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a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
active site structure with bound cofactor, the reduced pyrroloquinoline quinone (PQQ) transfers two electrons in single electron-transfer steps to cytochrome cL, creating a semiquinone form of the prosthetic group after the first electron transfer, electron transfer via enzyme residues Cys104, Asp105, and Asn52
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a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
catalytic mechanism, ping-pong kinetic schemes, and transition state structures, analysis by ab initio quantum mechanical methods, hydride transfer from the Calpha-position of the substrate alcohol or aldehyde directly to the C-5 carbon of PQQ is energetically feasible, detailed overview
a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
detailed reaction mechanism with direct hydride transfe, Glu177 plays the role of general base catalyst
a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
mechanism of methanol oxidation by QMDH, overview
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
additional information
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
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cytochrome c is the natural electron acceptor
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
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terminal electron acceptor is cytochrome cL
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
MDH catalyses the first reaction of an unusual periplasmic electron transport chain responsible for oxidation of methanol to formaldehyde in methylotrophic bacteria during growth on methane or methanol
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
flow of electrons from reduced pyrroloquinoline quinone to the heme of cytochrome cL
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
the reaction includes an electron transfer from the quinol PQQH2 to the electron acceptor cytochrome CL mediated by the disulfide structure of the active site, the active site of MDH involves Trp243 that forms the base of the active site chamber, and the Cys103-Cys104 disulfide ring and the pyrroloquinoline quinone prosthetic group, which is in the semiquinone form having the oxygen of the C4 carbonyl displaced out of the plane of the ring, overview
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
periplasmic electron transport chain responsible for oxidation of methanol to formaldehyde in methylotrophic bacteria: methanol, methanol dehydrogenase, cytochrome cL, cytochrome cH, oxidase, oxygen
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
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the physiological electron acceptor is cytochrome cL. Cytochrome cL is subsequently oxidized by the small class I c-type cytochrome cH
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additional information
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active site structure with important disulfide bridge of Cys103-Cys104, overview
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additional information
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active site structure, the Cys103-Cys104 disulfide bridge plays a role in the electron transfer during catalysis, overview
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additional information
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MDH is a soluble periplasmic enzyme, having cytochrome CL as electron acceptor, Ca2+ plays a role in maintaining PQQ in the correct configuration and may also be involved in the catalytic mechanism, overview
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additional information
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oxidation of alcohols by direct hydride transfer to the pyrroloquinoline quinone cofactor
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additional information
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1,6-dichlorophenolindophenol, N,N,N',N'-tetramethyl-4-phenylenediamine, and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfuric acid) can act as artificial electron acceptors. The artificial electron acceptors cannot be directly reduced by the enzyme. Their reduction requires the presence of phenazine ethosulfate or phenazine methosulfate. Electrons are transferred from an oxidizing substrate to the PQQ moiety, and protons are released into the cytoplasm. The reduced PQQ moiety donates electrons to cytochrome c one after the other, yielding the semiquinone form of PQQ
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
additional information
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MDH is a soluble periplasmic enzyme, having cytochrome CL as electron acceptor, Ca2+ plays a role in maintaining PQQ in the correct configuration and may also be involved in the catalytic mechanism, overview
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
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methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
