1G72

CATALYTIC MECHANISM OF QUINOPROTEIN METHANOL DEHYDROGENASE: A THEORETICAL AND X-RAY CRYSTALLOGRAPHIC INVESTIGATION

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	d1g72a_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	Methanol dehydrogenase, heavy chain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
C	d1g72c_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	Methanol dehydrogenase, heavy chain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
B	d1g72b_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	Methanol dehydrogenase, light chain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
D	d1g72d_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	Methanol dehydrogenase, light chain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	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	8036898	3001727	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8036898	3001727	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Methanol dehydrogenase subunit	8036900	3001764	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Methanol dehydrogenase subunit	8036900	3001764	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	e1g72A1	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	e1g72C1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
B	MDH	e1g72B1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
D	MDH	e1g72D1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	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)
B	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
D	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF13360	PQQ-like domain (PQQ_2)	PQQ-like domain	-	Repeat
B, D	PF02315	Methanol dehydrogenase beta subunit (MDH)	Methanol dehydrogenase beta subunit	Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein that oxidises methanol to formaldehyde. MDH is a tetramer of two alpha and two beta subunits. This family contains the small beta subunit.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	METHANOL DEHYDROGENASE HEAVY SUBUNIT	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors alcohol dehydrogenase (cytochrome c(L)) activity catalytic activity	organic hydroxy compound metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular process methanol metabolic process primary alcohol metabolic process	cell periphery cellular anatomical structure plasma membrane membrane outer membrane-bounded periplasmic space cell envelope periplasmic space
B, D	METHANOL DEHYDROGENASE LIGHT SUBUNIT	alcohol dehydrogenase [NAD(P)+] activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors alcohol dehydrogenase (NAD+) activity catalytic activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor alcohol dehydrogenase (cytochrome c(L)) activity	methanol oxidation organic hydroxy compound metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular process methanol metabolic process primary alcohol metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR018391	Pyrrolo-quinoline quinone beta-propeller repeat	Repeat
A, C	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A, C	IPR001479	Quinoprotein dehydrogenase, conserved site	Conserved Site
A, C	IPR017512	PQQ-dependent dehydrogenase, methanol/ethanol family	Family
A, C	IPR002372	Pyrrolo-quinoline quinone repeat	Repeat
B, D	IPR036557	Methanol dehydrogenase, beta subunit superfamily	Homologous Superfamily
B, D	IPR003420	Methanol dehydrogenase, beta subunit	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	methanol dehydrogenase (cytochrome c) M-CSA #99	Methanol dehydrogenase (MEDH) is a periplasmic quinoprotein. It catalyses the oxidation of methanol and other small alcohols to the corresponding aldehyde with the release of two protons and two electrons. The enzyme uses the pyrroloquinolinequinone (PQQ) cofactor. MEDH is an H2L2 heterotetramer, made of two heavy (H) chains and two light (L) chains. Each H subunit contains one molecule of the prosthetic group PQQ, which is non-covalently bound to the polypeptide chain, as well as one calcium ion which is catalytically essential. There is no interaction between the L chains which fold around the surface of the H chains.	Defined by 3 residues: GLU:A-173 [auth A-171]ASN:A-257 [auth A-255]ASP:A-299 [auth A-297] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.99.8 (PDB Primary Data) Search M-CSA Motif + EC 1.1.99.8 EC: 1.1.2.7 (UniProt) Search M-CSA Motif + EC 1.1.2.7

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.