Summary: Allinase

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Wikipedia: Alliinase
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Alliinase Edit Wikipedia article

alliin lyase

Identifiers

Databases

PDB structures

AmiGO / EGO

Search
PMC	articles
PubMed	articles
NCBI	proteins

Alliinase_C

crystal structure of alliinase from garlic- apo form

Identifiers

Symbol

Alliinase_C

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Alliinase EGF-like domain

crystal structure of alliinase from garlic- apo form

Identifiers

Symbol

EGF_alliinase

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

In enzymology, an alliin lyase (EC 4.4.1.4) is an enzyme that catalyzes the chemical reaction

an S-alkyl-L-cysteine S-oxide $\rightleftharpoons$ an alkyl sulfenate + 2-aminoacrylate

Hence, this enzyme has one substrate, S-alkyl-L-cysteine S-oxide, and two products, alkyl sulfenate and 2-aminoacrylate.

This enzyme belongs to the family of lyases, specifically the class of carbon-sulfur lyases. The systematic name of this enzyme class is S-alkyl-L-cysteine S-oxide alkyl-sulfenate-lyase (2-aminoacrylate-forming). Other names in common use include alliinase, cysteine sulfoxide lyase, alkylcysteine sulfoxide lyase, S-alkylcysteine sulfoxide lyase, L-cysteine sulfoxide lyase, S-alkyl-L-cysteine sulfoxide lyase, and alliin alkyl-sulfenate-lyase. It employs one cofactor, pyridoxal phosphate.

Many alliinases contain a novel N-terminal epidermal growth factor-like domain (EGF-like domain).^[1]

[edit] Occurrence

These enzymes are found in plants of the genus Allium, such as garlic and onions. Alliinase is responsible for catalyzing chemical reactions that produce the volatile chemicals that give these foods their flavors, odors, and tear-inducing properties. Alliinases are part of the plant's defense against herbivores. Alliinase is normally sequestered within a plant cell, but, when the plant is damaged by a feeding animal, the alliinase is released to catalyze the production of the pungent chemicals. This tends to have a deterrent effect on the animal. The same reaction occurs when onion or garlic is cut with a knife in the kitchen.

[edit] Chemistry

In garlic, an alliinase enzyme acts on the chemical alliin converting it into allicin. The process involves two stages: elimination of 2-propenesulfenic acid from the amino acid unit (with Î±-aminoacrylic acid as a byproduct), and then condensation of two of the sulfenic acid molecules.

Reaction scheme for the conversion: cysteine â†’ alliin â†’ allicin

Alliin and related substrates found in nature are chiral at the sulfoxide position (usually having the S absolute configuration, and alliin itself was the first natural product found to have both carbon- and sulfur-centered stereochemistry.^[2] However, the sulfenic acid intermediate is not chiral, and the final product's stereochemistry is not controlled.

There are a range of similar enzymes that can react with the cysteine-derived sulfoxides present in different species. In onions, an isomer of alliin, isoalliin, is converted to 1-propenesulfenic acid. A separate enzyme, the lachrymatory factor synthase or LFS, then converts this chemical to syn-propanethial-S-oxide, a potent lachrymator. The analogous butyl compound, syn-butanethial-S-oxide, is found in Allium siculum species.^[3]

[edit] Structural studies

As of late 2007, 3 structures have been solved for this class of enzymes, using X-ray crystallography. The PDB accession codes are 1LK9, 2HOR, and 2HOX.

[edit] References

^ Kuettner EB, Hilgenfeld R, Weiss MS (November 2002). "The active principle of garlic at atomic resolution". J. Biol. Chem. 277 (48): 46402â7. doi:10.1074/jbc.M208669200. PMID 12235163.
^ Block, Eric (2009). Garlic and Other Alliums: The Lore and the Science. Cambridge, Eng: Royal Society of Chemistry. pp. 100â106. ISBN 0-85404-190-7.
^ Kubec R, Cody RB, Dane AJ, Musah RA, Schraml J, Vattekkatte A, Block E (2010). "Applications of Direct Analysis in Real TimeâMass Spectrometry (DART-MS) in Allium Chemistry. (Z)-Butanethial S-Oxide and 1-Butenyl Thiosulfinates and their S-(E)-1-Butenylcysteine S-Oxide Precursor from Allium siculum". Journal of Agricultural and Food Chemistry 58 (2): 1121â1128. doi:10.1021/jf903733e. PMID 20047275.