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cytochrome c is the natural electron acceptor
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
MDH catalyses the first reaction of an unusual periplasmic electron transport chain responsible for oxidation of methanol to formaldehyde in methylotrophic bacteria during growth on methane or methanol
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
periplasmic electron transport chain responsible for oxidation of methanol to formaldehyde in methylotrophic bacteria: methanol, methanol dehydrogenase, cytochrome cL, cytochrome cH, oxidase, oxygen
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methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
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the physiological electron acceptor is cytochrome cL. Cytochrome cL is subsequently oxidized by the small class I c-type cytochrome cH
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heme c
part of cytochrome cL
cytochrome cL
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cytochrome cL
electron acceptor
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cytochrome cL
flow of electrons from reduced pyrroloquinoline quinone to the heme of cytochrome cL, binding and crystal structure determination and analysis at 1.6 A resolution, contains a disulfide bridge that tethers the long C-terminal extension to the body of the structure, overview
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pyrroloquinoline quinone
i.e. PQQ or 4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylaic acid, enzyme-bound to the active site, 1 molecule per alpha-subunit, required for catalytic activity
pyrroloquinoline quinone
PQQ
pyrroloquinoline quinone
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the enzyme is a type II PQQ-containing alcohol dehydrogenase, the cofactor is bound to the active site in an entirely planar conformation of the tricyclic PQQ cofactor ring, binding structure overview
pyrroloquinoline quinone
binding structure in the active site, overview
pyrroloquinoline quinone
dependent on, prosthetic group, the PQQ in the active site is held in place by a coplanar tryptophan and by a novel disulfide ring formed between adjacent cysteines which are bonded by an unusual non-planar trans peptide bond. One of the carbonyl oxygens of PQQ is bonded to the Ca2+ , probably facilitating attack on the substrate, and the other carbonyl oxygen is out of the plane of the ring, confirming the presence of the predicted free-radical semiquinone form of the prosthetic group
pyrroloquinoline quinone
flow of electrons from reduced pyrroloquinoline quinone to the heme of cytochrome cL, binding structure
pyrroloquinoline quinone
i.e. 2,7,9-tricarboxy-1H-pyrrolo[2,3-f]quinoline-4,5-dione, PQQ, structures of anionic PQQ, neutral PQQ, and reduced PQQ, overview
pyrroloquinoline quinone
PQQ, binding structure at the active site, overview, the active site contains a single Ca2 + ion whose coordination sphere contains PQQ and protein atoms, including both oxygens of the carboxylate of Glu177 and the amide oxygen of Asn261
pyrroloquinoline quinone
PQQ, prosthetic group
pyrroloquinoline quinone
PQQ, 2 mol of PQQ per mol of enzyme, the cofactor is predominantly in the semiquinone form, binding structure, overview
pyrroloquinoline quinone
PQQ, is the only prosthetic group, the PQQ is sandwiched between the indole ring of Trp243 and the disulfide ring structure, overview
pyrroloquinoline quinone
PQQ, one molecule per enzyme alpha-subunit. The PQQ ring is sandwiched between the indole ring of Trp243 and the two sulphur atoms of the disulfide ring structure
pyrroloquinoline quinone
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i.e. PQQ or 4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3f]quinoline-2,7,9-tricarboxylic acid, essentially required, binding structure
additional information
an NAD(P)-independent enzyme
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additional information
an NAD(P)-independent enzyme
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Fe2+
a cytochrome protein
Sr2+
Ca2+ can be replaced in the incorporation process by strontium or barium, the affinities for these ions being similar to that for Ca2+, Sr2+ shows 94% of the activity with Ca2+
additional information
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Mg2+ cannot substitute for Ca2+
Ba2+
can substitute for Ca2+, Ba-MDH has twice the maximum activity of the Ca-MDH but with a much lower affinity for its substrates
Ba2+
Ca2+ can be replaced in the incorporation process by strontium or barium, the affinities for these ions being similar to that for Ca2+, Ba2+ shows 102% of the activity with Ca2+
Ba2+
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modeling of Ba2+-containing MDH active site to investigate the proposed addition-elimination and hydride-transfer methanol oxidation mechanisms. For both mechanisms, almost all the free-energy barriers associated with all of the steps are reduced in the presence of Ba2+-MDH, and they are kinetically feasible. The free energy barriers for methanol oxidation by Ba2+-MDH, particularly for the rate-limiting steps of both mechanisms, are almost half the corresponding barriers calculated for the case of Ca2+-MDH
