Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
367  structures 8452  species 0  interactions 65249  sequences 692  architectures

Family: FAD_binding_4 (PF01565)

Summary: FAD binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

  1. 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

  2. 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

External database links

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.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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_5

Alignments

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...

View options

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)
RP15
(7257)
RP35
(28198)
RP55
(58050)
RP75
(97033)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(121)
Full
(65249)
Representative proteomes UniProt
(223477)
RP15
(7257)
RP35
(28198)
RP55
(58050)
RP75
(97033)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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)
RP15
(7257)
RP35
(28198)
RP55
(58050)
RP75
(97033)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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 View help on the curation process

Seed source: Pfam-B_352 (release 4.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A
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 View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.4 26.4
Trusted cut-off 26.4 26.4
Noise cut-off 26.3 26.3
Model length: 139
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096QRL3 View 3D Structure Click here
A0A0N7KQK9 View 3D Structure Click here
A0A0P0V5D2 View 3D Structure Click here
A0A0P0VE34 View 3D Structure Click here
A0A0P0VGV3 View 3D Structure Click here
A0A0P0W932 View 3D Structure Click here
A0A0P0W9H9 View 3D Structure Click here
A0A0P0WXN6 View 3D Structure Click here
A0A0P0XEY6 View 3D Structure Click here
A0A0R0ETX2 View 3D Structure Click here
A0A0R0G721 View 3D Structure Click here
A0A0R0G9Z9 View 3D Structure Click here
A0A0R0HMH0 View 3D Structure Click here
A0A0R0I2I0 View 3D Structure Click here
A0A0R0IC18 View 3D Structure Click here
A0A0R0JH42 View 3D Structure Click here
A0A0R0JLB6 View 3D Structure Click here
A0A0R0JUD5 View 3D Structure Click here
A0A0R0K0E5 View 3D Structure Click here
A0A0R0K2X4 View 3D Structure Click here
A0A0R4J3W6 View 3D Structure Click here
A0A1D6EIA5 View 3D Structure Click here
A0A1D6F9W7 View 3D Structure Click here
A0A1D6GMF7 View 3D Structure Click here
A0A1D6H4L4 View 3D Structure Click here
A0A1D6HUM7 View 3D Structure Click here
A0A1D6HUM7 View 3D Structure Click here
A0A1D6IKF9 View 3D Structure Click here
A0A1D6JAL0 View 3D Structure Click here
A0A1D6KES9 View 3D Structure Click here
A0A1D6KQI1 View 3D Structure Click here
A0A1D6LT92 View 3D Structure Click here
A0A1D6LTC0 View 3D Structure Click here
A0A1D6LTC1 View 3D Structure Click here
A0A1D6MHW3 View 3D Structure Click here
A0A1D6NA77 View 3D Structure Click here
A0A1D6P228 View 3D Structure Click here
A0A1D6PSW8 View 3D Structure Click here
A0A1D6QA56 View 3D Structure Click here
A0A1D6QQD6 View 3D Structure Click here
A0A1D6QQD7 View 3D Structure Click here
A0A1D8PGR9 View 3D Structure Click here
A0A1D8PJK5 View 3D Structure Click here
A0A368UGT4 View 3D Structure Click here
A0A368UH07 View 3D Structure Click here
A0A368ULS0 View 3D Structure Click here
A1L258 View 3D Structure Click here
A3AVP1 View 3D Structure Click here
A4HXL3 View 3D Structure Click here
A4I0D2 View 3D Structure Click here
A4I309 View 3D Structure Click here
A4I481 View 3D Structure Click here
A4I507 View 3D Structure Click here
B4FR64 View 3D Structure Click here
B6V8F7 View 3D Structure Click here
B7EDV2 View 3D Structure Click here
C0PHW4 View 3D Structure Click here
E3T1X0 View 3D Structure Click here
E3T1X1 View 3D Structure Click here
E3T1X3 View 3D Structure Click here
F1QC72 View 3D Structure Click here
