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49  structures 4696  species 1  interaction 8070  sequences 27  architectures

Family: Flavoprotein (PF02441)

Summary: Flavoprotein

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Flavoprotein Edit Wikipedia article

Flavoprotein
PDB 1e20 EBI.jpg
the fmn binding protein athal3
Identifiers
Symbol Flavoprotein
Pfam PF02441
InterPro IPR003382
SCOP 1e20
SUPERFAMILY 1e20

Flavoproteins are proteins that contain a nucleic acid derivative of riboflavin: the flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN).

Flavoproteins are involved in a wide array of biological processes, including, but by no means limited to, bioluminescence, removal of radicals contributing to oxidative stress, photosynthesis, DNA repair, and apoptosis. The spectroscopic properties of the flavin cofactor make it a natural reporter for changes occurring within the active site; this makes flavoproteins one of the most-studied enzyme families.

Discovery[edit]

The first mention of a flavoprotein in the scientific literature dates back to 1879, when the work on the composition of cow’s milk resulted in the isolation of a bright-yellow pigment, that we now know as flavin, but termed lactochrome at the time. By the early 1930s, this same pigment had been isolated from a range of sources, and recognised as a component of the vitamin B complex. Its structure was determined almost simultaneously by two groups in 1934, and given the name riboflavin, derived from the ribityl side chain and yellow colour of the conjugated ring system.[1]

The first evidence for the requirement of flavin as an enzyme cofactor came in 1935. Hugo Theorell and coworkers showed that a bright-yellow-coloured yeast protein, identified previously as essential for cellular respiration, could be separated into apoprotein and a bright-yellow pigment. Neither apoprotein nor pigment alone could catalyse the oxidation of NADH, but mixing of the two restored the enzyme activity. However, replacing the isolated pigment with riboflavin did not restore enzyme activity, despite their being indistinguishable under spectroscopy. This led to the discovery that the protein studied required not riboflavin but flavin mononucleotide to be catalytically active[1][2]

Similar experiments with D-amino acid oxidase[3] led to the identification of flavin adenine dinucleotide (FAD) as a second form of flavin utilised by enzymes.[4]

Examples[edit]

The flavoprotein family contains a diverse range of enzymes, including:

See also[edit]

References[edit]

  1. ^ a b Massey, V. (2000) The chemical and biological versatility of riboflavin, Biochem. Soc. Trans. 28, 283-296.
  2. ^ Theorell, H. (1935) Preparation in pure state of the effect group of yellow enzymes, Biochemische Zeitschrift 275, 344-346.
  3. ^ Warburg, O., and Christian, W. (1938) Isolation of the prosthetic group of the amino acid oxydase, Biochemische Zeitschrift 298, 150-168.
  4. ^ Christie, S. M. H., Kenner, G. W., and Todd, A. R. (1954) NUCLEOTIDES .25. A SYNTHESIS OF FLAVIN ADENINE DINUCLEOTIDE, Journal of the Chemical Society, 46-52.
  5. ^ Kupke T, Stevanovic S, Sahl HG, Gotz F (August 1992). "Purification and characterization of EpiD, a flavoprotein involved in the biosynthesis of the lantibiotic epidermin". J. Bacteriol. 174 (16): 5354–61. PMC 206373. PMID 1644762. 
  6. ^ Daniel RA, Errington J (July 1993). "Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis". J. Mol. Biol. 232 (2): 468–83. doi:10.1006/jmbi.1993.1403. PMID 8345520. 
  7. ^ Clausen M, Lamb CJ, Megnet R, Doerner PW (May 1994). "PAD1 encodes phenylacrylic acid decarboxylase which confers resistance to cinnamic acid in Saccharomyces cerevisiae". Gene 142 (1): 107–12. doi:10.1016/0378-1119(94)90363-8. PMID 8181743. 

External links[edit]

  • Flavoprotein at eMedicine Dictionary
  • The menu "science" of the program STRAP provides A comprehensive collection of all flavo-proteins with known 3D-structure. It compares the protein structures to elucidate phylogenetic relationships.

This article incorporates text from the public domain Pfam and InterPro IPR003382

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.

Flavoprotein Provide feedback

This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD P30197 which has been shown to be a flavoprotein that binds FMN [1]. This enzyme catalyses the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance [2]. dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase P33751 ( EC:4.1.1.-) [3].

Literature references

  1. Kupke T, Stevanovic S, Sahl HG, Gotz F; , J Bacteriol 1992;174:5354-5361.: Purification and characterization of EpiD, a flavoprotein involved in the biosynthesis of the lantibiotic epidermin. PUBMED:1644762 EPMC:1644762

  2. Daniel RA, Errington J; , J Mol Biol 1993;232:468-483.: Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis. PUBMED:8345520 EPMC:8345520

  3. Clausen M, Lamb CJ, Megnet R, Doerner PW; , Gene 1994;142:107-112.: PAD1 encodes phenylacrylic acid decarboxylase which confers resistance to cinnamic acid in Saccharomyces cerevisiae. PUBMED:8181743 EPMC:8181743


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003382

This entry contains a diverse range of flavoprotein enzymes, including epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN [PUBMED:1644762]. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance [PUBMED:8345520]. Dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenylacrylic acid decarboxylase EC [PUBMED:8181743].

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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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...

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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
(143)
Full
(8070)
Representative proteomes NCBI
(5827)
Meta
(2565)
RP15
(675)
RP35
(1384)
RP55
(1855)
RP75
(2213)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(143)
Full
(8070)
Representative proteomes NCBI
(5827)
Meta
(2565)
RP15
(675)
RP35
(1384)
RP55
(1855)
RP75
(2213)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(143)
Full
(8070)
Representative proteomes NCBI
(5827)
Meta
(2565)
RP15
(675)
RP35
(1384)
RP55
(1855)
RP75
(2213)
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.

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Seed source: Pfam-B_1622 (release 5.4)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 143
Number in full: 8070
Average length of the domain: 130.60 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 43.39 %

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 22.2 22.2
Trusted cut-off 22.2 22.2
Noise cut-off 21.9 22.1
Model length: 129
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Flavoprotein

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 Flavoprotein domain has been found. There are 49 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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