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11  structures 714  species 1  interaction 2113  sequences 23  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
Symbol RPE65
Pfam PF03055
InterPro IPR004294
SCOP 2biw
SUPERFAMILY 2biw
OPM superfamily 111
OPM protein 2biw

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 a receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein.

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 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.[5]

Human proteins containing this domain[edit]

BCDO2; BCMO1; RPE65;

References[edit]

  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): –. 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. 
  5. ^ Lee JS, Horwitz J, Travis GH, Mata NL, Moghrabi WN, Bui TV, Radu RA (2004). "Rpe65 is a retinyl ester binding protein that presents insoluble substrate to the isomerase in retinal pigment epithelial cells". J. Biol. Chem. 279 (1): 635–643. doi:10.1074/jbc.M310042200. PMID 14532273. 

Further reading[edit]

  • 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[edit]

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


External database links

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].

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
(151)
Full
(2113)
Representative proteomes NCBI
(1992)
Meta
(868)
RP15
(234)
RP35
(534)
RP55
(747)
RP75
(903)
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Format an alignment

  Seed
(151)
Full
(2113)
Representative proteomes NCBI
(1992)
Meta
(868)
RP15
(234)
RP35
(534)
RP55
(747)
RP75
(903)
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
(151)
Full
(2113)
Representative proteomes NCBI
(1992)
Meta
(868)
RP15
(234)
RP35
(534)
RP55
(747)
RP75
(903)
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.

Pfam alignments:

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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
Author: Griffiths-Jones SR
Number in seed: 151
Number in full: 2113
Average length of the domain: 396.50 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 89.26 %

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 17.4 17.4
Trusted cut-off 17.9 18.3
Noise cut-off 16.4 17.3
Model length: 486
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

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

RPE65

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 11 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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