (Anthony & Zatman; ref 2) did not find the unknown redox cofactor in ‘alcohol dehydrogenase’. The link to alcohol dehydrogenase is not correct. Perhaps this is a weakness of Wikipedia articles; if there is an article already written with a title that is the same as a word used then we are linked to it. In this case the reader is referred to an article on typical NAD-linked alcohol dehydrogenase; but the whole point of the enzyme containing PQQ (actual name is methanol dehydrogenase) is that it is NOT a typical alchohol dehydrogenase; it is one of a completely new class of enzymes (quinoproteins).
In fact we extracted this prosthetic group from methanol dehydrogenase of methylotrophs.
My suggested rewrite:
Pyrroloquinoline quinone (PQQ) was discovered by J.G. Hauge as the third redox cofactor after after nicotinamide and flavin derivatives in bacteria (although he hypothesised that it was naphthoquinone). Anthony and Zatman purified and characterised this prosthetic group from methanol dehydrogenase of methylotrophs . In 1979, using this prosthetic group, Duine and colleagues showed its unusual quinone structure, and Salisbury and colleagues identified its molecular structure by X-ray crystallography, suggesting the name Methoxatin (not now used). In 1981 Adachi and colleagues identified that PQQ was also found in the membrane alcohol dehydrogenase of Acetobacter.
Controversy section in the Wikipedia article
“Anthony further states on his website that "No mammalian PQQ-containing enzyme (quinoprotein) has been described" and that PQQ therefore cannot be called a "vitamin". The latter statement is an exaggeration, since there are at least four human quinoproteins, the enzyme activity of which is dependent on PQQ”.
The author then lists the four enzymes. I have listed them here with my comments. My conclusion is that there is no evidence at all that these are quinoproteins.
Quote from the Uniprot entry: Broad specificity oxidoreductase that catalyzes the NADPH-dependent reduction of a variety of flavins, such as riboflavin, FAD or FMN, biliverdins, methemoglobin and PQQ (pyrroloquinoline quinone). Contributes to heme catabolism and metabolizes linear tetrapyrroles. Can also reduce the complexed Fe3+ iron to Fe2+ in the presence of FMN and NADPH. In the liver, converts biliverdin to bilirubin.
This says that Flavin reductase can use PQQ as a substrate. It does not say PQQ is part of the enzyme. To suggest this enzyme is a PQQ-containing enzyme is like saying the substrate glucose is part of glucose kinase.
I can find no mention of PQQ as substrate in any of the references from Uniprot, including the reference given for the mention of PQQ as substrate: Orla CUNNINGHAM*1, Michael G. GORE† and Timothy J. MANTLE (2000). Initial-rate kinetics of the flavin reductase reaction catalysed by human biliverdin-IXbreductase (BVR-B). Biochem. J. 345 (393–399).
This is very confused. The enzyme referred to in Uniprot is not AAS dehydrogenase; it is (as stated) Acyl-CoA synthetase. The presumed PQQ enzyme referred to here is published by Wang et al. Wang et al (2005). Cloning and characterization of a novel human homolog of mouse U26, a putative PQQ-dependent AAS dehydrogenase. Mol. Biol. Rep. 32:47-53.
The mU26 protein said to be a putative PQQ-dependent AAS dehydrogenase (Amino adipate semialdehyde dehydrogenase) is the enzyme involved in lysine degradation. BUT Kasahara & Kato were not dealing with this enzyme. They started by assuming that the yeast enzyme involved in lysine biosynthesis (amino adipic acid reductase; AAA reductase) could work in reverse and be involved in lysine degradation, and this is the enzyme used in their work.
This entry states that there is a binding site for PQQ. This is one of the dangers of using database searches. All this does is to say that there is a tiny sequence in the amino acid sequence similar to a sequence involved in PQQ binding. This is not evidence that PQQ does bind.
A thorough review of the enzymes (referred to in the Uniprot article) is: ST Prigge, RE Mains, BA Eipper, LM Amzel (2000). "New insights into copper monooxygenases and peptide amidation: structure, mechanism and function.". Cellular and Molecular Life Sciences. 57: 1236–1259. This does not mention PQQ.
So none of the four enzymes is a PQQ-containing quinoprotein
The final statement in the Controversy section of the Wikipedia article:
This analysis is the reply to our Nature paper refuting the conclusions of Kasahara & Kato which claimed to have found a PQQ-containing enzyme in mice and thus proposing PQQ as a new vitamin.
