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138  structures 2170  species 0  interactions 8705  sequences 112  architectures

Family: RPE65 (PF03055)

Summary: Retinal pigment epithelial membrane protein

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 "Carotenoid oxygenase". More...

Carotenoid oxygenase Edit Wikipedia article

Retinal pigment epithelial membrane protein
PDB 1bix EBI.jpg
The Structure of a Retinal-Forming Carotenoid Oxygenase.[1]
Identifiers
SymbolRPE65
PfamPF03055
InterProIPR004294
SCOPe2biw / SUPFAM
OPM superfamily103
OPM protein2biw

Carotenoid oxygenases are a family of enzymes involved in the cleavage of carotenoids to produce, for example, retinol, commonly known as vitamin A. This family includes an enzyme known as RPE65 which is abundantly expressed in the retinal pigment epithelium where it catalyzed the formation of 11-cis-retinol from all-trans-retinyl esters.

Carotenoids such as beta-carotene, lycopene, lutein and beta-cryptoxanthine are produced in plants and certain bacteria, algae and fungi, where they function as accessory photosynthetic pigments and as scavengers of oxygen radicals for photoprotection. They are also essential dietary nutrients in animals. Carotenoid oxygenases cleave a variety of carotenoids into a range of biologically important products, including apocarotenoids in plants that function as hormones, pigments, flavours, floral scents and defence compounds, and retinoids in animals that function as vitamins, visual pigments and signalling molecules.[2] Examples of carotenoid oxygenases include:

  • Beta-carotene 15,15'-monooxygenase (BCDO1; EC 1.14.99.36) from animals, which cleaves beta-carotene symmetrically at the central double bond to yield two molecules of retinal.[2]
  • Beta-carotene-9',10'-dioxygenase (BCDO2) from animals, which cleaves beta-carotene asymmetrically to apo-10'-beta-carotenal and beta-ionone, the latter being converted to retinoic acid. Lycopene is also oxidatively cleaved.[2]
  • 9-cis-epoxycarotenoid dioxygenase from plants, which cleaves 9-cis xanthophylls to xanthoxin, a precursor of the hormone abscisic acid.[3]
  • Apocarotenoid-15,15'-oxygenase from bacteria and cyanobacteria, which converts beta-apocarotenals rather than beta-carotene into retinal. This protein has a seven-bladed beta-propeller structure with four hisitidines that hold the iron active centre.[4]
  • Retinal pigment epithelium 65 kDa protein (RPE65) from vertebrates which is important for the production of 11-cis retinal during visual pigment regeneration.

Human proteins containing this domain

BCDO2; BCMO1; RPE65;

References

  1. ^ Kloer DP, Ruch S, Al-Babili S, Beyer P, Schulz GE (April 2005). "The structure of a retinal-forming carotenoid oxygenase". Science. 308 (5719): 267–9. doi:10.1126/science.1108965. PMID 15821095.
  2. ^ a b c Wyss A (2004). "Carotene oxygenases: a new family of double bond cleavage enzymes". J. Nutr. 134 (1): 246S–250S. PMID 14704328.
  3. ^ Cline K, Liu L, Li QB, Tan BC, Joseph LM, Deng WT, Mccarty DR (2003). "Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family". Plant J. 35 (1): 44–56. doi:10.1046/j.1365-313X.2003.01786.x. PMID 12834401.
  4. ^ Schulz GE, Kloer DP, Ruch S, Al-Babili S, Beyer P (2005). "The structure of a retinal-forming carotenoid oxygenase". Science. 308 (5719): 267–269. doi:10.1126/science.1108965. PMID 15821095.

Further reading

  • Nicoletti A, Wong DJ, Kawase K, Gibson LH, Yang-Feng TL, Richards JE, Thompson DA (April 1995). "Molecular characterization of the human gene encoding an abundant 61 kDa protein specific to the retinal pigment epithelium". Hum. Mol. Genet. 4 (4): 641–9. doi:10.1093/hmg/4.4.641. PMID 7633413.

