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Chlorophyllase Edit Wikipedia article
||This article is written like a personal reflection or opinion essay rather than an encyclopedic description of the subject. (July 2008)|
||This article's tone or style may not reflect the encyclopedic tone used on Wikipedia. (July 2008)|
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Chlorophyllase (klawr-uh-fil-eys) is the key enzyme in chlorophyll metabolism. It is a membrane protein that is commonly known as Chlase (EC 126.96.36.199, CLH) and systematically known as chlorophyll chlorophyllidohydrolase. Chlorophyllase can be found in the chloroplast, thylakoid membrane and etioplast of at least higher plants such as ferns, mosses, brown and red algae and diatoms. Chlase is the catalyst for the hydrolysis of chlorophyll to produce chlorophyllide (also called Chlide) and phytol. It is also known to function in the esterification of Chlide and transesterification. The enzyme functions optimally at pH 8.5 and 50°C. 
Role of chlorophyllase in chlorophyll breakdown
Of high importance to all photogenic organisms is chlorophyll, and so, its synthesis and breakdown are closely regulated throughout the entire life cycle of the plant. Chlorophyll breakdown is most evident in seasonal changes as the plants lose their green color in the autumn; it is also evident in fruit ripening, leaf senescence and flowering. In this first step, chlorophyllase initiates the catabolism of chlorophyll to from chlorophyllide. Chlorophyll degradation occurs in the turnover of chlorophyll, as well as in the event of cell death caused by injuries, pathogenic attack, and other external factors.
Chlorophyllase’s role is two-fold as it functions in both de-greening processes, such as autumnal coloration, and is also thought to be involved in turnover and homeostasis of chlorophylls. Chlorophyllase catalysis of the initial step of chlorophyll breakdown is important for plant development and survival. The breakdown serves as a prerequisite in the detoxification of the potentially phototoxic chlorophyll and chlorophyll intermediates as it accompanies leaf senescence to non-fluorescent catabolites. Rapid degradation of chlorophyll and its intermediates is therefore necessary to prevent cell damage due to the potential phototoxicity of chlorophyll. 
Reaction and mechanism catalyzed by chlorophyllase
Chlorophyllase catalyzes the hydrolysis of ester bond to yield chlorophyllide and phytol. It reacts via tranesterification or hydrolysis of a carboxylic ester in which its natural substrates are 13-OH-chlorophyll a, bacteriochlorophyll and chlorophyll a.
Hydrolysis of chlorophyll starts with the attack of a carbonyl group of chlorophyll by the oxygen of the hydroxyl group of the crucial serine residue of the chlorophyllase. This attack forms a tetrahedral transition state. The double bond of the attacked carbonyl reforms and the serine is then esterified to chlorophyllide. The phytol group consequently leaves the compound and replaces the serine residue on the chlorophyllase enzyme. The addition of water to the reaction cleaves the phytol off the enzyme. Next, through the reverse reaction, the oxygen on the hydroxy group from the water in the previous step attacks the carbonyl of the intermediate in order to form another tetrahedral transition state. The double bond of the carbonyl forms again and the serine residue returns to chlorophyllase and the ester of the chlorophyll is now a carboxylic acid. This product is chlorophyllide. 
Chlorophyllide is then broken down to Pheophorbide A. After Pheophorbide a is formed, the poryphin ring is cleaved by Pheophorbide an oxide to form RCC causing the plant to lose its green color. RCC is then broken down into pFCC.
Citrus sinesis and Chenopodium album were the first plants from which the genes encoding chlorophyllase were isolated. These experiments revealed an uncharacteristic encoded sequence (21 amino acids in Citrus sinensis and 30 amino acids in Chenopodium album) located on the N-terminal that was absent from the mature protein. The chlorophyllase enzyme is a smart choice as the rate limiting enzyme of the catabolic pathway since degreening and the expression of chlorophyllase is induced in ethylene-treated Citrus. Recent data, however, suggests that chlorophyllase is expressed at low levels during natural fruit development, when chlorophyll catabolism usually takes place. Also, some data suggests that chlorophyllase activity is not consistent with degreening during natural senescence. Finally, there is evidence that chlorophyllase has been found in the inner envelope membrane of chloroplast where it does not come in contact with chlorophyll. Recent studies inspired by inconsistent data revealed that chlorophyllase in Citrus lacking the 21 amino sequence on the N-terminal results in extensive chlorophyll breakdown and the degreening effect that should occur in vivo. This cleavage occurs in the chloroplast membrane fraction. Both the full chlorophyllase and the cleaved, mature chlorophyllase, however, experienced similar levels of activity in an in vitro assay. This data suggests that the mature protein comes in contact with its substrate more readily because of the N-terminal sequence and some natural regulation occurs that directly affects enzyme activity. Another possibility is that the suborganelle compartments breaking down allowing a greater amount of enzyme activity. 
