6FKW

Europium-containing methanol dehydrogenase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6fkwa_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	automated matches	automated matches	(Methylacidiphilum fumariolicum SolV ) [TaxId: 1156937 ],	SCOPe (2.08)
B	d6fkwb_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	automated matches	automated matches	(Methylacidiphilum fumariolicum SolV ) [TaxId: 1156937 ],	SCOPe (2.08)
C	d6fkwc_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	automated matches	automated matches	(Methylacidiphilum fumariolicum SolV ) [TaxId: 1156937 ],	SCOPe (2.08)
D	d6fkwd_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	automated matches	automated matches	(Methylacidiphilum fumariolicum SolV ) [TaxId: 1156937 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076952	3001727	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076952	3001727	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076952	3001727	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076952	3001727	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PQQ_2	e6fkwA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
B	PQQ_2	e6fkwB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
C	PQQ_2	e6fkwC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
D	PQQ_2	e6fkwD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
B	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
C	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
D	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13360	PQQ-like domain (PQQ_2)	PQQ-like domain	-	Repeat
A, B, C, D	PF13570	PQQ-like domain (PQQ_3)	PQQ-like domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Methanol dehydrogenase	oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor oxidoreductase activity alcohol dehydrogenase (cytochrome c) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding alcohol dehydrogenase (cytochrome c(L)) activity	-	membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018391	Pyrrolo-quinoline quinone beta-propeller repeat	Repeat
A, B, C, D	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A, B, C, D	IPR017512	PQQ-dependent dehydrogenase, methanol/ethanol family	Family
A, B, C, D	IPR002372	Pyrrolo-quinoline quinone repeat	Repeat

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	lanthanide-dependent methanol dehydrogenase M-CSA #997	Lanthanide-dependent methanol dehydrogenase is a widespread enzyme used by methylotrophic bacteria to oxidise methanol for carbon and energy. The enzyme requires early lanthanide (Ln) metals in the 3+ oxidation state for catalytic activity. Across the series (La-Lu), catalytic activity of Ln-MDH decreases; Eu-MDH shows significantly lower catalytic activity than Ce-MDH, and Yb-MDH shows no catalytic activity. This is attributed to the lanthanide contraction effect whereby the ionic radius of Ln ions decreases as atomic number increases. In turn metal-ligand bond lengths decreases and Lewis acidity increases. Despite this, however, we observe a decrease in activity across the series. Nearly all strains of Methylobacterium have at least two types of MDHs, such as MxaFI, a Ca²⁺-dependent MDH, and XoxF, an Ln-dependent MDH. In contrast to Ca²⁺-dependent MDH (EC 1.1.2.7), Ln-dependent MDH shows little activity with Ca²⁺.	Defined by 4 residues: GLU:A-172ASN:A-256ASP:A-299ASP:A-301 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.2.7 (PDB Primary Data) Search M-CSA Motif + EC 1.1.2.7 EC: 1.1.2.8 (PDB Primary Data) Search M-CSA Motif + EC 1.1.2.8 EC: 1.1.2.10 (UniProt) Search M-CSA Motif + EC 1.1.2.10

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.