2BBK | pdb_00002bbk

CRYSTAL STRUCTURE OF THE QUINOPROTEIN METHYLAMINE DEHYDROGENASE FROM PARACOCCUS DENITRIFICANS AT 1.75 ANGSTROMS

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
Protein Modification Annotation
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 [auth H]	d2bbkh_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	Methylamine dehydrogenase, H-chain	Methylamine dehydrogenase, H-chain	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C [auth J]	d2bbkj_	All beta proteins	7-bladed beta-propeller	YVTN repeat-like/Quinoprotein amine dehydrogenase	Methylamine dehydrogenase, H-chain	Methylamine dehydrogenase, H-chain	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B [auth L]	d2bbkl_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D [auth M]	d2bbkm_	Small proteins	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase, L chain	Methylamine dehydrogenase	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth H]	SCOP2 Family	Methylamine dehydrogenase, H-chain	8030467	4002731	SCOP2 (2022-06-29)
A [auth H]	SCOP2 Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2 (2022-06-29)
C [auth J]	SCOP2B Superfamily	YVTN repeat-like/Quinoprotein amine dehydrogenase	8042846	3001671	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	Methylamine dehydrogenase, L chain	8041821	3000932	SCOP2B (2022-06-29)
D [auth M]	SCOP2B Superfamily	Methylamine dehydrogenase, L chain	8041821	3000932	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 [auth H]	Me-amine-dh_H	e2bbkH1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
C [auth J]	Me-amine-dh_H	e2bbkJ1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Me-amine-dh_H	ECOD (1.6)
B [auth L]	Me-amine-dh_L	e2bbkL1	A: few secondary structure elements	X: Methylamine dehydrogenase, L chain (From Topology)	H: Methylamine dehydrogenase, L chain (From Topology)	T: Methylamine dehydrogenase, L chain	F: Me-amine-dh_L	ECOD (1.6)
D [auth M]	Me-amine-dh_L	e2bbkM1	A: few secondary structure elements	X: Methylamine dehydrogenase, L chain (From Topology)	H: Methylamine dehydrogenase, L chain (From Topology)	T: Methylamine dehydrogenase, L chain	F: Me-amine-dh_L	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C [auth J]	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B [auth L]	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.3.0)
D [auth M]	2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H], C [auth J]	PF06433	Methylamine dehydrogenase heavy chain (MADH) (Me-amine-dh_H)	Methylamine dehydrogenase heavy chain (MADH)	-	Repeat
B [auth L], D [auth M]	PF02975	Methylamine dehydrogenase, L chain (Me-amine-dh_L)	Methylamine dehydrogenase, L chain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth J]	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity methylamine dehydrogenase (amicyanin) activity oxidoreductase activity, acting on the CH-NH2 group of donors, with a copper protein as acceptor catalytic activity aliphatic amine dehydrogenase activity	amine metabolic process methylamine metabolic process metabolic process cellular process primary amino compound metabolic process	cellular anatomical structure periplasmic space
B [auth L], D [auth M]	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity methylamine dehydrogenase (amicyanin) activity oxidoreductase activity, acting on the CH-NH2 group of donors, with a copper protein as acceptor catalytic activity aliphatic amine dehydrogenase activity	amine metabolic process metabolic process cellular process	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H], C [auth J]	IPR009451	Amine dehydrogenase heavy chain	Family
A [auth H], C [auth J]	IPR011044	Quinoprotein amine dehydrogenase, beta chain-like	Homologous Superfamily
A [auth H], C [auth J]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A [auth H], C [auth J]	IPR013476	Methylamine dehydrogenase heavy chain	Family
B [auth L], D [auth M]	IPR004229	Methylamine dehydrogenase light chain	Family
B [auth L], D [auth M]	IPR016008	Amine dehydrogenase light chain	Family
B [auth L], D [auth M]	IPR036560	Methylamine/Aralkylamine dehydrogenase light chain superfamily	Homologous Superfamily
B [auth L], D [auth M]	IPR013504	Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth L], D [auth M]	TRQ	Parent Component: TRP RESID: AA0148 PSI-MOD : oxidation of tryptophan to L-tryptophyl quinone MOD:00157

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

Chains	Enzyme Name	Description	Catalytic Residues
A [auth H], B [auth L]	amine dehydrogenase M-CSA #13	Methylamine dehydrogenase is a heterotetrameric, periplasmic quinoprotein found in several forms of constitutive and facultative methylotrophic bacteria. The enzyme catalyses the oxidative deamination of primary amines to their corresponding aldehydes with the release of two electrons and two protons. The enzyme is induced when the methylotrophic bacteria are grown on media containing methylamine as the sole carbon, and therefore energy, source. The electron acceptor, Amicyanin, binds first to MADH to be reduced and then dissociates from MADH to react with cytochrome c-551i or cytochrome aa3 via the same binding site to be regenerated. Electrons can reach the terminal oxidase via different routes, and it cannot be concluded that one specific interaction is preferred.	Defined by 7 residues: PHE:A-48 [auth H-66]ASP:B-26 [auth L-32]TRP:B-51 [auth L-57]ASP:B-70 [auth L-76]TRP:B-102 [auth L-108]TYR:B-113 [auth L-119]THR:B-116 [auth L-122] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.4.99.3 (PDB Primary Data) Search M-CSA Motif + EC 1.4.99.3 EC: 1.4.9.1 (UniProt) Search M-CSA Motif + EC 1.4.9.1

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.