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144  structures 4278  species 6  interactions 14779  sequences 159  architectures

Family: FAD_binding_6 (PF00970)

Summary: Oxidoreductase FAD-binding domain

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

Oxidoreductase FAD-binding domain Edit Wikipedia article

Oxidoreductase FAD-binding domain
Identifiers
Symbol FAD_binding_6
Pfam PF00970
InterPro IPR008333
SCOP 1cne
SUPERFAMILY 1cne

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[edit]

Human genes encoding proteins containing this domain inlclude:

References[edit]

  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. 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 contain an oxidoreductase FAD-binding domain.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(115)
Full
(14779)
Representative proteomes NCBI
(11998)
Meta
(1730)
RP15
(1115)
RP35
(2425)
RP55
(3487)
RP75
(4286)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(115)
Full
(14779)
Representative proteomes NCBI
(11998)
Meta
(1730)
RP15
(1115)
RP35
(2425)
RP55
(3487)
RP75
(4286)
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
(115)
Full
(14779)
Representative proteomes NCBI
(11998)
Meta
(1730)
RP15
(1115)
RP35
(2425)
RP55
(3487)
RP75
(4286)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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
Author: Finn RD, Bateman A, Griffiths-Jones SR
Number in seed: 115
Number in full: 14779
Average length of the domain: 96.10 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 26.84 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -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: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 6 interactions for this family. More...

DHO_dh FAD_binding_6 Globin NAD_binding_1 DHODB_Fe-S_bind Fer2

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 144 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 seqence.

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