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8  structures 47  species 2  interactions 95  sequences 2  architectures

Family: Carot_N (PF09150)

Summary: Orange carotenoid protein, N-terminal

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This is the Wikipedia entry entitled "Orange carotenoid N-terminal domain". More...

Orange carotenoid N-terminal domain Edit Wikipedia article

Carot_N
PDB 1m98 EBI.jpg
crystal structure of orange carotenoid protein
Identifiers
Symbol Carot_N
Pfam PF09150
InterPro IPR015233
SCOP 1m98
SUPERFAMILY 1m98

In molecular biology the orange carotenoid N-terminal domain is a protein domain found predominantly at the N-terminus of prokaryotic orange carotenoid proteins and in related carotenoid-binding proteins. It adopts an alpha-helical structure consisting of two four-helix bundles.[1]

Orange carotenoid-binding proteins (OCP) were first identified in cyanobacterial species, where they occur associated with phycobilisome in the cellular thylakoid membrane. These proteins function in photoprotection, and are essential for inhibiting white and blue-green light non-photochemical quenching (NPQ).[2][3] Carotenoids improve the photoprotectant activity by broadening OCP's absorption spectrum and facilitating the dissipation of absorbed energy. OCP acts as a homodimer, and binds one molecule of carotenoid (3'-hydroxyechinenone) and one chloride ion per subunit, where the carotenoid binding site is lined with a striking number of methionine residues. The carotenoid 3'-hydroxyechinenone is not found in higher plants. OCP has two domains: an N-terminal helical domain and a C-terminal domain that resembles a NTF2 (nuclear transport factor 2) domain. OCP can be proteolytically cleaved into a red form (RCP), which lacks 15 residues from the N terminus and approximately 150 residues from the C terminus.[4]

References[edit]

  1. ^ Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO (January 2003). "The crystal structure of a cyanobacterial water-soluble carotenoid binding protein". Structure 11 (1): 55–65. doi:10.1016/S0969-2126(02)00936-X. PMID 12517340. 
  2. ^ Wilson A, Boulay C, Wilde A, Kerfeld CA, Kirilovsky D (February 2007). "Light-induced energy dissipation in iron-starved cyanobacteria: roles of OCP and IsiA proteins". Plant Cell 19 (2): 656–72. doi:10.1105/tpc.106.045351. PMC 1867334. PMID 17307930. 
  3. ^ Wilson A, Ajlani G, Verbavatz JM, Vass I, Kerfeld CA, Kirilovsky D (April 2006). "A soluble carotenoid protein involved in phycobilisome-related energy dissipation in cyanobacteria". Plant Cell 18 (4): 992–1007. doi:10.1105/tpc.105.040121. PMC 1425857. PMID 16531492. 
  4. ^ Kerfeld CA (2004). "Structure and function of the water-soluble carotenoid-binding proteins of cyanobacteria". Photosyn. Res. 81 (3): 215–25. doi:10.1023/B:PRES.0000036886.60187.c8. PMID 16034528. 

This article incorporates text from the public domain Pfam and InterPro IPR015233

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Orange carotenoid protein, N-terminal Provide feedback

Members of this family adopt an alpha-helical structure consisting of two four-helix bundles. They are predominantly found in prokaryotic orange carotenoid protein, and carotenoid binding proteins [1].

Literature references

  1. Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO; , Structure. 2003;11:55-65.: The crystal structure of a cyanobacterial water-soluble carotenoid binding protein. PUBMED:12517340 EPMC:12517340


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015233

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. Orange carotenoid-binding proteins (OCP) were first identified in cyanobacterial species, where they occur associated with phycobilisome in the cellular thylakoid membrane. These proteins function in photoprotection, and are essential for inhibiting white and blue-green light non-photochemical quenching (NPQ) [PUBMED:17307930, PUBMED:16531492]. Carotenoids improve the photoprotectant activity by broadening OCP's absorption spectrum and facilitating the dissipation of absorbed energy. OCP acts as a homodimer, and binds one molecule of carotenoid (3'-hydroxyechinenone) and one chloride ion per subunit, where the carotenoid binding site is lined with a striking number of methionine residues. The carotenoid 3'-hydroxyechinenone is not found in higher plants. OCP has two domains: an N-terminal helical domain and a C-terminal domain that resembles a NTF2 (nuclear transport factor 2) domain. OCP can be proteolytically cleaved into a red form (RCP), which lacks 15 residues from the N terminus and approximately 150 residues from the C terminus [PUBMED:16034528].

This entry represents the N-terminal domain found predominantly in prokaryotic orange carotenoid proteins and related carotenoid-binding proteins. It adopts an alpha-helical structure consisting of two four-helix bundles [PUBMED:12517340].

Gene Ontology

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Domain organisation

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Alignments

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(8)
Full
(95)
Representative proteomes NCBI
(100)
Meta
(4)
RP15
(5)
RP35
(27)
RP55
(42)
RP75
(43)
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  Seed
(8)
Full
(95)
Representative proteomes NCBI
(100)
Meta
(4)
RP15
(5)
RP35
(27)
RP55
(42)
RP75
(43)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

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Curation View help on the curation process

Seed source: pdb_1m98
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 8
Number in full: 95
Average length of the domain: 155.00 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 65.57 %

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 25.0 25.0
Trusted cut-off 64.6 64.6
Noise cut-off 23.4 19.8
Model length: 159
Family (HMM) version: 5
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Species distribution

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Interactions

There are 2 interactions for this family. More...

NTF2 Carot_N

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 Carot_N domain has been found. There are 8 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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