InterPro domain: IPR036318

This entry represents a FAD-binding domain superfamily. This domain consists of two alpha+beta subdomains.

Flavoenzymes have the ability to catalyse a wide range of biochemical reactions. They are involved in the dehydrogenation of a variety of metabolites, in electron transfer from and to redox centres, in light emission, in the activation of oxygen for oxidation and hydroxylation reactions [ 1 ]. About 1% of all eukaryotic and prokaryotic proteins are predicted to encode a flavin adenine dinucleotide (FAD)-binding domain [ 2 ].

According to structural similarities and conserved sequence motifs,FAD-binding domains have been grouped in three main families: (i) theferredoxin reductase (FR)-type FAD-binding domain (see PDOC51384 ),(ii) the FAD-binding domains that adopt a Rossmann fold and (iii) the p-cresol methylhydroxylase (PCMH)-type FAD-binding domain [ 3 ].

The FAD cofactor consists of adenosine monophosphate (AMP) linked to flavin mononucleotide (FMN) by a pyrophosphate bond. The AMP moiety is composed of the adenine ring bonded to a ribose that is linked to a phosphate group. The FMN moiety is composed of the isoalloxazine-flavin ring linked to a ribitol, which is connected to a phosphate group. The flavin functions mainly in a redox capacity, being able to take up two electrons from one substrate and release them two at a time to a substrate or coenzyme, or one at a time to an electron acceptor. The catalytic function of the FAD is concentrated in the isoalloxazine ring, whereas the ribityl phosphate and the AMP moiety mainly stabilise cofactor binding to protein residues [ 4 ].

The PCMH-type FAD-binding domain consists of two alpha-beta subdomains: one is composed of three parallel beta-strands (B1-B3) surrounded by alpha-helices, and is packed against the second subdomain containing five antiparallel beta-strands (B4-B8) surrounded by alpha-helices [ 4 ]. The two subdomains accommodate the FAD cofactor between them [ 5 ]. In the PCMH proteins the coenzyme FAD is also covalently attached to a tyrosine located outside the FAD-binding domain in the C-terminal catalytic domain [ 5 ].

This domain is found in:

• FAD-linked oxidases (N-terminal domain), such as vanillyl-alochol oxidase ( 1.1.3.38 ) [ 6 ], flavoprotein subunit of p-cresol methylhydroxylase ( 1.17.99.1 ) [ 7 ], D-lactate dehydrogenases ( 1.1.1.28 , 1.1.2.4 -cytochrome) [ 8 ], cholesterol oxidases ( 1.1.3.6 ) [ 9 ], and cytokinin dehydrogenase 1 ( 1.5.99.12 ) [ 10 ].
• Uridine diphospho-N-acetylenolpyruvylglucosamine reductase (MurB) (N-terminal domain) [ 11 ].
• CO dehydrogenase flavoprotein (N-terminal domain; [ 12 ]) family, which includes xanthine oxidase (domain 3) ( 1.17.3.2 ) [ 13 ], subunit A of xanthine dehydrogenase (domain 3) ( 1.17.1.4 ) [ 14 ], medium subunit of quinoline 2-oxidoreductase (QorM) ( 1.3.99.17 ) [ 15 ], and the beta-subunit of 4-hydroxybenzoyl-CoA reductase (HrcB) (N-terminal domain) ( 1.3.99.20 ) [ 16 ].

1. Flavoenzymes: diverse catalysts with recurrent features. Trends Biochem. Sci. 25, 126-32
2. To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes. Trends Biochem. Sci. 31, 276-83
3. Sequence-structure analysis of FAD-containing proteins. Protein Sci. 10, 1712-28
4. Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism. J. Mol. Biol. 295, 357-74
5. 8 alpha-(O-Tyrosyl)flavin adenine dinucleotide, the prosthetic group of bacterial p-cresol methylhydroxylase. Biochemistry 20, 3068-75
6. Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase. J. Biol. Chem. 274, 35514-20
7. p-Cresol methylhydroxylase: alteration of the structure of the flavoprotein subunit upon its binding to the cytochrome subunit. Biochemistry 44, 2963-73
8. The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. Proc. Natl. Acad. Sci. U.S.A. 97, 9413-8
9. Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair. J. Biol. Chem. 276, 30435-41
10. Structures of Michaelis and product complexes of plant cytokinin dehydrogenase: implications for flavoenzyme catalysis. J. Mol. Biol. 341, 1237-49
11. X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution. Biochemistry 36, 806-11
12. The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase. J. Mol. Biol. 301, 1221-35
13. The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition. Proc. Natl. Acad. Sci. U.S.A. 101, 7931-6
14. Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus. Structure 10, 115-25
15. Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase. Structure 12, 1425-35
16. Structure of a xanthine oxidase-related 4-hydroxybenzoyl-CoA reductase with an additional [4Fe-4S] cluster and an inverted electron flow. Structure 12, 2249-56