Other forms of regulation
Chlorophyllide, the product of the reaction catalyzed by chlorophyllase, spontaneously combines with plant lipids such as phophatidylcholine liposomes along with aulphoquinovosyldiacylglycerol. These two lipids cooperatively inhibit the activity of chlorophyllase, but this inhibition can be reversed by the presence of Mg++, a divalent cation.  The activity of chlorophyllase also depends on the pH and ionic content of the medium. The values of kcat and kcat/km of chlorophyllase in the presence of chlorophyll showed pKa values of 6.3 and 6.7, respectively. Temperature also affects chlorophyllase activity. Wheat chlorophyllase is active from 25 to 75 °C. The enzyme is inactivated at temperatures above 85 °C. Wheat chlorophyllase is stable 20 °C higher than other chlorophyllases. These other chlorophyllases can stay active at temperatures up to 55 °C. 
Ethylene induces the synthesis of chlorophyllase and promotes the degreening of citrus fruits. Chlorophyllase was detected in protein extracts of ethylene treated fruit. Ethylene treated fruits had chlorophyllase activity increased by 5 fold in 24 hours. Ethylene, more specifically, induces increased rates of transcription of the chlorophyllase gene.
There is also evidence of a highly conserved serine lipase domain in the chlorophyllase enzyme that contains a serine residue that is essential for enzyme activity. Histidne and aspartic acid residues are also a part of the catalytic triad of chlorophyllase as a serine hydrolase. Specific inhibitors for the serine hydrolase mechanism, therefore, effectively inhibit the chlorophyllase enzyme. Also, mutations at these specific amino acid residues causes complete loss of function since the mutations change the catalytic site of the chlorophyllase enzyme. 
References and Further Reading
- chlorophyllase - Definitions from Dictionary.com
- Yi Y, Kermasha S, Neufeld R (December 2006). "Characterization of sol-gel entrapped chlorophyllase". Biotechnol. Bioeng. 95 (5): 840–9. doi:10.1002/bit.21027. PMID 16804946.
- Hornero-Méndez D, Mínguez-Mosquera MI (2001). "Properties of chlorophyllase from Capsicum annuum L. fruits". Z. Naturforsch., C, J. Biosci. 56 (11–12): 1015–21. PMID 11837653.
- Tsuchiya T, Ohta H, Okawa K, et al. (December 1999). "Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: Finding of a lipase motif and the induction by methyl jasmonate". Proc. Natl. Acad. Sci. U.S.A. 96 (26): 15362–7. doi:10.1073/pnas.96.26.15362. PMC 24824. PMID 10611389.
- Hörtensteiner S (October 1999). "Chlorophyll breakdown in higher plants and algae". Cell. Mol. Life Sci. 56 (3–4): 330–47. doi:10.1007/s000180050434. PMID 11212360.
- Okazawa A, Tango L, Itoh Y, Fukusaki E, Kobayashi A (2006). "Characterization and subcellular localization of chlorophyllase from Ginkgo biloba". Z. Naturforsch., C, J. Biosci. 61 (1–2): 111–7. PMID 16610227.
- Fang Z, Bouwkamp J, Solomos T (1998). "Chlorophyllase activities and chlorophyll degradation during leaf senescence in non-yellowing mutant and wild type of Phaseolus vulgaris L.". J. Exp. Bot. 49 (320): 503–10. doi:10.1093/jexbot/49.320.503.
- Tsuchiya T, Suzuki T, Yamada T, et al. (January 2003). "Chlorophyllase as a serine hydrolase: identification of a putative catalytic triad". Plant Cell Physiol. 44 (1): 96–101. doi:10.1093/pcp/pcg011. PMID 12552153.