External links

This article incorporates text from the public domain Pfam and InterPro: IPR004294

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.

Retinal pigment epithelial membrane protein Provide feedback

This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria.

Literature references

  1. Nicoletti A, Wong DJ, Kawase K, Gibson LH, Yang-Feng TL, Richards JE, Thompson DA; , Hum Mol Genet 1995;4:641-649.: Molecular characterization of the human gene encoding an abundant 61 kDa protein specific to the retinal pigment epithelium. PUBMED:7633413 EPMC:7633413


This tab holds annotation information from the InterPro database.

InterPro entry IPR004294

Carotenoids such as beta-carotene, lycopene, lutein and beta-cryptoxanthine are produced in plants and certain bacteria, algae and fungi, where they function as accessory photosynthetic pigments and as scavengers of oxygen radicals for photoprotection. They are also essential dietary nutrients in animals. Carotenoid oxygenases cleave a variety of carotenoids into a range of biologically important products, including apocarotenoids in plants that function as hormones, pigments, flavours, floral scents and defence compounds, and retinoids in animals that function as vitamins, visual pigments and signalling molecules [ PUBMED:14704328 ]. Examples of carotenoid oxygenases include:

  • Beta-carotene-15,15'-monooxygenase (BCDO1; EC ) from animals, which cleaves beta-carotene symmetrically at the central double bond to yield two molecules of retinal [ PUBMED:14704328 ].
  • Beta-carotene-9',10'-dioxygenase (BCDO2) from animals, which cleaves beta-carotene asymmetrically to apo-10'-beta-carotenal and beta-ionone, the latter being converted to retinoic acid. Lycopene is also oxidatively cleaved [ PUBMED:14704328 ].
  • 9-cis-epoxycarotenoid dioxygenase from plants, which cleaves 9-cis xanthophylls to xanthoxin, a precursor of the hormone abscisic acid [ PUBMED:12834401 ].
  • Apocarotenoid-15,15'-oxygenase from bacteria and cyanobacteria, which converts beta-apocarotenals rather than beta-carotene into retinal. This protein has a seven-bladed beta-propeller structure with four hisitidines that hold the iron active centre [ PUBMED:15821095 ].
  • Retinal pigment RPE65 from animals, which in its soluble form binds all-trans retinol, and in its membrane-bound form binds all-trans retinyl esters. RPE65 is important for the production of 11-cis retinal during visual pigment regeneration [ PUBMED:14532273 ].

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
(499)
Full
(8705)
Representative proteomes UniProt
(21831)
RP15
(1181)
RP35
(4029)
RP55
(7478)
RP75
(11058)
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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
(499)
Full
(8705)
Representative proteomes UniProt
(21831)
RP15
(1181)
RP35
(4029)
RP55
(7478)
RP75
(11058)
Alignment:
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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
(499)
Full
(8705)
Representative proteomes UniProt
(21831)
RP15
(1181)
RP35
(4029)
RP55
(7478)
RP75
(11058)
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_947 (release 6.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 499
Number in full: 8705
Average length of the domain: 424.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 87.88 %

