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87  structures 3021  species 0  interactions 11095  sequences 255  architectures

Family: FAD_binding_1 (PF00667)

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.

This is the Wikipedia entry entitled "Flavoprotein pyridine nucleotide cytochrome reductases". More...

Flavoprotein pyridine nucleotide cytochrome reductases Edit Wikipedia article

FAD binding domain
Identifiers
SymbolFAD_binding_1
PfamPF00667
InterProIPR003097
SCOPe1amo / SUPFAM

Flavoprotein pyridine nucleotide cytochrome reductases[1] catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin-NADP+ reductases,[2] plant and fungal NAD(P)H:nitrate reductases,[1][3] cytochrome b5 reductases,[4] cytochrome P450 reductases,[5] sulphite reductases,[6] nitric oxide synthases,[7] phthalate dioxygenase reductase,[8] and various other flavoproteins.

Human proteins containing this domain

MTRR; NDOR1; NOS1; NOS2A; NOS3; NR1; POR;

References

  1. ^ a b Hyde GE, Crawford NM, Campbell WH (1991). "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". J. Biol. Chem. 266 (35): 23542–23547. PMID 1748631.
  2. ^ Karplus PA, Bruns CM (1994). "Structure-function relations for ferredoxin reductase". J. Bioenerg. Biomembr. 26 (1): 89–99. doi:10.1007/BF00763221. PMID 8027025.
  3. ^ Siverio JM (2002). "Assimilation of nitrate by yeasts". FEMS Microbiol. Rev. 26 (3): 277–284. doi:10.1111/j.1574-6976.2002.tb00615.x. PMID 12165428.
  4. ^ Iwanaga S, Miyata T, Yubisui T, Tamura M, Takeshita M (1986). "Complete amino acid sequence of NADH-cytochrome b5 reductase purified from human erythrocytes". J. Biochem. 99 (2): 407–422. PMID 3700359.
  5. ^ Porter TD (1991). "An unusual yet strongly conserved flavoprotein reductase in bacteria and mammals" (PDF). Trends Biochem. Sci. 16 (4): 154–158. doi:10.1016/0968-0004(91)90059-5. PMID 1908607.
  6. ^ Siegel LM, Ostrowski J, Rueger DC, Miller BE, Kredich NM, Barber MJ (1989). "Characterization of the flavoprotein moieties of NADPH-sulfite reductase from Salmonella typhimurium and Escherichia coli. Physicochemical and catalytic properties, amino acid sequence deduced from DNA sequence of cysJ, and comparison with NADPH-cytochrome P-450 reductase". J. Biol. Chem. 264 (27): 15796–15808. PMID 2550423.
  7. ^ Snyder SH, Reed RR, Bredt DS, Hwang PM, Glatt CE, Lowenstein C (1991). "Cloned and expressed nitric oxide synthase structurally resembles cytochrome P-450 reductase". Nature. 351 (6329): 714–718. doi:10.1038/351714a0. PMID 1712077.
  8. ^ Karplus PA, Bruns CM, Correll CC, Ludwig ML (1993). "Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin". Protein Sci. 2 (12): 2112–2133. doi:10.1002/pro.5560021212. PMC 2142325. PMID 8298460.
This article incorporates text from the public domain Pfam and InterPro: IPR003097

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.

FAD binding domain Provide feedback

This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase.

Literature references

  1. Eschenbrenner M, Coves J, Fontecave M; , J Biol Chem 1995;270:20550-20555.: The flavin reductase activity of the flavoprotein component of sulfite reductase from Escherichia coli. A new model for the protein structure. PUBMED:7657631 EPMC:7657631

  2. Eschenbrenner M, Coves J, Fontecave M; , FEBS Lett 1995;374:82-84.: NADPH-sulfite reductase flavoprotein from Escherichia coli: contribution to the flavin content and subunit interaction. PUBMED:7589518 EPMC:7589518

  3. Smith GC, Tew DG, Wolf CR; , Proc Natl Acad Sci U S A 1994;91:8710-8714.: Dissection of NADPH-cytochrome P450 oxidoreductase into distinct functional domains. PUBMED:8078947 EPMC:8078947

  4. Wang M, Roberts DL, Paschke R, Shea TM, Masters BS, Kim JJ; , Proc Natl Acad Sci U S A 1997;94:8411-8416.: Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes. PUBMED:9237990 EPMC:9237990


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003097

This FAD-binding domain can be found in sulfite reductase [NADPH] flavoprotein alpha-component CysJ, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. CysJ is a component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide [ PUBMED:10860732 ]. The structure of the nitric oxide synthase FAD-binding domain has been solved [ PUBMED:11473123 ].

