6FKW | pdb_00006fkw

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)
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)
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)

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)
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)
B	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)
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)
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)

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)
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)
B	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	Outer membrane protein assembly factor BamB (PQQ_2)	Outer membrane protein assembly factor BamB	-	Repeat
A, B, C, D	PF13570	Beta-alanine-activating enzyme, beta-propeller (Beta-prop_ACSF4)	Beta-alanine-activating enzyme, beta-propeller	-	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	alcohol metabolic process small molecule metabolic process metabolic process cellular process methanol metabolic process primary alcohol metabolic process	cellular anatomical structure membrane periplasmic space

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	IPR002372	Pyrrolo-quinoline quinone repeat domain	Domain
A, B, C, D	IPR017512	PQQ-dependent dehydrogenase, methanol/ethanol family	Family

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.