In their reply to our paper (and that of Rucker refuting their claims on nutritional grounds in the same journal) (ref 52) they say “Rucker et al.3 find that the aminoadipic 6-semialdehyde (AAS) dehydrogenase activity in their samples with and without PQQ does not change, nor does the ratio of plasma 2-aminoadipic acid (AAA)/lysine between PQQ-deprived and PQQ-supplemented rodents3. They are here discussing the enzyme that is involved in lysine metabolism in mice, and it is the one with the link L-aminoadipate-semialdehyde dehydrogenase. However this enzyme is NOT the proposed ‘enzyme’ mU26 which is the subject of their original paper. That enzyme (wrongly identified as being a PQQ enzyme) was proposed on the basis of similarity (26%) to an enzyme: Aminoadipic acid reductase (AAA reductase). This functions in the biosynthesis of lysine in yeast, not its degradation. It requires NADPH and ATP for activity. It is NOT reversible and It does not occur in mammals.
Their false argument, based on sequence:
All trees are green; My coat is green: Therefore my coat is a tree].
All quinoproteins have propellers; My protein has a propeller; Therefore my protein is a quinoprotein
The Wikipedia writer refers to the Kasahara & Kato response in Nature (ref. 52) which says “Felton and Anthony2 assert that the repeated sequences we find in mouse U26 (mU26) represent a β-propeller protein and not a PQQ-dependent enzyme. Anthony and a colleague claimed previously that the ‘tryptophan docking motif’, a partial sequence of the PQQ enzyme repeat, is present only in PQQ-dependent enzymes that have a different number of blades and a unique manner of closure compared with other β-propeller proteins4”.
Ref. 4. Anthony, C. & Ghosh, M. (1988). The structure and function of the PQQ-containing quinoprotein dehydrogenases. Progr. Biophys.Mol. Biol. 69, 1–21.
They are quoting this as justification for their conclusion. The statement is true but not relevant as an argument against the truth. At the time of our 1988 review the only proteins that had such a structure were the PQQ-containing quinoproteins so what we said was true. This does not mean that other proteins could never be found with this structure but which are not quinoproteins.
For anyone interested in these proteins the structure mU26 (predicted from a gene sequence, never seen as a protein) does have a (predicted) 8-bladed propeller structure with the blades held together by a tryptophan-docking motif, previously only seen in quinoproteins. What is very remarkable about this structure is that it is the smallest possible 8-bladed structure with only the smallest possible blades and the smallest possible distances between them.
My website links:
=Anthony, C. and Zatman, L.J. (1967). The microbial oxidation of methanol: The prosthetic group of alcohol dehydrogenase of Pseudomonas sp. M27; A new oxidoreductase prosthetic group. Biochemical Journal 104, 960-969.
Anthony, C. (1971). Prosthetic group of the alcohol dehydrogenase of a Pseudomonad. Methods in Enzymology 18, 808-813.
Nunn, D.N. and Anthony, C. (1988). The nucleotide sequence and deduced amino acid sequence of the genes for cytochrome cL and a hypothetical second subunit of the methanol dehydrogenase of Methylobacterium AM1. Nucleic Acids Research 16, 7722-7722.
Nunn, D.N., Day, D.J. and Anthony, C. (1989). The second subunit of methanol dehydrogenase of Methylobacterium extorquens AM1. Biochemical Journal 260, 857-862.
Anderson, D.J., Morris, C.J., Nunn, D.N., Anthony, C. and Lidstrom, M.E. (1990). Nucleotide sequence of the Methylobacterium extorquens AM1 moxF and moxJ genes involved in methanol oxidation. Gene 90, 173-176.
Ghosh, M., Harlos, K., Blake, C.C.F., Richardson, I. & Anthony, C. (1992). Crystallization and preliminary crystallographic investigation of methanol dehydrogenase from Methylobacterium-extorquens AM1. J Mol Biol 228, 302-305.
Blake, C.C.F., Ghosh, M., Harlos, K., Avezoux, A. & Anthony, C. (1994). The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues. Nature, Structural Biology 1, 102-105.
Avezoux, A., Goodwin, M.G. & Anthony, C. (1995). The role of the novel disulphide ring in the active site of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens. Biochemical Journal 307, 735-741.
Cozier, G.E., Giles, I.G. & Anthony, C. (1995). The structure of the quinoprotein alcohol dehydrogenase of Acetobacter aceti modelled on that of methanol dehydrogenase from Methylobacterium extorquens. Biochemical Journal 308, 375-379.
Cozier, G.E. & Anthony, C. (1995). The structure of the quinoprotein glucose dehydrogenase of Escherichia coli modelled on that of methanol dehydrogenase from Methylobacterium extorquens. Biochemical Journal 312, 679-685.
Ghosh, M., Anthony, C., Harlos, K., Goodwin, M.G. & Blake, C.C.F. (1995). The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94Å. Structure 3, 177-187.
Anthony, C. (1998). The pyrroloquinoline quinone (PQQ)-containing quinoprotein dehydrogenases. Biochemical Society Transactions 26, 413-417.
Cozier, G.E., Salleh, R. A. & Anthony, C. (1998). The structure and function of glucose dehydrogenase. Biochemical Society Transactions 26, S270.
