4TQO | pdb_00004tqo

The crystal structure of methanol dehydrogenase from Methylococcus capsulatus (Bath)

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
P	d4tqop_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
N [auth O]	d4tqoo_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
L [auth N]	d4tqon_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
J [auth M]	d4tqom_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
H [auth L]	d4tqol_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
F [auth K]	d4tqok_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
D [auth J]	d4tqoj_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
B [auth I]	d4tqoi_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Methanol dehydrogenase subunit	Methanol dehydrogenase subunit	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
O [auth H]	d4tqoh_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
M [auth G]	d4tqog_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
K [auth F]	d4tqof_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
I [auth E]	d4tqoe_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
G [auth D]	d4tqod_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
E [auth C]	d4tqoc_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
C [auth A]	d4tqoa_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)
A [auth B]	d4tqob_	All beta proteins	8-bladed beta-propeller	Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	automated matches	(Methylococcus capsulatus str. Bath ) [TaxId: 243233 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
N [auth O]	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
L [auth N]	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
J [auth M]	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
H [auth L]	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
F [auth K]	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2B (2022-06-29)
B [auth I]	SCOP2 Family	methanol dehydrogenase subunit	8077626	4004028	SCOP2 (2022-06-29)
B [auth I]	SCOP2 Superfamily	Methanol dehydrogenase subunit	8077627	3001764	SCOP2 (2022-06-29)
O [auth H]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2B (2022-06-29)
K [auth F]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2B (2022-06-29)
C [auth A]	SCOP2 Family	Quinoprotein alcohol dehydrogenase-like	8076949	4002772	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	3001727	SCOP2 (2022-06-29)
A [auth B]	SCOP2B Superfamily	Quinoprotein alcohol dehydrogenase-like	8076950	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)
P	MDH	e4tqoP1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
N [auth O]	MDH	e4tqoO1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
L [auth N]	MDH	e4tqoN1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
J [auth M]	MDH	e4tqoM1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
H [auth L]	MDH	e4tqoL1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
F [auth K]	MDH	e4tqoK1	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 [auth J]	MDH	e4tqoJ1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
B [auth I]	MDH	e4tqoI1	A: extended segments	X: Methanol dehydrogenase subunit (From Topology)	H: Methanol dehydrogenase subunit (From Topology)	T: Methanol dehydrogenase subunit	F: MDH	ECOD (1.6)
O [auth H]	PQQ_2	e4tqoH1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
M [auth G]	PQQ_2	e4tqoG1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
K [auth F]	PQQ_2	e4tqoF1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
I [auth E]	PQQ_2	e4tqoE1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
G [auth D]	PQQ_2	e4tqoD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
E [auth C]	PQQ_2	e4tqoC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
C [auth A]	PQQ_2	e4tqoA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: PQQ_2	ECOD (1.6)
A [auth B]	PQQ_2	e4tqoB1	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)
P	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
N [auth O]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
L [auth N]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
J [auth M]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
H [auth L]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
F [auth K]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
D [auth J]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
B [auth I]	4.10.160.10	Few Secondary Structures	Irregular	Methanol Dehydrogenase	Chain B	CATH (4.3.0)
O [auth H]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
M [auth G]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
K [auth F]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
I [auth E]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
G [auth D]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
E [auth C]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
C [auth A]	2.140.10.10	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
A [auth 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
B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], L [auth N], N [auth O], P	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
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	PF13360	Outer membrane protein assembly factor BamB (PQQ_2)	Outer membrane protein assembly factor BamB	-	Repeat
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	PF01011	Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain (PQQ)	Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], L [auth N], N [auth O], P	Methanol dehydrogenase, small 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 alcohol metabolic process small molecule metabolic process metabolic process cellular process methanol metabolic process primary alcohol metabolic process	-
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	Methanol dehydrogenase protein, large subunit	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity tetrapyrrole binding heme binding organic acid binding anion binding carboxylic acid binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity tetrapyrrole binding heme binding organic acid binding anion binding carboxylic acid binding heterocyclic compound binding pyrroloquinoline quinone binding	-	cellular anatomical structure membrane outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], L [auth N], N [auth O], P	IPR036557	Methanol dehydrogenase, beta subunit superfamily	Homologous Superfamily
B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], B [auth I], D [auth J], F [auth K], H [auth L], J [auth M], L [auth N], N [auth O], P	IPR003420	Methanol dehydrogenase, beta subunit	Family
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR018391	Pyrrolo-quinoline quinone beta-propeller repeat	Repeat
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR001479	Quinoprotein dehydrogenase, conserved site	Conserved Site
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR002372	Pyrrolo-quinoline quinone repeat domain	Domain
A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], A [auth B], C [auth A], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	IPR017512	PQQ-dependent dehydrogenase, methanol/ethanol family	Family

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.