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Information on EC 1.1.2.7 - methanol dehydrogenase (cytochrome c) and Organism(s) Methylorubrum extorquens and UniProt Accession P14775

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IUBMB Comments
A periplasmic quinoprotein alcohol dehydrogenase that only occurs in methylotrophic bacteria. It uses the novel specific cytochrome cL as acceptor. Acts on a wide range of primary alcohols, including ethanol, duodecanol, chloroethanol, cinnamyl alcohol, and also formaldehyde. Activity is stimulated by ammonia or methylamine. It is usually assayed with phenazine methosulfate. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulfide ring structure in close proximity to the PQQ. It differs from EC 1.1.2.8, alcohol dehydrogenase (cytochrome c), in having a high affinity for methanol and in having a second essential small subunit (no known function).
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Methylorubrum extorquens
UNIPROT: P14775 not found.
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The taxonomic range for the selected organisms is: Methylorubrum extorquens
The enzyme appears in selected viruses and cellular organisms
Synonyms
type i mdh, hd-mdh, pqq-dependent methanol dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
methanol dehydrogenase
PQQ-dependent methanol dehydrogenase
-
-
quinohemoprotein (type II) alcohol dehydrogenase
-
quinohemoprotein alcohol dehydrogenase
-
quinone-dependent alcohol dehydrogenase
-
-
quinoprotein alcohol dehydrogenase
-
quinoprotein dehydrogenase
-
quinoprotein methanol dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a primary alcohol + 2 ferricytochrome cL = an aldehyde + 2 ferrocytochrome cL + 2 H+
show the reaction diagram
SYSTEMATIC NAME
IUBMB Comments
methanol:cytochrome c oxidoreductase
A periplasmic quinoprotein alcohol dehydrogenase that only occurs in methylotrophic bacteria. It uses the novel specific cytochrome cL as acceptor. Acts on a wide range of primary alcohols, including ethanol, duodecanol, chloroethanol, cinnamyl alcohol, and also formaldehyde. Activity is stimulated by ammonia or methylamine. It is usually assayed with phenazine methosulfate. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulfide ring structure in close proximity to the PQQ. It differs from EC 1.1.2.8, alcohol dehydrogenase (cytochrome c), in having a high affinity for methanol and in having a second essential small subunit (no known function).
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
show the reaction diagram
methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
methanol + 2 ferricytochrome cL
formaldehyde + 2 ferrocytochrome cL + 2 H+
show the reaction diagram
methanol + ferricytochrome cL
formaldehyde + ferrocytochrome cL
show the reaction diagram
additional information
?
-
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
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cytochrome cL
-
heme c
part of cytochrome cL
pyrroloquinoline quinone
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
-
Mg2+ cannot substitute for Ca2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ammonia
ammonia affects the rate-limiting step of breaking of the methyl C-H bond
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
steady-state analysis using stopped-flow kinetics, molecular dynamics, overview
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 10.5
pH profile, overview
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.8
sequence calculation
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
A0A2N9AL61_METEX
96
1
10512
TrEMBL
-
A0A1S1P5J7_METEX
96
1
10512
TrEMBL
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
62000
x * 62000, alpha-subunit, + x * 7500, beta-subunit, SDS-PAGE
66000
7500
x * 62000, alpha-subunit, + x * 7500, beta-subunit, SDS-PAGE
8500
2 * 66000 + 2 * 8500, alpha2beta2, crystal structure determination
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 62000, alpha-subunit, + x * 7500, beta-subunit, SDS-PAGE
tetramer
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ba2+-containing MDH active site model to investigate the two proposed addition-elimination and hydride-transfer methanol oxidation mechanisms
-
crystal structure analysis
purified holoenzyme, hanging-drop vapour-diffusion method, 3 ml of 15 mg/ml protein solution, 20 mM Tris buffer, pH 8.0, are placed on siliconized cover slips and mixed with an equal volume of well solution, the cover slip is sealed with high-vacuum grease over a 1 ml well containing 20% PEG 8000, pH 9.0, large crystals after two weeks, X-ray diffraction structure determination and analysis at 1.2 A resolution, modeling
-
X-ray diffraction structure determination
X-ray diffraction structure determination and analysis at 1.94 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
EDTA, DTT, and Ca2+ are slightly stabilizing
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, purified native enzyme, 20 mM phosphate, pH 7.0, negligible loss of activity in 6 months
4°C, purified native enzyme, 20 mM phosphate, pH 7.0, loss of 80% activity within 1 week
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native enzyme 22fold from strain AM1 in a single cation exchange chromatographical step, followed by ultrafiltration and buffer exchange, over 97% purity
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
incubation in a calcium salt solution leads to full restoration of the Ca2+-lacking mutant enzymes to active holoenzymes, overview
reconstitution of the active holoenzyme by incorporation of two exogenous Ca2+ into the active sites of the alpha-subunits of the alpha2beta2 tetramer, time course of Ca2+ incorporation, overview
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Anthony, C.
The quinoprotein dehydrogenases for methanol and glucose
Arch. Biochem. Biophys.
428
2-9
2004
Methylophilus sp., Methylorubrum extorquens (P16027 and P14775)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team