Summary: FAD binding domain
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FAD binding domain Provide feedback
This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].
Literature references
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Mattevi A, Fraaije MW, Mozzarelli A, Olivi L, Coda A, van Berkel WJ; , Structure 1997;5:907-920.: Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity. PUBMED:9261083 EPMC:9261083
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Benson TE, Walsh CT, Hogle JM; , Structure 1996;4:47-54.: The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls. PUBMED:8805513 EPMC:8805513
Internal database links
SCOOP: | BBE FAD_binding_5 |
Similarity to PfamA using HHSearch: | FAD_binding_5 |
External database links
HOMSTRAD: | FAD-oxidase_NC FAD_binding_4 |
PROSITE: | PDOC00674 |
SCOP: | 2vao |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006094
Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, EC ) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [ PUBMED:10984479 ]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. Other enzymes included in this family are MurB family members UDP-N-acetylenolpyruvoylglucosamine reductases involved in the biosynthesis of peptidoglycan [ PUBMED:8805513 ], D-lactate dehydrogenases among many others oxidoreductases.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | flavin adenine dinucleotide binding (GO:0050660) |
oxidoreductase activity (GO:0016491) | |
Biological process | oxidation-reduction process (GO:0055114) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan FAD_PCMH (CL0077), which has the following description:
The FAD-binding domains contained in this family fall within the PCMH (p-cresol methyl-hydroxylase) family of FAD binding proteins as defined in [1]. In this family, the structure of the FAD binding domain is comprised of two subdomains. Both of these subdomains have an alpha-beta fold. The first subdomain is comprised of three parallel beta strands, surrounded by alpha helices. The second subdomain contains five antiparallel beta strands, also surrounded by alpha helices. The junction between these two subdomains forms the FAD bind pocket, where the ligand is bound by hydrogen and van der Waals bonds [1].
The clan contains the following 2 members:
FAD_binding_4 FAD_binding_5Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (121) |
Full (65249) |
Representative proteomes | UniProt (223477) |
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RP15 (7257) |
RP35 (28198) |
RP55 (58050) |
RP75 (97033) |
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HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (121) |
Full (65249) |
Representative proteomes | UniProt (223477) |
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RP15 (7257) |
RP35 (28198) |
RP55 (58050) |
RP75 (97033) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_352 (release 4.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bashton M |
Number in seed: | 121 |
Number in full: | 65249 |
Average length of the domain: | 135.60 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 26.12 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 139 | ||||||||||||
Family (HMM) version: | 25 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the FAD_binding_4 domain has been found. There are 367 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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