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 18.7 18.7
Trusted cut-off 18.7 18.8
Noise cut-off 18.6 18.6
Model length: 475
Family (HMM) version: 17
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 RPE65 domain has been found. There are 138 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
A0A0P0WT80 View 3D Structure Click here
A0A0P0WT80 View 3D Structure Click here
A0A0P0XF96 View 3D Structure Click here
A0A0P0XFB0 View 3D Structure Click here
A0A0P0XLA9 View 3D Structure Click here
A0A0P0XST1 View 3D Structure Click here
A0A0P0YD24 View 3D Structure Click here
A0A0R0INQ1 View 3D Structure Click here
A0A0R0INQ1 View 3D Structure Click here
A0A0R0JDV9 View 3D Structure Click here
A0A0R0KG82 View 3D Structure Click here
A0A0R4IFG6 View 3D Structure Click here
A0A0R4IH96 View 3D Structure Click here
A0A0R4J2L5 View 3D Structure Click here
A0A1D6E3X3 View 3D Structure Click here
A0A1D6F9F2 View 3D Structure Click here
A0A1D6FED1 View 3D Structure Click here
A0A1D6FIJ1 View 3D Structure Click here
A0A1D6GLI1 View 3D Structure Click here
A0A1D6HHH7 View 3D Structure Click here
A0A1D6I0E9 View 3D Structure Click here
A0A1D6I1X3 View 3D Structure Click here
A0A1D6I1X3 View 3D Structure Click here
A0A1D6IPX2 View 3D Structure Click here
A0A1D6ITE2 View 3D Structure Click here
A0A1D6IUU2 View 3D Structure Click here
A0A1D6JN83 View 3D Structure Click here
A0A1D6JN83 View 3D Structure Click here
A0A1D6JNU2 View 3D Structure Click here
A0A1D6KGE1 View 3D Structure Click here
A0A1D6KX21 View 3D Structure Click here
A0A1D6L5B2 View 3D Structure Click here
A0A1D6LI49 View 3D Structure Click here
A0A1D6MVG7 View 3D Structure Click here
A0A1D6N121 View 3D Structure Click here
A0A1D6NU77 View 3D Structure Click here
A0A1D6NUR0 View 3D Structure Click here
A0A1D6NUR0 View 3D Structure Click here
A0A1D6Q1S6 View 3D Structure Click here
A0A1X7YEQ7 View 3D Structure Click here
A0A1X7YFJ3 View 3D Structure Click here
A2BGP6 View 3D Structure Click here
A3KN98 View 3D Structure Click here
A9C3R8 View 3D Structure Click here
A9C3R9 View 3D Structure Click here
B4FBA4 View 3D Structure Click here
B6SV18 View 3D Structure Click here
C0PIX7 View 3D Structure Click here
C4PJN4 View 3D Structure Click here
F1QU45 View 3D Structure Click here
H2L060 View 3D Structure Click here
I1JUV6 View 3D Structure Click here
I1K3F0 View 3D Structure Click here
I1KRU0 View 3D Structure Click here
I1LVC9 View 3D Structure Click here
I1M0X0 View 3D Structure Click here
I6Y551 View 3D Structure Click here
K7K2H0 View 3D Structure Click here
K7KIW6 View 3D Structure Click here
K7KTX3 View 3D Structure Click here
K7KTY4 View 3D Structure Click here
K7L8V1 View 3D Structure Click here
K7U7K6 View 3D Structure Click here
O24592 View 3D Structure Click here
O49505 View 3D Structure Click here
O49675 View 3D Structure Click here
O65572 View 3D Structure Click here
O70276 View 3D Structure Click here
P9WPR5 View 3D Structure Click here
Q16518 View 3D Structure Click here
Q1RLW1 View 3D Structure Click here
Q5MBR3 View 3D Structure Click here
Q5MBR5 View 3D Structure Click here
Q5MBR6 View 3D Structure Click here
Q69NX5 View 3D Structure Click here
Q6PBW5 View 3D Structure Click here
Q6YVJ0 View 3D Structure Click here
Q7XJM2 View 3D Structure Click here
Q7XRP0 View 3D Structure Click here
Q7XU29 View 3D Structure Click here
Q8LIY8 View 3D Structure Click here
Q8VY26 View 3D Structure Click here
Q91XT5 View 3D Structure Click here
Q91ZQ5 View 3D Structure Click here
Q93VD5 View 3D Structure Click here
Q99NF1 View 3D Structure Click here
Q9BYV7 View 3D Structure Click here
Q9C6Z1 View 3D Structure Click here
Q9HAY6 View 3D Structure Click here
Q9JJS6 View 3D Structure Click here
Q9LRM7 View 3D Structure Click here
Q9LRR7 View 3D Structure Click here
Q9M9F5 View 3D Structure Click here
Q9TXT9 View 3D Structure Click here
Q9U2E4 View 3D Structure Click here
Q9VFS2 View 3D Structure Click here