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33  structures 422  species 0  interactions 2672  sequences 22  architectures

Family: Chloroa_b-bind (PF00504)

Summary: Chlorophyll A-B binding protein

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This is the Wikipedia entry entitled "Light-harvesting complexes of green plants". More...

Light-harvesting complexes of green plants Edit Wikipedia article

2bhw.gif
Light-Harvesting Complex II
Identifiers
Symbol Chloroa_b-bind
Pfam PF00504
InterPro IPR001344
SCOP 1rwt
SUPERFAMILY 1rwt
OPM superfamily 1
OPM protein 1rwt

The light-harvesting (or antenna) complex of plants is an array of protein and chlorophyll molecules embedded in the thylakoid membrane which transfer light energy to one chlorophyll a molecule at the reaction center of a photosystem.

The antenna pigments are predominantly chlorophyll b, xanthophylls, and carotenoids. Chlorophyll a is known as the core pigment. Their absorption spectra are non-overlapping in order to broaden the range of light that can be absorbed in photosynthesis. The carotenoids have another role as an antioxidant to prevent photo-oxidative damage of chlorophyll molecules. Each antenna complex has between 250 and 400 pigment molecules and the energy they absorb is shuttled by resonance energy transfer to a specialized chlorophyll-protein complex known as the reaction center of each photosystem[citation needed]. The reaction center initiates a complex series of chemical reactions that capture energy in the form of chemical bonds.

For photosystem II, when either of the two chlorophyll a molecules at the reaction center absorb energy, an electron is excited and transferred to an electron acceptor molecule, phaeophytin, leaving the chlorophyll a in an oxidized state. The oxidised chlorophyll a replaces the electrons by photolysis that involves the reduction of water molecules to oxygen, protons and electrons.

Under changing light conditions, the reversible phosphorylation of light harvesting chlorophyll a/b binding proteins (LHCII) represents a system for balancing the excitation energy between the two photosystems.[1]

The N-terminus of the chlorophyll A-B binding protein extends into the stroma where it is involved with adhesion of granal membranes and photo-regulated by reversible phosphorylation of its threonine residues.[2] Both these processes are believed to mediate the distribution of excitation energy between photosystems I and II.

This family also includes the photosystem II protein PsbS, which plays a role in energy-dependent quenching that increases thermal dissipation of excess absorbed light energy in the photosystem.[3]

References[edit]

  1. ^ Liu XD, Shen YG (2004). "NaCl-induced phosphorylation of light harvesting chlorophyll a/b proteins in thylakoid membranes from the halotolerant green alga, Dunaliella salina". FEBS Lett. 569 (1–3): 337–340. doi:10.1016/j.febslet.2004.05.065. PMID 15225658. 
  2. ^ Andersson B, Yang DH, Paulsen H (2000). "The N-terminal domain of the light-harvesting chlorophyll a/b-binding protein complex (LHCII) is essential for its acclimative proteolysis". FEBS Lett. 466 (2–3): 385–388. doi:10.1016/S0014-5793(00)01107-8. PMID 10682866. 
  3. ^ Kramer D, Bassi R, Li XP, Gilmore AM, Caffarri S, Golan T, Niyogi KK (2004). "Regulation of photosynthetic light harvesting involves intrathylakoid lumen pH sensing by the PsbS protein". J. Biol. Chem. 279 (22): 22866–22874. doi:10.1074/jbc.M402461200. PMID 15033974. 

See also[edit]

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.

Chlorophyll A-B binding protein Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022796

The light-harvesting complex (LHC) consists of chlorophylls A and B and the chlorophyll A-B binding protein. LHC functions as a light receptor that captures and delivers excitation energy to photosystems I and II with which it is closely associated. Under changing light conditions, the reversible phosphorylation of light harvesting chlorophyll a/b binding proteins (LHCII) represents a system for balancing the excitation energy between the two photosystems [PUBMED:15225658].

The N terminus of the chlorophyll A-B binding protein extends into the stroma where it is involved with adhesion of granal membranes and photo-regulated by reversible phosphorylation of its threonine residues [PUBMED:10682866]. Both these processes are believed to mediate the distribution of excitation energy between photosystems I and II.

This family also includes the photosystem II protein PsbS, which plays a role in energy-dependent quenching that increases thermal dissipation of excess absorbed light energy in the photosystem [PUBMED:15033974].

Domain organisation

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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
(157)
Full
(2672)
Representative proteomes NCBI
(2617)
Meta
(772)
RP15
(418)
RP35
(719)
RP55
(840)
RP75
(911)
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  Seed
(157)
Full
(2672)
Representative proteomes NCBI
(2617)
Meta
(772)
RP15
(418)
RP35
(719)
RP55
(840)
RP75
(911)
Alignment:
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  Seed
(157)
Full
(2672)
Representative proteomes NCBI
(2617)
Meta
(772)
RP15
(418)
RP35
(719)
RP55
(840)
RP75
(911)
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_54 (release 1.0) & Pfam-B_5772 (Release 7.5)
Previous IDs: chloroa_b-bind;
Type: Family
Author: Finn RD, Bateman A
Number in seed: 157
Number in full: 2672
Average length of the domain: 131.40 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 66.18 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 156
Family (HMM) version: 16
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 Chloroa_b-bind domain has been found. There are 33 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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