F1QUM4 View 3D Structure Click here
F1QXM5 View 3D Structure Click here
F4HV09 View 3D Structure Click here
G5EE46 View 3D Structure Click here
H7BRI4 View 3D Structure Click here
H9D2G5 View 3D Structure Click here
I1JFY3 View 3D Structure Click here
I1JS35 View 3D Structure Click here
I1JVN2 View 3D Structure Click here
I1JVN4 View 3D Structure Click here
I1K2W7 View 3D Structure Click here
I1K2W8 View 3D Structure Click here
I1K2W9 View 3D Structure Click here
I1K2X2 View 3D Structure Click here
I1K2X4 View 3D Structure Click here
I1K2X6 View 3D Structure Click here
I1K2X7 View 3D Structure Click here
I1KFV4 View 3D Structure Click here
I1KFV5 View 3D Structure Click here
I1KHQ7 View 3D Structure Click here
I1KQQ2 View 3D Structure Click here
I1KQQ3 View 3D Structure Click here
I1KRA7 View 3D Structure Click here
I1KRA9 View 3D Structure Click here
I1KRB0 View 3D Structure Click here
I1KRB1 View 3D Structure Click here
I1KRB3 View 3D Structure Click here
I1KRB4 View 3D Structure Click here
I1KRB5 View 3D Structure Click here
I1KRB6 View 3D Structure Click here
I1L0D6 View 3D Structure Click here
I1L0H6 View 3D Structure Click here
I1L0H7 View 3D Structure Click here
I1L0H8 View 3D Structure Click here
I1L0H9 View 3D Structure Click here
I1L0I0 View 3D Structure Click here
I1L0I8 View 3D Structure Click here
I1L0J0 View 3D Structure Click here
I1L1H8 View 3D Structure Click here
I1L1J0 View 3D Structure Click here
I1L5I9 View 3D Structure Click here
I1LC19 View 3D Structure Click here
I1LIV5 View 3D Structure Click here
I1LL79 View 3D Structure Click here
I1LPL0 View 3D Structure Click here
I1LXZ6 View 3D Structure Click here
I1M956 View 3D Structure Click here
I1MG66 View 3D Structure Click here
I1MG67 View 3D Structure Click here
I1MG68 View 3D Structure Click here
I1MG76 View 3D Structure Click here
I1MG79 View 3D Structure Click here
I1MG80 View 3D Structure Click here
I1MH82 View 3D Structure Click here
I1MKD9 View 3D Structure Click here
I1MKE0 View 3D Structure Click here
I1MKE1 View 3D Structure Click here
I1MSG8 View 3D Structure Click here
I1N8X2 View 3D Structure Click here
I1NCQ4 View 3D Structure Click here
I1NID0 View 3D Structure Click here
K7K4A7 View 3D Structure Click here
K7KI99 View 3D Structure Click here
K7L2L9 View 3D Structure Click here
K7L5I0 View 3D Structure Click here
K7LSE0 View 3D Structure Click here
K7LYV0 View 3D Structure Click here
K7MB53 View 3D Structure Click here
K7MMN7 View 3D Structure Click here
K7U150 View 3D Structure Click here
K7U1M0 View 3D Structure Click here
K7UFJ8 View 3D Structure Click here
K7V1U5 View 3D Structure Click here
K7VE94 View 3D Structure Click here
K7VHU9 View 3D Structure Click here
K7VI02 View 3D Structure Click here
K7VPF4 View 3D Structure Click here
L0TBR2 View 3D Structure Click here
O00116 View 3D Structure Click here
O05784 View 3D Structure Click here
O07406 View 3D Structure Click here
O17397 View 3D Structure Click here
O22213 View 3D Structure Click here
O23240 View 3D Structure Click here
O33177 View 3D Structure Click here
O45218 View 3D Structure Click here
O50381 View 3D Structure Click here
O53608 View 3D Structure Click here
O64743 View 3D Structure Click here
O64745 View 3D Structure Click here
O69686 View 3D Structure Click here
O81030 View 3D Structure Click here
O81032 View 3D Structure Click here
O93852 View 3D Structure Click here
O96759 View 3D Structure Click here
P06149 View 3D Structure Click here
P08373 View 3D Structure Click here
P0AEP9 View 3D Structure Click here
P10867 View 3D Structure Click here
P32891 View 3D Structure Click here
P39976 View 3D Structure Click here
P46681 View 3D Structure Click here
P52073 View 3D Structure Click here
P54783 View 3D Structure Click here
P58710 View 3D Structure Click here
P71984 View 3D Structure Click here
P77748 View 3D Structure Click here
P84850 View 3D Structure Click here