Ca2+
bound to the active site, required for catalytic activity
Ca2+
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required, bound at the active site, interaction with the cofactor and the active site residues Arg331, Asp303, and Glu177, but not Asn261, structure overview
Ca2+
binding structure at the active site, overview, the active site contains a single Ca2+ ion whose coordination sphere contains PQQ and protein atoms, including both oxygens of the carboxylate of Glu177 and the amide oxygen of Asn261
Ca2+
binding strucure in the active site, overview
Ca2+
one molecule per enzyme alpha-subunit, binding involves Glu177 and Asn261, Ca2+ plays a role in maintaining PQQ in the correct configuration and may also be involved in the catalytic mechanism
Ca2+
required for activity, functional role analysis, overview
Ca2+
the active site contains a single Ca2+ whose coordination sphere contains PQQ and protein atoms
Ca2+
tightly bound close to the inner heme propionate, Ca2+ is involved in stabilization of the redox potential, and is important in the flow of electrons from reduced pyrroloquinoline quinone in methanol dehydrogenase to the heme of cytochrome cL
Ca2+
2 Ca2+ ions are irreversibly incorporated per alpha2beta2 tetramer. Calcium can be replaced in the incorporation process by strontium or barium, the affinities for these ions being similar to that for Ca2+
Ca2+
one molecule of Ca2+ per enzyme tetramer. Ca2+ is directly or indirectly involved in the biding of pyrroloquinoline quinone. Methanol oxidation mutants MoxA-, K- and L- contain no Ca2+. The MoxA, K and L proteins may be involved in maintaining a high Ca2+ concentration in the periplasm. It is more likely, that they fill a chaperone function, stabilizing a configuration of methanol dehydrogenase which permits incorporation of low concentrations of Ca2+ into the protein
Ca2+
one molecule per enzyme alpha-subunit. Neither the quinone form of pyrroloquinoline quinone, nor the disulfide ring or its reduced form are absolutely essential for calcium incorporation into the active site
Ca2+
required for activity, one of the carbonyl oxygens of PQQ is bonded to the Ca2+, probably facilitating attack on the substrate, and the other carbonyl oxygen is out of the plane of the ring, confirming the presence of the predicted free-radical semiquinone form of the prosthetic group
Ca2+
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active site of QMDH contains one Ca2+ ion, removal of Ca2+ ions results in the loss of the enzyme activity, important role of Ca2+ in the catalysis
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x * 62000, alpha-subunit, + x * 7500, beta-subunit, SDS-PAGE
tetramer
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alpha2beta2 subunit conposition, structure model of an alphabeta unit from crystal structure determination, overview
tetramer
2 * 66000 + 2 * 8500, alpha2beta2, crystal structure determination
tetramer
4 * 66000, alpha2beta2, crystal structure
tetramer
alpha2beta2, comparison of wild-type and mutant enzyme structures, overview
tetramer
alpha2beta2, the alpha-subunit has an 8fold radial symmetry, with its eight 3-sheets stabilized by a novel tryptophan docking motif. The PQQ in the active site is held in place by a coplanar tryptophan and by a novel disulfide ring formed between adjacent cysteines which are bonded by an unusual non-planar trans peptide bond, subunit structures and interactions, overview
tetramer
alpha2beta2, three-dimensional structure, modelling, overview
additional information
the large alpha-subunit has a propeller fold making up a superbarrel of eight radially arranged beta-sheets, i.e. the propeller blades, containing the tryptophan-docking motifs that link together the eight beta-sheets, and the presence in the active site of a unique eight-membered disulfide ring structure formed from adjacent cysteine residues 103 and 104, joined by an atypical non-planar peptide bond
additional information
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the periplasmic protein contains both a PQQ-containing domain, folded into a beta-propeller fold, and a smaller cytochrome c domain, which is analogous to a typical class I c-type cytochrome, these two domains are connected via a proline-rich linker region, which lacks any secondary structure, structure model of the electron-transfer complex formed by MDH and cytochrome cL, overview
additional information
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the enzyme shows a propeller structure, QMDH contains a disulfide structure that is similar to the analogous structure in QEDH, EC 1.1.5.5
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Liu, Q.; Kirchhoff, J.R.; Faehnle, C.R.; Viola, R.E.; Hudson, R.A.
A rapid method for the purification of methanol dehydrogenase from Methylobacterium extorquens
Protein Expr. Purif.
