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

Ghosh, M.; Anthony, C.; Harlos, K.; Goodwin, M.G.; Blake, C.; Structure 3, 177-187 (1995)

Data extracted from this reference:

Crystallization (Commentary)

Crystallization	Organism
X-ray diffraction structure determination and analysis at 1.94 A resolution	Methylobacterium extorquens NCIMB 9133
X-ray diffraction structure determination and analysis at 1.94 A resolution	Methylobacterium extorquens

Localization

Localization	Commentary	Organism	GeneOntology No.	Textmining
periplasm	-	Methylobacterium extorquens	-	-
periplasm	-	Methylobacterium extorquens NCIMB 9133	-	-

Metals/Ions

Metals/Ions	Commentary	Organism	Structure
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	Methylobacterium extorquens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Commentary (Nat. Sub.)	Natural Products	Commentary (Nat. Pro.)	Organism (Nat. Pro.)	Reversibility
methanol + ferricytochrome cL	Methylobacterium extorquens	-	formaldehyde + ferrocytochrome cL	-	-	?

Organism

Organism	Primary Accession No. (UniProt)	Commentary	Textmining
Methylobacterium extorquens	P16027 and P14775	P16027 (large subunit, alpha) and P14775 (small subunit, beta)	-

Substrates and Products (Substrate)

Substrates	Commentary Substrates	Literature (Substrates)	Organism	Products	Commentary (Products)	Literature (Products)	Organism (Products)	Reversibility
methanol + ferricytochrome cL	-	690095	Methylobacterium extorquens	formaldehyde + ferrocytochrome cL	-	-	-	?
More	active site structure with important disulfide bridge of Cys103-Cys104, overview	690095	Methylobacterium extorquens	?	-	-	-	-
More	active site structure with important disulfide bridge of Cys103-Cys104, overview	690095	Methylobacterium extorquens NCIMB 9133	?	-	-	-	-

Subunits

Subunits	Commentary	Organism
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	Methylobacterium extorquens
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	Methylobacterium extorquens NCIMB 9133

Cofactor

Cofactor	Commentary	Organism	Structure
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	Methylobacterium extorquens

Cofactor (protein specific)

Cofactor	Commentary	Organism	Structure
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	Methylobacterium extorquens

Crystallization (Commentary) (protein specific)

Crystallization	Organism
X-ray diffraction structure determination and analysis at 1.94 A resolution	Methylobacterium extorquens
X-ray diffraction structure determination and analysis at 1.94 A resolution	Methylobacterium extorquens NCIMB 9133

Localization (protein specific)

Localization	Commentary	Organism	GeneOntology No.	Textmining
periplasm	-	Methylobacterium extorquens	-	-
periplasm	-	Methylobacterium extorquens NCIMB 9133	-	-

Metals/Ions (protein specific)

Metals/Ions	Commentary	Organism	Structure
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	Methylobacterium extorquens

Natural Substrates/ Products (Substrates) (protein specific)

Natural Substrates	Organism	Commentary (Nat. Sub.)	Natural Products	Commentary (Nat. Pro.)	Organism (Nat. Pro.)	Reversibility
methanol + ferricytochrome cL	Methylobacterium extorquens	-	formaldehyde + ferrocytochrome cL	-	-	?

Substrates and Products (Substrate) (protein specific)

Substrates	Commentary Substrates	Literature (Substrates)	Organism	Products	Commentary (Products)	Literature (Products)	Organism (Products)	Reversibility
methanol + ferricytochrome cL	-	690095	Methylobacterium extorquens	formaldehyde + ferrocytochrome cL	-	-	-	?
More	active site structure with important disulfide bridge of Cys103-Cys104, overview	690095	Methylobacterium extorquens	?	-	-	-	-
More	active site structure with important disulfide bridge of Cys103-Cys104, overview	690095	Methylobacterium extorquens NCIMB 9133	?	-	-	-	-

Subunits (protein specific)

Subunits	Commentary	Organism
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	Methylobacterium extorquens
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	Methylobacterium extorquens NCIMB 9133

See also following references to EC number 1.1.2.7 (sorted by year of publication):