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...

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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
(11)
Full
(11095)
Representative proteomes UniProt
(30586)
RP15
(1731)
RP35
(4764)
RP55
(9039)
RP75
(13857)
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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
(11)
Full
(11095)
Representative proteomes UniProt
(30586)
RP15
(1731)
RP35
(4764)
RP55
(9039)
RP75
(13857)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(11)
Full
(11095)
Representative proteomes UniProt
(30586)
RP15
(1731)
RP35
(4764)
RP55
(9039)
RP75
(13857)
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_180 (release 2.1)
Previous IDs: FAD_binding;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 11
Number in full: 11095
Average length of the domain: 203.00 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 25.82 %

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 32.3 32.3
Trusted cut-off 32.3 32.3
Noise cut-off 32.2 32.2
Model length: 222
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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_1 domain has been found. There are 87 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
A0A0R0L4H1 View 3D Structure Click here
A0A0R0L4H1 View 3D Structure Click here
A0A0R4IQG7 View 3D Structure Click here
A0A0R4J338 View 3D Structure Click here
A0A0R4J4Q1 View 3D Structure Click here
A0A0R4J5H8 View 3D Structure Click here
A0A1D6DVQ5 View 3D Structure Click here
A0A1D6IAL1 View 3D Structure Click here
A0A1D6ND25 View 3D Structure Click here
A0A1D8PIF6 View 3D Structure Click here
A0A1D8PLR7 View 3D Structure Click here
A0A2R8QQ95 View 3D Structure Click here
A2AI05 View 3D Structure Click here
A2BIN8 View 3D Structure Click here
A4I3K3 View 3D Structure Click here
A4IA43 View 3D Structure Click here
A4IBG5 View 3D Structure Click here
A4IDQ0 View 3D Structure Click here
C0H553 View 3D Structure Click here
C0HFL6 View 3D Structure Click here
D4ABT4 View 3D Structure Click here
F1Q7F3 View 3D Structure Click here
F1QML0 View 3D Structure Click here
F8W4Z6 View 3D Structure Click here
I1K9R6 View 3D Structure Click here
I1MB07 View 3D Structure Click here
I1N5D0 View 3D Structure Click here
K7LAX4 View 3D Structure Click here
K7THB1 View 3D Structure Click here
K7TVP4 View 3D Structure Click here
M1ZMI3 View 3D Structure Click here
O94613 View 3D Structure Click here
P00388 View 3D Structure Click here
P16435 View 3D Structure Click here
P16603 View 3D Structure Click here
P29474 View 3D Structure Click here
P29475 View 3D Structure Click here
P29476 View 3D Structure Click here
P29477 View 3D Structure Click here
P35228 View 3D Structure Click here
P36587 View 3D Structure Click here
P37040 View 3D Structure Click here
P38038 View 3D Structure Click here
P39692 View 3D Structure Click here
P70313 View 3D Structure Click here
Q06518 View 3D Structure Click here
Q09590 View 3D Structure Click here
Q09744 View 3D Structure Click here
Q09878 View 3D Structure Click here
Q0J705 View 3D Structure Click here
Q12181 View 3D Structure Click here
Q17574 View 3D Structure Click here
Q27571 View 3D Structure Click here
Q27597 View 3D Structure Click here
Q2FUZ8 View 3D Structure Click here
Q498R1 View 3D Structure Click here
Q4D617 View 3D Structure Click here
Q4DLF5 View 3D Structure Click here
Q4DPU7 View 3D Structure Click here
Q4DS22 View 3D Structure Click here
Q54B10 View 3D Structure Click here
Q54JL0 View 3D Structure Click here
Q54L96 View 3D Structure Click here
Q54L96 View 3D Structure Click here
Q55CT1 View 3D Structure Click here
Q55G48 View 3D Structure Click here
Q5AD27 View 3D Structure Click here
Q5JL61 View 3D Structure Click here
Q62600 View 3D Structure Click here
Q653S9 View 3D Structure Click here
Q6NPS8 View 3D Structure Click here
Q6PFP6 View 3D Structure Click here
Q7X7K8 View 3D Structure Click here
Q8C1A3 View 3D Structure Click here
Q9SB48 View 3D Structure Click here
Q9SUM3 View 3D Structure Click here
Q9UBK8 View 3D Structure Click here
Q9UHB4 View 3D Structure Click here
Q9US28 View 3D Structure Click here
Q9VEV2 View 3D Structure Click here
Q9VSJ5 View 3D Structure Click here
Q9Z0J4 View 3D Structure Click here