[edit] Bibliography

Durbin RD and Uchytil TF (1971). "Purification and properties of alliin lyase from the fungus Penicillium corymbiferum". Biochim. Biophys. Acta â Enzymology 235 (3): 518â520. doi:10.1016/0005-2744(71)90293-2.
Goryachenkova, E. V. (1952). "Ð¤ÐµÑÐ¼ÐµÐ½Ñ Ð² ÑÐµÑÐ½Ð¾ÐºÐµ, ÐºÐ¾ÑÐ¾ÑÑÐ¹ ÑÐ¾ÑÐ¼Ð¸ÑÑÐµÑ allycine (allyinase), Ð±ÐµÐ»Ð¾Ðº Ñ phosphopyridoxal" [Enzyme in garlic which forms allycine (allyinase), a protein with phosphopyridoxal]. Doklady Akademii Nauk SSSR (in Russian) 87: 457â460.
Jacobsen JV, Yamaguchi M, Howard FD and Bernhard RA (1968). "Product inhibition of the cysteine sulfoxide lyase of tulbaghia violacea". Arch. Biochem. Biophys. 127: 252â258. doi:10.1016/0003-9861(68)90223-3.

[edit] External links

Genuine Garlic:Alliinase from Allium sativum.

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.

Allinase Provide feedback

Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulfoxide cysteine derivatives by alliinase ( EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system.

Literature references

Kuettner EB, Hilgenfeld R, Weiss MS; , J Biol Chem 2002;0:0-0.: The active principle of garlic at atomic resolution. PUBMED:12235163 EPMC:12235163

Internal database links

Similarity to PfamA using HHSearch:

Aminotran_1_2

External database links

PANDIT:	PF04864
Pseudofam:	PF04864
SCOP:	1lk9
SYSTERS:	Alliinase_C

This tab holds annotation information from the InterPro database.

InterPro entry IPR006948

Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system [PUBMED:12235163].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function

carbon-sulfur lyase activity (GO:0016846)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PLP_aminotran (CL0061), which contains the following 15 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SHMT SLA_LP_auto_ag

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...

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.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

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 (10)	Full (180)	Representative proteomes				NCBI (718)	Meta (304)
	Seed (10)	Full (180)	RP15 (14)	RP35 (57)	RP55 (67)	RP75 (77)	NCBI (718)	Meta (304)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (10)	Full (180)	Representative proteomes				NCBI (718)	Meta (304)
	Seed (10)	Full (180)	RP15 (14)	RP35 (57)	RP55 (67)	RP75 (77)	NCBI (718)	Meta (304)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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 (10)	Full (180)	Representative proteomes				NCBI (718)	Meta (304)
	Seed (10)	Full (180)	RP15 (14)	RP35 (57)	RP55 (67)	RP75 (77)	NCBI (718)	Meta (304)
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.

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

Seed source:

Pfam-B_4527 (release 7.6)

Previous IDs:

none

Type:

Domain

Author:

Mifsud W

Number in seed:

10

Number in full:

180

Average length of the domain:

318.40 aa

Average identity of full alignment:

46 %

Average coverage of the sequence by the domain:

79.58 %

HMM information

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	22.0	22.0
Trusted cut-off	22.0	22.0
Noise cut-off	21.9	21.9

Model length:

363

Family (HMM) version:

8

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. 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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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".

Sub-species

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.

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

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.

Interactive tree

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.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
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Interactions

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

EGF_alliinase Alliinase_C

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 Alliinase_C domain has been found. There are 19 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Alliinase_C (PF04864)

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Summary: Allinase

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Alliinase Edit Wikipedia article

Contents

[edit] Occurrence

[edit] Chemistry

[edit] Structural studies

[edit] References

[edit] Bibliography

[edit] External links

Allinase Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR006948

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures