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100  structures 8169  species 0  interactions 15796  sequences 93  architectures

Family: Flavoprotein (PF02441)

Summary: Flavoprotein

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This is the Wikipedia entry entitled "Flavoprotein". More...

Flavoprotein Edit Wikipedia article

Flavoprotein
PDB 1e20 EBI.jpg
the fmn binding protein athal3
Identifiers
SymbolFlavoprotein
PfamPF02441
InterProIPR003382
SCOPe1e20 / SUPFAM

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 removal of radicals contributing to oxidative stress, photosynthesis, and DNA repair. The flavoproteins are some of the most-studied families of enzymes.

Flavoproteins have either FMN or FAD as a prosthetic group or as a cofactor. The flavin is generally tightly bound (see example adrenodoxin reductase wherein the FAD is deeply buried in the enzyme).[1] About 5-10% of flavoproteins have a covalently linked FAD.[2] Based on the available structural data, FAD-binding sites can be divided into more than 200 different types.[3]

90 flavoproteins are encoded in the human genome; about 84% require FAD, and around 16% require FMN, whereas 5 proteins require both.[4] Flavoproteins are mainly located in the mitochondria.[4] Of all flavoproteins, 90% perform redox reactions and the other 10% are transferases, lyases, isomerases, ligases.[5]

Discovery

Flavoproteins were first mentioned in 1879, when they isolated as a bright-yellow pigment from cow's milk. They were initially termed lactochrome. 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 was reported in 1935 and given the name riboflavin, derived from the ribityl side chain and yellow colour of the conjugated ring system.[6]

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.[6][7]

Similar experiments with D-amino acid oxidase[8] led to the identification of flavin adenine dinucleotide (FAD) as a second form of flavin utilised by enzymes.[9]

Examples

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

  • Adrenodoxin reductase that is involved in steroid hormone synthesis in vertebrate species, and has a ubiquitous distribution in metazoa and prokaryotes.[1]

See also

References

  1. ^ a b Hanukoglu I (2017). "Conservation of the Enzyme-Coenzyme Interfaces in FAD and NADP Binding Adrenodoxin Reductase-A Ubiquitous Enzyme". Journal of Molecular Evolution. 85 (5): 205–218. doi:10.1007/s00239-017-9821-9. PMID 29177972.
  2. ^ Abbas, Charles A.; Sibirny, Andriy A. (2011-06-01). "Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers". Microbiology and Molecular Biology Reviews. 75 (2): 321–360. doi:10.1128/MMBR.00030-10. ISSN 1092-2172. PMC 3122625. PMID 21646432.
  3. ^ Garma, Leonardo D.; Medina, Milagros; Juffer, André H. (2016-11-01). "Structure-based classification of FAD binding sites: A comparative study of structural alignment tools". Proteins: Structure, Function, and Bioinformatics. 84 (11): 1728–1747. doi:10.1002/prot.25158. ISSN 1097-0134. PMID 27580869.
  4. ^ a b Lienhart, Wolf-Dieter; Gudipati, Venugopal; Macheroux, Peter (2013-07-15). "The human flavoproteome". Archives of Biochemistry and Biophysics. 535 (2): 150–162. doi:10.1016/j.abb.2013.02.015. PMC 3684772. PMID 23500531.
  5. ^ Macheroux, Peter; Kappes, Barbara; Ealick, Steven E. (2011-08-01). "Flavogenomics – a genomic and structural view of flavin-dependent proteins". FEBS Journal. 278 (15): 2625–2634. doi:10.1111/j.1742-4658.2011.08202.x. ISSN 1742-4658. PMID 21635694.
  6. ^ a b Massey, V (2000). "The chemical and biological versatility of riboflavin". Biochemical Society Transactions. 28 (4): 283–96. doi:10.1042/0300-5127:0280283. PMID 10961912.
  7. ^ Theorell, H. (1935). "Preparation in pure state of the effect group of yellow enzymes". Biochemische Zeitschrift. 275: 344–46.
  8. ^ Warburg, O.; Christian, W. (1938). "Isolation of the prosthetic group of the amino acid oxydase". Biochemische Zeitschrift. 298: 150–68.
  9. ^ Christie, S. M. H.; Kenner, G. W.; Todd, A. R. (1954). "Nucleotides. Part XXV. A synthesis of flavin?adenine dinucleotide". Journal of the Chemical Society: 46–52. doi:10.1039/JR9540000046.
  10. ^ Kupke, T; Stevanović, S; Sahl, H. G.; Götz, F (1992). "Purification and characterization of EpiD, a flavoprotein involved in the biosynthesis of the lantibiotic epidermin". Journal of Bacteriology. 174 (16): 5354–61. doi:10.1128/jb.174.16.5354-5361.1992. PMC 206373. PMID 1644762.
  11. ^ Daniel, R.A.; Errington, J. (1993). "Cloning, DNA Sequence, Functional Analysis and Transcriptional Regulation of the Genes Encoding Dipicolinic Acid Synthetase Required for Sporulation in Bacillus subtilis". Journal of Molecular Biology. 232 (2): 468–83. doi:10.1006/jmbi.1993.1403. PMID 8345520.
  12. ^ Clausen, Monika; Lamb, Christopher J.; Megnet, Roland; Doerner, Peter W. (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

  • 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(89)
Full
(15796)
Representative proteomes UniProt
(69807)
RP15
(2121)
RP35
(7402)
RP55
(15327)
RP75
(26121)
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Format an alignment

  Seed
(89)
Full
(15796)
Representative proteomes UniProt
(69807)
RP15
(2121)
RP35
(7402)
RP55
(15327)
RP75
(26121)
Alignment:
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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
(89)
Full
(15796)
Representative proteomes UniProt
(69807)
RP15
(2121)
RP35
(7402)
RP55
(15327)
RP75
(26121)
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_1622 (release 5.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 89
Number in full: 15796
Average length of the domain: 176.70 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 57.01 %

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 22.7 22.7
Trusted cut-off 22.8 22.8
Noise cut-off 22.6 22.6
Model length: 157
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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 Flavoprotein domain has been found. There are 100 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
A0A0R0IFH2 View 3D Structure Click here
A0A1D6MHF9 View 3D Structure Click here
A0A1D8PKD2 View 3D Structure Click here
A0A1D8PQ84 View 3D Structure Click here
A4I5I3 View 3D Structure Click here
B4FCR1 View 3D Structure Click here
B4FI60 View 3D Structure Click here
C6SZ50 View 3D Structure Click here
C6TA59 View 3D Structure Click here
D3ZZZ5 View 3D Structure Click here
I1N3H3 View 3D Structure Click here
K7LGA7 View 3D Structure Click here
K7LGA8 View 3D Structure Click here
K7MU20 View 3D Structure Click here
K7MU23 View 3D Structure Click here
K7MU24 View 3D Structure Click here
P0ABQ0 View 3D Structure Click here
P0AG03 View 3D Structure Click here
P33751 View 3D Structure Click here
P36024 View 3D Structure Click here
P36076 View 3D Structure Click here
P91988 View 3D Structure Click here
P94063 View 3D Structure Click here
P9WNZ1 View 3D Structure Click here
Q08438 View 3D Structure Click here
Q1LWK2 View 3D Structure Click here
Q2FXB5 View 3D Structure Click here
Q2G268 View 3D Structure Click here
Q4DB42 View 3D Structure Click here
Q4DVU1 View 3D Structure Click here
Q54Y51 View 3D Structure Click here
Q57566 View 3D Structure Click here
Q57661 View 3D Structure Click here
Q58140 View 3D Structure Click here
Q58323 View 3D Structure Click here
Q5A868 View 3D Structure Click here
Q69K55 View 3D Structure Click here
Q8BZB2 View 3D Structure Click here
Q8IAZ8 View 3D Structure Click here
Q8MKK3 View 3D Structure Click here
Q96CD2 View 3D Structure Click here
Q9SWE5 View 3D Structure Click here
Q9UTI7 View 3D Structure Click here