No.	1st author	Pub Med	title	organims	journal	volume	pages	year	Activating Compound	Application	Cloned(Commentary)	Crystallization (Commentary)	Engineering	General Stability	Inhibitors	KM Value [mM]	Localization	Metals/Ions	Molecular Weight [Da]	Natural Substrates/ Products (Substrates)	Organic Solvent Stability	Organism	Oxidation Stability	Posttranslational Modification	Purification (Commentary)	Reaction	Renatured (Commentary)	Source Tissue	Specific Activity [micromol/min/mg]	Storage Stability	Substrates and Products (Substrate)	Subunits	Temperature Optimum [�C]	Temperature Range [�C]	Temperature Stability [�C]	Turnover Number [1/s]	pH Optimum	pH Range	pH Stability	Cofactor	Ki Value [mM]	pI Value	IC50 Value	Activating Compound (protein specific)	Application (protein specific)	Cloned(Commentary) (protein specific)	Cofactor (protein specific)	Crystallization (Commentary) (protein specific)	Engineering (protein specific)	General Stability (protein specific)	IC50 Value (protein specific)	Inhibitors (protein specific)	Ki Value [mM] (protein specific)	KM Value [mM] (protein specific)	Localization (protein specific)	Metals/Ions (protein specific)	Molecular Weight [Da] (protein specific)	Natural Substrates/ Products (Substrates) (protein specific)	Organic Solvent Stability (protein specific)	Oxidation Stability (protein specific)	Posttranslational Modification (protein specific)	Purification (Commentary) (protein specific)	Renatured (Commentary) (protein specific)	Source Tissue (protein specific)	Specific Activity [micromol/min/mg] (protein specific)	Storage Stability (protein specific)	Substrates and Products (Substrate) (protein specific)	Subunits (protein specific)	Temperature Optimum [�C] (protein specific)	Temperature Range [�C] (protein specific)	Temperature Stability [�C] (protein specific)	Turnover Number [1/s] (protein specific)	pH Optimum (protein specific)	pH Range (protein specific)	pH Stability (protein specific)	pI Value (protein specific)	Expression	General Information	General Information (protein specific)	Expression (protein specific)	KCat/KM [mM/s]	KCat/KM [mM/s] (protein specific)
712855	Idupulapati		Quantum chemical modeling of m ...	Methylobacterium extorquens	J. Phys. Chem. A	114	1887-1896	2010	-	-	-	3	-	-	-	-	-	1	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	3	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
687417	Kalyuzhnaya		Characterization of a novel me ...	Methylibium petroleiphilum, Methyloversatilis universalis	J. Bacteriol.	190	3817-3823	2008	2	-	2	-	-	-	-	8	2	-	-	2	-	7	-	-	-	-	-	-	-	-	10	2	2	-	-	-	2	-	-	4	-	-	-	2	-	2	4	-	-	-	-	-	-	8	2	-	-	2	-	-	-	-	-	-	-	-	10	2	2	-	-	-	2	-	-	-	-	-	-	-	-	-
673047	Leopoldini		The preferred reaction path fo ...	Methylophilus methylotrophus	Chem. Eur. J.	13	2109-2117	2007	-	-	-	-	-	-	-	1	1	1	-	-	-	1	-	-	-	3	-	-	-	-	-	1	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	-	-	-	-	-	-	1	1	1	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-
676902	Zhang		Mechanism of methanol oxidatio ...	Methylophilus methylotrophus	Proc. Natl. Acad. Sci. USA	104	745-749	2007	-	-	-	-	-	-	-	-	-	1	-	-	-	2	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
667721	Nojiri		Crystal structures of cytochro ...	Hyphomicrobium denitrificans, Hyphomicrobium denitrificans A3151	Biochemistry	45	3481-3492	2006	-	-	-	2	-	-	-	11	-	-	2	2	-	5	-	-	2	-	-	-	3	-	3	3	2	-	-	12	1	1	-	4	-	-	-	-	-	-	4	2	-	-	-	-	-	11	-	-	2	2	-	-	-	2	-	-	3	-	3	2	2	-	-	12	1	1	-	-	-	-	-	-	-	-
670785	Liu		A rapid method for the purific ...	Methylobacterium extorquens	Protein Expr. Purif.	46	316-320	2006	-	-	-	-	-	2	-	-	-	2	-	-	-	1	-	-	2	-	-	-	2	4	-	2	-	-	-	-	1	-	-	2	-	1	-	-	-	-	2	-	-	2	-	-	-	-	-	2	-	-	-	-	-	2	-	-	2	4	-	2	-	-	-	-	1	-	-	1	-	-	-	-	-	-
688333	Williams		The 1.6A X-ray structure of th ...	Methylobacterium extorquens	J. Mol. Biol.	357	151-162	2006	-	-	-	-	-	-	-	-	-	1	-	1	-	4	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	3	-	-	-	-	-	-	3	-	-	-	-	-	-	-	-	1	-	1	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
671068	Williams		The atomic resolution structur ...	Methylobacterium extorquens	Acta Crystallogr. Sect. D	D61	75-79	2005	-	-	-	3	-	-	-	-	3	2	-	1	-	1	-	-	-	1	-	-	-	-	2	2	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	3	-	-	-	-	-	-	3	2	-	1	-	-	-	-	-	-	-	-	2	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-
