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99  structures 6937  species 0  interactions 26097  sequences 333  architectures

Family: FAD_binding_6 (PF00970)

Summary: Oxidoreductase 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.

This is the Wikipedia entry entitled "Oxidoreductase FAD-binding domain". More...

Oxidoreductase FAD-binding domain Edit Wikipedia article

Oxidoreductase FAD-binding domain
Identifiers
SymbolFAD_binding_6
PfamPF00970
InterProIPR008333
SCOPe1cne / SUPFAM
CDDcd00322

The oxidoreductase FAD-binding domain is an evolutionary conserved protein domain.

To date, the 3D-structures of the flavoprotein domain of Zea mays nitrate reductase[1] and of pig NADH:cytochrome b5 reductase[2] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase:[3] the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).

Examples

Human genes encoding proteins containing this domain include:

References

  1. ^ Lindqvist Y, Schneider G, Campbell WH, Lu G (1994). "Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 A resolution: relationship to other flavoprotein reductases". Structure. 2 (9): 809–821. doi:10.1016/s0969-2126(94)00082-4. PMID 7812715.
  2. ^ Miki K, Nishida H, Inaka K, Yamanaka M, Kaida S, Kobayashi K (1995). "Crystal structure of NADH-cytochrome b5 reductase from pig liver at 2.4 A resolution". Biochemistry. 34 (9): 2763–2767. doi:10.1021/bi00009a004. PMID 7893687.
  3. ^ Karplus PA, Bruns CM (1994). "Structure-function relations for ferredoxin reductase". J. Bioenerg. Biomembr. 26 (1): 89–99. doi:10.1007/BF00763221. PMID 8027025.
This article incorporates text from the public domain Pfam and InterPro: IPR008333


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

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No Pfam abstract.

Literature references

  1. Lu G, Campbell WH, Schneider G, Lindqvist Y; , Structure 1994;2:809-821.: Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 A resolution: relationship to other flavoprotein reductases. PUBMED:7812715 EPMC:7812715

  2. Hyde GE, Crawford NM, Campbell W; , J Biol Chem 1991;266:23542-23547.: The sequence of squash NADH:nitrate reductase and its relationship to the sequences of other flavoprotein oxidoreductases. A family of flavoprotein pyridine nucleotide cytochrome reductases. PUBMED:1748631 EPMC:1748631


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008333

These sequences represent the FAD-binding domain found in NADH:cytochrome b5 reductases and nitrate reductases.

To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [ PUBMED:7812715 ] and of pig NADH:cytochrome b5 reductase [ PUBMED:7893687 ] have been solved. The overall fold is similar to that of ferredoxin:NADP + reductase [ PUBMED:8027025 ]: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).

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_Lum_binding (CL0076), which has the following description:

Riboflavin nucleotide coenzymes and flavin adenine dinucleotide (FAD) are essential cofactors for a large number of flavoproteins involved in a diverse set of redox reactions. There are thought to be four different FAD-binding folds [1].The FAD-binding fold of this clan is a cylindrical beta-fold. More specifically, the domain forms a flattened six-stranded antiparallel beta-barrel organised into two orthogonal sheets (1-2-5 and 4-3-6) separated by one alpha-helix. The cylinder is open between strands strand 4 and 5. This opening of the cylinder makes space for the isoalloxazine and ribityl moieties of the FAD, to which hydrogen bonds are formed from the open edges of the strands. The other end of the cylinder is covered by the only helix of the domain, which is essential for the binding of the pyrophosphate groups of the FAD [1].The structural differences in the FAD-binding domain are manifested mainly as loops of different length and extra extending structural elements, which may be important for interactions with their redox partners [1]. The structural core of all clan members is highly conserved.

The clan contains the following 5 members:

FAD_binding_1 FAD_binding_6 FAD_binding_8 FAD_binding_9 Lum_binding

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
(35)
Full
(26097)
Representative proteomes UniProt
(109429)
RP15
(3029)
RP35
(10666)
RP55
(24337)
RP75
(44567)
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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
(35)
Full
(26097)
Representative proteomes UniProt
(109429)
RP15
(3029)
RP35
(10666)
RP55
(24337)
RP75
(44567)
Alignment:
Format:
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Sequence:
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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
(35)
Full
(26097)
Representative proteomes UniProt
(109429)
RP15
(3029)
RP35
(10666)
RP55
(24337)
RP75
(44567)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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_143 (release 3.0)
Previous IDs: Cyt_reductase;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 35
Number in full: 26097
Average length of the domain: 96.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 24.95 %

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 99
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Selections