P9WIT1 View 3D Structure Click here
P9WIT3 View 3D Structure Click here
P9WJF1 View 3D Structure Click here
P9WJL9 View 3D Structure Click here
Q0DBM6 View 3D Structure Click here
Q0JQ12 View 3D Structure Click here
Q10I64 View 3D Structure Click here
Q11061 View 3D Structure Click here
Q15392 View 3D Structure Click here
Q2G069 View 3D Structure Click here
Q2PMD5 View 3D Structure Click here
Q2QXY1 View 3D Structure Click here
Q2R3Y8 View 3D Structure Click here
Q2RAP0 View 3D Structure Click here
Q39085 View 3D Structure Click here
Q46911 View 3D Structure Click here
Q4ADV8 View 3D Structure Click here
Q4CRU8 View 3D Structure Click here
Q4CYF3 View 3D Structure Click here
Q4D224 View 3D Structure Click here
Q4DPS1 View 3D Structure Click here
Q4DPZ5 View 3D Structure Click here
Q4DQH9 View 3D Structure Click here
Q54H55 View 3D Structure Click here
Q54N34 View 3D Structure Click here
Q54R94 View 3D Structure Click here
Q54U09 View 3D Structure Click here
Q55BQ4 View 3D Structure Click here
Q55CU9 View 3D Structure Click here
Q55DP7 View 3D Structure Click here
Q55E52 View 3D Structure Click here
Q55GL1 View 3D Structure Click here
Q5ABC8 View 3D Structure Click here
Q5ADT6 View 3D Structure Click here
Q5BQE6 View 3D Structure Click here
Q5JLP4 View 3D Structure Click here
Q5Z620 View 3D Structure Click here
Q5Z7I1 View 3D Structure Click here
Q5Z7I5 View 3D Structure Click here
Q5Z7I6 View 3D Structure Click here
Q5Z956 View 3D Structure Click here
Q5Z957 View 3D Structure Click here
Q5ZAY9 View 3D Structure Click here
Q67YU0 View 3D Structure Click here
Q6NQ66 View 3D Structure Click here
Q6YW50 View 3D Structure Click here
Q6YW51 View 3D Structure Click here
Q6YXT5 View 3D Structure Click here
Q6Z955 View 3D Structure Click here
Q709Q5 View 3D Structure Click here
Q75K78 View 3D Structure Click here
Q7EZA7 View 3D Structure Click here
Q7K511 View 3D Structure Click here
Q7TNG8 View 3D Structure Click here
Q7TPJ4 View 3D Structure Click here
Q7XI14 View 3D Structure Click here
Q84PV5 View 3D Structure Click here
Q84PV6 View 3D Structure Click here
Q84PV7 View 3D Structure Click here
Q869M2 View 3D Structure Click here
Q86WU2 View 3D Structure Click here
Q8C0I1 View 3D Structure Click here
Q8CIM3 View 3D Structure Click here
Q8I4K2 View 3D Structure Click here
Q8LNV6 View 3D Structure Click here
Q8N465 View 3D Structure Click here
Q8S9W7 View 3D Structure Click here
Q8VCH6 View 3D Structure Click here
Q93ZA3 View 3D Structure Click here
Q94AX4 View 3D Structure Click here
Q9C1X2 View 3D Structure Click here
Q9C614 View 3D Structure Click here
Q9EQR2 View 3D Structure Click here
Q9FI21 View 3D Structure Click here
Q9FI25 View 3D Structure Click here
Q9FKU8 View 3D Structure Click here
Q9FKU9 View 3D Structure Click here
Q9FKV0 View 3D Structure Click here
Q9FKV2 View 3D Structure Click here
Q9FM82 View 3D Structure Click here
Q9FUJ1 View 3D Structure Click here
Q9FUJ2 View 3D Structure Click here
Q9FUJ3 View 3D Structure Click here
Q9FZC4 View 3D Structure Click here
Q9FZC5 View 3D Structure Click here
Q9FZC6 View 3D Structure Click here
Q9FZC7 View 3D Structure Click here
Q9FZC8 View 3D Structure Click here
Q9HDX8 View 3D Structure Click here
Q9LPC3 View 3D Structure Click here
Q9LTS3 View 3D Structure Click here
Q9LY71 View 3D Structure Click here
Q9LYD8 View 3D Structure Click here
Q9SA85 View 3D Structure Click here
Q9SA86 View 3D Structure Click here
Q9SA87 View 3D Structure Click here
Q9SA88 View 3D Structure Click here
Q9SA89 View 3D Structure Click here
Q9SA99 View 3D Structure Click here
Q9SU56 View 3D Structure Click here
Q9SUC6 View 3D Structure Click here
Q9SVG3 View 3D Structure Click here
Q9SVG4 View 3D Structure Click here
Q9SVG5 View 3D Structure Click here
Q9SVG7 View 3D Structure Click here
Q9T0N8 View 3D Structure Click here
Q9V778 View 3D Structure Click here
Q9XVZ2 View 3D Structure Click here