46
316-320
2006
Methylorubrum extorquens (P16027 and P14775), Methylorubrum extorquens ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 (P16027 and P14775)
brenda
Williams, P.A.; Coates, L.; Mohammed, F.; Gill, R.; Erskine, P.T.; Coker, A.; Wood, S.P.; Anthony, C.; Cooper, J.B.
The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens
Acta Crystallogr. Sect. D
D61
75-79
2005
Methylorubrum extorquens
brenda
Anthony, C.
The quinoprotein dehydrogenases for methanol and glucose
Arch. Biochem. Biophys.
428
2-9
2004
Methylophilus sp., Methylorubrum extorquens (P16027 and P14775)
brenda
Richardson, I.W.; Anthony, C.
Characterization of mutant forms of the quinoprotein methanol dehydrogenase lacking an essential calcium ion
Biochem. J.
287
709-715
1992
Methylorubrum extorquens (P16027 and P14775), Methylorubrum extorquens NCIMB 9133 (P16027 and P14775)
brenda
Avezoux, A.; Goodwin, M.G.; Anthony, C.
The role of the novel disulphide ring in the active site of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens
Biochem. J.
307
735-741
1995
Methylorubrum extorquens (P16027 and P14775), Methylorubrum extorquens ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 (P16027 and P14775)
brenda
Goodwin, M.G.; Avezoux, A.; Dales, S.L.; Anthony, C.
Reconstitution of the quinoprotein methanol dehydrogenase from inactive Ca(2+)-free enzyme with Ca2+, Sr2+ or Ba2+
Biochem. J.
319
839-842
1996
Methylorubrum extorquens (P16027 and P14775)
brenda
Anthony, C.; Williams, P.
The structure and mechanism of methanol dehydrogenase
Biochim. Biophys. Acta
1647
18-23
2003
Methylophilus sp., Methylorubrum extorquens (P16027 and P14775)
brenda
Jongejan, A.; Jongejan, J.A.; Hagen, W.R.
Direct hydride transfer in the reaction mechanism of quinoprotein alcohol dehydrogenases: a quantum mechanical investigation
J. Comput. Chem.
22
1732-1749
2001
Methylorubrum extorquens (P16027 and P14775), Methylophilus methylotrophus (P38539 and P38540)
brenda
Williams, P.; Coates, L.; Mohammed, F.; Gill, R.; Erskine, P.; Bourgeois, D.; Wood, S.P.; Anthony, C.; Cooper, J.B.
The 1.6A X-ray structure of the unusual c-type cytochrome, cytochrome cL, from the methylotrophic bacterium Methylobacterium extorquens
J. Mol. Biol.
357
151-162
2006
Methylorubrum extorquens (P16027 and P14775)
brenda
Blake, C.C.; Ghosh, M.; Harlos, K.; Avezoux, A.; Anthony, C.
The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues
Nat. Struct. Biol.
1
102-105
1994
Methylorubrum extorquens (P16027 and P14775)
brenda
Ghosh, M.; Anthony, C.; Harlos, K.; Goodwin, M.G.; Blake, C.
The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A
Structure
3
177-187
1995
Methylorubrum extorquens (P16027 and P14775)
brenda
Cozier, G.E.; Giles, I.G.; Anthony, C.
The structure of the quinoprotein alcohol dehydrogenase of Acetobacter aceti modelled on that of methanol dehydrogenase from Methylobacterium extorquens
Biochem. J.
308
375-379
1995
Methylorubrum extorquens (P16027 and P14775)
brenda
Idupulapati, N.B.; Mainardi, D.S.
Quantum chemical modeling of methanol oxidation mechanisms by methanol dehydrogenase enzyme: effect of substitution of calcium by barium in the active site
J. Phys. Chem. A
114
1887-1896
2010
Methylorubrum extorquens
brenda
Gvozdev, A.; Tukhvatullin, I.; Gvozdev, R.
Quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases
Biochemistry
77
843-856
2012
Diplococcus sp., Methylophilus methylotrophus, Methylophilus methylotrophus W3A1, Methylorubrum extorquens, Paracoccus denitrificans, Paracoccus pantotrophus, Pseudomonas sp., Rhodoblastus acidophilus
brenda