673048	Nojiri	-	Preparation and characterizati ...	Hyphomicrobium denitrificans, Hyphomicrobium denitrificans A3151	Chem. Lett.	34	1036-1037	2005	-	-	2	-	2	-	-	-	-	2	-	-	-	2	-	-	2	2	-	-	5	-	-	2	-	-	-	-	-	-	-	2	-	-	-	-	-	2	2	-	2	-	-	-	-	-	-	2	-	-	-	-	-	2	-	-	5	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-
684666	Anthony		The quinoprotein dehydrogenase ...	Methylobacterium extorquens, Methylophilus sp.	Arch. Biochem. Biophys.	428	2-9	2004	-	-	-	4	-	-	-	4	4	4	-	3	-	4	-	-	-	4	-	-	-	-	6	3	-	-	-	-	1	-	-	7	-	-	-	-	-	-	7	4	-	-	-	-	-	4	4	4	-	3	-	-	-	-	-	-	-	-	6	3	-	-	-	-	1	-	-	-	-	-	-	-	-	-
685313	Anthony		The structure and mechanism of ...	Methylobacterium extorquens, Methylophilus sp.	Biochim. Biophys. Acta	1647	18-23	2003	4	-	-	4	2	-	-	-	4	4	-	3	-	2	-	-	-	-	-	-	-	-	6	-	-	-	-	-	-	-	-	3	-	-	-	4	-	-	3	4	2	-	-	-	-	-	4	4	-	3	-	-	-	-	-	-	-	-	6	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
687993	Jongejan		Direct hydride transfer in the ...	Methylobacterium extorquens, Methylophilus methylotrophus	J. Comput. Chem.	22	1732-1749	2001	-	-	-	-	-	-	-	-	-	2	-	-	-	2	-	-	-	2	-	-	-	-	3	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	3	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
689818	Zheng		Catalytic mechanism of quinopr ...	Methylophilus methylotrophus	Proc. Natl. Acad. Sci. USA	98	432-434	2001	-	-	-	-	-	-	-	-	-	1	-	-	-	3	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
687432	Grosse		Purification and properties of ...	Methylosinus sp., Methylosinus sp. WI 14	J. Basic Microbiol.	38	189-196	1998	4	-	-	-	-	-	5	14	2	-	2	1	-	2	-	-	2	-	-	-	2	4	12	2	2	-	2	-	1	-	-	2	-	-	-	4	-	-	2	-	-	-	-	5	-	14	2	-	2	1	-	-	-	2	-	-	2	4	12	2	2	-	2	-	1	-	-	-	-	-	-	-	-	-
689815	Zheng		Conformation of coenzyme pyrro ...	Methylophilus methylotrophus	Proc. Natl. Acad. Sci. USA	94	11881-11886	1997	-	-	-	-	-	-	-	-	-	1	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
684950	Goodwin		Reconstitution of the quinopro ...	Methylobacterium extorquens	Biochem. J.	319	839-842	1996	-	-	-	-	2	-	-	-	3	3	-	1	-	3	-	-	-	-	2	-	-	-	1	-	2	-	-	-	1	1	-	3	-	-	-	-	-	-	3	-	2	-	-	-	-	-	3	3	-	1	-	-	-	-	2	-	-	-	1	-	2	-	-	-	1	1	-	-	-	-	-	-	-	-
684948	Avezoux		The role of the novel disulphi ...	Methylobacterium extorquens	Biochem. J.	307	735-741	1995	-	-	-	-	2	-	-	-	-	3	-	-	-	4	-	-	-	-	-	-	-	-	1	-	2	-	-	-	1	-	-	4	-	-	-	-	-	-	4	-	2	-	-	-	-	-	-	3	-	-	-	-	-	-	-	-	-	-	1	-	2	-	-	-	1	-	-	-	-	-	-	-	-	-
690095	Ghosh		The refined structure of the q ...	Methylobacterium extorquens	Structure	3	177-187	1995	-	-	-	2	-	-	-	-	2	1	-	1	-	4	-	-	-	-	-	-	-	-	3	2	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	2	-	-	-	-	-	-	2	1	-	1	-	-	-	-	-	-	-	-	3	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-
690794	Cozier		The structure of the quinoprot ...	Methylobacterium extorquens	Biochem. J.	308	375-379	1995	-	-	-	2	-	-	-	-	3	3	-	2	-	1	-	-	-	-	-	-	-	-	2	2	-	-	-	-	-	-	-	4	-	-	-	-	-	-	4	2	-	-	-	-	-	-	3	3	-	2	-	-	-	-	-	-	-	-	2	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-
689139	Blake		The active site of methanol de ...	Methylobacterium extorquens	Nat. Struct. Biol.	1	102-105	1994	-	-	-	-	-	-	-	-	-	2	-	2	-	4	-	-	-	-	-	-	-	-	4	1	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	2	-	2	-	-	-	-	-	-	-	-	4	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-
685050	White		The active site structure of t ...	Methylophilus sp., Methylophilus sp. W3A1	Biochemistry	32	12955-12958	1993	-	-	-	-	-	-	-	-	-	2	-	-	-	3	-	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	2	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-
684947	Richardson		Characterization of mutant for ...	Methylobacterium extorquens, Methylobacterium extorquens NCIMB 9133	Biochem. J.	287	709-715	1992	-	-	-	-	2	-	2	-	-	1	-	-	-	7	-	-	-	-	2	-	-	-	-	2	2	-	-	-	1	-	-	1	-	-	-	-	-	-	1	-	2	-	-	2	-	-	-	1	-	-	-	-	-	-	2	-	-	-	-	2	2	-	-	-	1	-	-	-	-	-	-	-	-	-
687486	Xia		The three-dimensional structur ...	Methylophilus methylotrophus	J. Biol. Chem.	267	22289-22297	1992	-	-	-	1	-	-	-	-	1	-	1	-	-	1	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	1	-	-	-	-	-	-	1	-	1	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-