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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_6 domain has been found. There are 99 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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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
A0A0R0EM30 View 3D Structure Click here
A0A0R0KKK6 View 3D Structure Click here
A0A0R4J5H2 View 3D Structure Click here
A0A1D6HBR0 View 3D Structure Click here
A0A1D6M6Z3 View 3D Structure Click here
A0A1D6N8X4 View 3D Structure Click here
A0A1D8PTX6 View 3D Structure Click here
A0A1D8PU81 View 3D Structure Click here
A0A368UIE7 View 3D Structure Click here
A1ZBK6 View 3D Structure Click here
A4HUT9 View 3D Structure Click here
A4HVN4 View 3D Structure Click here
A4HWA2 View 3D Structure Click here
A4HZV4 View 3D Structure Click here
A4HZV5 View 3D Structure Click here
A4I589 View 3D Structure Click here
A4I862 View 3D Structure Click here
A4IAY0 View 3D Structure Click here
A4IB12 View 3D Structure Click here
B1AS42 View 3D Structure Click here
B6TCK3 View 3D Structure Click here
C6TKA3 View 3D Structure Click here
D3ZZ05 View 3D Structure Click here
E9AHE4 View 3D Structure Click here
F1QJ75 View 3D Structure Click here
I1K1F4 View 3D Structure Click here
I1KVY3 View 3D Structure Click here
I1LW34 View 3D Structure Click here
I1MAM4 View 3D Structure Click here
I1MAM5 View 3D Structure Click here
K7LX30 View 3D Structure Click here
O13809 View 3D Structure Click here
O16521 View 3D Structure Click here
O16522 View 3D Structure Click here
O74557 View 3D Structure Click here
P00387 View 3D Structure Click here
P0AEN1 View 3D Structure Click here
P11035 View 3D Structure Click here
P11832 View 3D Structure Click here
P16081 View 3D Structure Click here
P17571 View 3D Structure Click here
P20070 View 3D Structure Click here
P24232 View 3D Structure Click here
P28861 View 3D Structure Click here
P36060 View 3D Structure Click here
P38626 View 3D Structure Click here
P38909 View 3D Structure Click here
P39676 View 3D Structure Click here
P39870 View 3D Structure Click here
P39871 View 3D Structure Click here
P41344 View 3D Structure Click here
P49102 View 3D Structure Click here
P54233 View 3D Structure Click here
P71846 View 3D Structure Click here
P75824 View 3D Structure Click here
P76081 View 3D Structure Click here
P76254 View 3D Structure Click here
P83291 View 3D Structure Click here
P95277 View 3D Structure Click here
P9WJ93 View 3D Structure Click here
P9WNE9 View 3D Structure Click here
Q04516 View 3D Structure Click here
Q0P487 View 3D Structure Click here
Q12746 View 3D Structure Click here
Q2G2P2 View 3D Structure Click here
Q3KNK3 View 3D Structure Click here
Q3TDX8 View 3D Structure Click here
Q4CKI1 View 3D Structure Click here
Q4CM25 View 3D Structure Click here
Q4CMU8 View 3D Structure Click here
Q4CUP8 View 3D Structure Click here
Q4CYX1 View 3D Structure Click here
Q4D0C0 View 3D Structure Click here
Q4D778 View 3D Structure Click here
Q4DA56 View 3D Structure Click here
Q4DEP6 View 3D Structure Click here
Q4DHD7 View 3D Structure Click here
Q4DL41 View 3D Structure Click here
Q4DLP7 View 3D Structure Click here
Q4DNM4 View 3D Structure Click here
Q4DRG8 View 3D Structure Click here
Q4DYC3 View 3D Structure Click here
Q502I6 View 3D Structure Click here
Q54D73 View 3D Structure Click here
Q54NC1 View 3D Structure Click here
Q54XV1 View 3D Structure Click here
Q59M70 View 3D Structure Click here
Q59MV6 View 3D Structure Click here
Q59MV9 View 3D Structure Click here
Q59P03 View 3D Structure Click here
Q5AG85 View 3D Structure Click here
Q5EB81 View 3D Structure Click here
Q5N760 View 3D Structure Click here
Q5VR12 View 3D Structure Click here
Q68EJ0 View 3D Structure Click here
Q6AVN1 View 3D Structure Click here
Q6AY12 View 3D Structure Click here
Q6BCY4 View 3D Structure Click here
Q6IPT4 View 3D Structure Click here
Q6NYE6 View 3D Structure Click here
Q6ZC33 View 3D Structure Click here
Q6ZHH7 View 3D Structure Click here
Q7ARS9 View 3D Structure Click here
Q7L1T6 View 3D Structure Click here
Q8ID33 View 3D Structure Click here
Q9DB73 View 3D Structure Click here
Q9DCN2 View 3D Structure Click here
Q9SLP6 View 3D Structure Click here
Q9SYR0 View 3D Structure Click here
Q9UAG7 View 3D Structure Click here
Q9UHQ9 View 3D Structure Click here
Q9URY5 View 3D Structure Click here
Q9VWK8 View 3D Structure Click here
Q9XWF1 View 3D Structure Click here
Q9ZNT1 View 3D Structure Click here
X2JGK6 View 3D Structure Click here