Cozier, G.E., Salleh, R.A. & Anthony, C. (1999). Characterisation of the membrane glucose dehydrogenase from Escherichia coli and characterisation of a site directed mutant in which His262 has been changed to tyrosine. Biochem. J. 340, 639-647.
Afolabi, P.R. Mohammed, F., Amaratunga, K., Majekodunmi, O., Dales, S.L., Gill, R., thompson, D., cooper, J.B., Wood, S.OP., Goodwin, P.M. and Anthony, C. (2001). Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor cytochrome c. Biochemistry 40, 9799-9809.
Anthony, C. and Williams, P.W. (2003). The structure and function of methanol dehydrogenase. Biochim. Biophys. Acta 1467, 18-23.
Felton, L. M. & Anthony, C.(2005). Role of PQQ as a mammalian enzyme cofactor? Nature doi:10.1038/nature03322
P A Williams, L Coates, F Mohammed, R Gill, P T Erskine, A Coker, S P Wood, C Anthony, J B Cooper (2005). The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallogr D Biol Crystallogr. 61:75-9
Book chapters and Reviews
Anthony, C., John, R.A. and Wilmot, C.M. (2003). Third international Symposium on vitamin B6, PQQ, Carbonyl Catalysis and Quinoproteins. Biochim. Biophys. Acta 1647, 1-410.
Anthony, C. (1990). The oxidation of methanol in Gram-negative bacteria. FEMS Microbiology Reviews 87, 209-214.
Anthony, C. (1992a). The structure of bacterial quinoprotein dehydrogenases. Int J Biochem 24, 29-39.
Anthony, C. (1993a). The role of quinoproteins in bacterial energy transduction. In Principles and applications of quinoproteins, pp. 223-244.Davidson.V.L.New York, Marcel Dekker.
Anthony, C. (1993b). Methanol dehydrogenase in Gram-negative bacteria. In Principles and applications of quinoproteins, pp. 17-45.Davidson.V.L.New York, Marcel Dekker.
Anthony, C. (1994). The structure and function of quinoprotein dehydrogenases. In Biochemistry of Vitamin B6 and PQQ, pp. 277-281. Marino.G., Sannia.G. & Bossa.F.Basel, Switzerland, Birkhauser Verlag.
Anthony, C., Ghosh, M. & Blake, C.C.F. (1994). The structure and function of methanol dehydrogenase and related PQQ-containing quinoproteins. Biochem J 304, 665-674.
Anthony, C. (1996). Quinoprotein-catalysed reactions. Biochem.J. 320, 697-711.
Anthony, C. and Ghosh, M. (1996). The structure and function of PQQ-containing quinoproteins. Current Science (India) 72, 716-727.
Goodwin, P.M. & Anthony, C. (1998). The biochemistry, physiology and genetics of PQQ and PQQ-containing enzymes. Advances in Microbial Physiology 40, 1-80.
Anthony, C. (1998). Quinoprotein-catalysed reactions. In Comprehensive Biological Catalysis, Academic Press (Ed, M. Sinnott), 155-180.
Anthony, C. & Ghosh, M. (1998). The structure and function of the PQQ-containing quinoprotein dehydrogenases. Progress in Biophysics and Molecular Biology 69, 1-21.
Anthony, C. (1999). An unusual role for tryptophan in PQQ-containing quinoproteins. Adv Exp Med Biol 467, 597-602.
Anthony, C., Salleh, R.A., James, P.L. & Cozier, G.E. (2000) the membrane glucose dehydrogenase of E. coli. In Vitamin B6, carbonyl catalysis, PQQ and Quinoproteins (Ed. M Martinez-Carrion) Birkhauser Verlag AG.
Anthony, C. (2000). Methanol dehydrogenase; a PQQ-containing quinoprotein dehydrogenase. In Enzyme-catalysed electron and radical transfers. Subcellular Biochemistry 35, 73-118.
Anthony, C. (2001). Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes. Antioxidants and Redox Signalling 3, 757-774.
Anthony, C. and Williams, P.W. (2003). The structure and function of methanol dehydrogenase. Biochim. Biophys. Acta 1467, 18-23.
Anthony, C. (2003) Guest Editor of Biochim. Biophys. Acta Special Issue : 3rd International Symposium on Vitamin B6, PQQ, Carbonyl catalysis and Quinoproteins Biochim. Biophys. Acta 1647, 1-408 (2003).
Anthony, C. (2004) The Pyrroloquinoline Quinone (PQQ)-Containing Dehydrogenases. In Zannoni D. (ed): Respiration in Archaea and Bacteria. Vol. 1. Diversity of Prokaryotic Electron Transport Carriers, pp. 203-225. Kluwer Academic Publishers. Printed in The Netherlands.
Anthony, C. (2004). The quinoprotein dehydrogenases for methanol and glucose. Archives of Biochemistry and Biophysics 428, 2–9.