- Harpaz-Saad S, Azoulay T, Arazi T, et al. (March 2007). "Chlorophyllase Is a Rate-Limiting Enzyme in Chlorophyll Catabolism and Is Posttranslationally Regulated". Plant Cell 19 (3): 1007–22. doi:10.1105/tpc.107.050633. PMC 1867358. PMID 17369368.
- Lambers JW, Terpstra W (October 1985). "Inactivation of chlorophyllase by negatively charged plant membrane lipids". Biochim. Biophys. Acta 831 (2): 225–35. doi:10.1016/0167-4838(85)90039-1. PMID 4041468.
- Arkus KA, Cahoon EB, Jez JM (June 2005). "Mechanistic analysis of wheat chlorophyllase". Arch. Biochem. Biophys. 438 (2): 146–55. doi:10.1016/j.abb.2005.04.019. PMID 15913540.
- Trebitsh T, Goldschmidt EE, Riov J (October 1993). "Ethylene induces de novo synthesis of chlorophyllase, a chlorophyll degrading enzyme, in Citrus fruit peel". Proc. Natl. Acad. Sci. U.S.A. 90 (20): 9441–5. doi:10.1073/pnas.90.20.9441. PMC 47584. PMID 11607429.
- Jacob-Wilk D, Holland D, Goldschmidt EE, Riov J, Eyal Y (December 1999). "Chlorophyll breakdown by chlorophyllase: isolation and functional expression of the Chlase1 gene from ethylene-treated Citrus fruit and its regulation during development". Plant J. 20 (6): 653–61. doi:10.1046/j.1365-313X.1999.00637.x. PMID 10652137.
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.
Chlorophyllase Provide feedback
This family consists of several plant specific Chlorophyllase proteins ( EC:188.8.131.52). Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of ester bond to yield chlorophyllide and phytol .
Tsuchiya T, Ohta H, Okawa K, Iwamatsu A, Shimada H, Masuda T, Takamiya K; , Proc Natl Acad Sci U S A 1999;96:15362-15367.: Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. PUBMED:10611389 EPMC:10611389
Tsuchiya T, Suzuki T, Yamada T, Shimada H, Masuda T, Ohta H, Takamiya K; , Plant Cell Physiol 2003;44:96-101.: Chlorophyllase as a serine hydrolase: identification of a putative catalytic triad. PUBMED:12552153 EPMC:12552153
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR010821
This family consists of several chlorophyllase proteins (EC). Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll degradation and catalyses the hydrolysis of the ester bond to yield chlorophyllide and phytol [PUBMED:10611389, PUBMED:15598807, PUBMED:17369368].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||chlorophyllase activity (GO:0047746)|
|Biological process||chlorophyll catabolic process (GO:0015996)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
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This catalytic domain is found in a very wide range of enzymes.
The clan contains the following 67 members:Abhydro_lipase Abhydrolase_1 Abhydrolase_2 Abhydrolase_3 Abhydrolase_4 Abhydrolase_5 Abhydrolase_6 Abhydrolase_7 Abhydrolase_8 Acyl_transf_2 Arb2 AXE1 BAAT_C Chlorophyllase Chlorophyllase2 COesterase Cutinase DLH DUF1057 DUF1100 DUF1350 DUF1400 DUF1749 DUF2048 DUF2235 DUF2305 DUF2424 DUF2920 DUF2974 DUF3089 DUF3141 DUF3530 DUF452 DUF676 DUF726 DUF818 DUF829 DUF900 DUF915 EHN Esterase Esterase_phd FSH1 Hydrolase_4 LCAT LIP Lipase Lipase_2 Lipase_3 Ndr PAF-AH_p_II Palm_thioest PE-PPE Peptidase_S10 Peptidase_S15 Peptidase_S28 Peptidase_S37 Peptidase_S9 PGAP1 PhaC_N PHB_depo_C PhoPQ_related Ser_hydrolase Tannase Thioesterase UPF0227 VirJ
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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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You can see the alignments as HTML or in three different sequence viewers:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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.
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...
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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.
|Seed source:||Pfam-B_17130 (release 10.0)|
|Number in seed:||4|
|Number in full:||48|
|Average length of the domain:||233.40 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||75.56 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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