Summary: Isocitrate lyase family

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Isocitrate lyase Edit Wikipedia article

Isocitrate Lyase

Homotetrameric structure of Isocitrate lyase from E. coli. Based on PDB 1IGW.^[1]

Identifiers

Databases

PDB structures

AmiGO / EGO

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PubMed	articles
NCBI	proteins

Isocitrate lyase family

Identifiers

Symbol

ICL

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

Isocitrate lyase (EC 4.1.3.1), or ICL, is an enzyme in the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate.^[2]^[3] Together with malate synthase, it bypasses the two decarboxylation steps of the tricarboxylic acid cycle (TCA cycle) and is used by bacteria, fungi, and plants.^[4]

The systematic name of this enzyme class is isocitrate glyoxylate-lyase (succinate-forming). Other names in common use include isocitrase, isocitritase, isocitratase, threo-Ds-isocitrate glyoxylate-lyase, and isocitrate glyoxylate-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism.

[edit] Mechanism

This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. Other enzymes also belong to this family including carboxyvinyl-carboxyphosphonate phosphorylmutase (EC 2.7.8.23) which catalyses the conversion of 1-carboxyvinyl carboxyphosphonate to 3-(hydrohydroxyphosphoryl) pyruvate carbon dioxide, and phosphoenolpyruvate mutase (EC 5.4.2.9), which is involved in the biosynthesis of phosphinothricin tripeptide antibiotics.

During catalysis, isocitrate is deprotonated, and an aldol cleavage results in the release of succinate and glyoxylate. This reaction mechanism functions much like that of aldolase in glycolysis, where a carbon-carbon bond is cleaved and an aldehyde is released.^[5]

In the glyoxylate cycle, malate synthase then catalyzes the condensation of glyoxylate and acetyl-CoA to form malate so the cycle can continue.

ICL competes with isocitrate dehydrogenase, an enzyme found in the TCA cycle, for isocitrate processing. Flux through these enzymes is controlled by phosphorylation of isocitrate dehydrogenase, which has a much higher affinity for isocitrate as compared to ICL.^[6] Deactivation of isocitrate dehydrogenase by phosphorylation thus leads to increased isocitrate channeling through ICL, as seen when bacteria are grown on acetate, a two-carbon compound.^[6]

[edit] Enzyme Structure

As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1DQU, 1F61, 1F8I, 1F8M, and 1IGW.

ICL is composed of four identical chains and requires a Mg²⁺ or Mn²⁺ and a thiol for activity.^[4] In Escherichia coli, Lys-193, Lys-194, Cys-195, His-197, and His-356 are thought to be catalytic residues, while His-184 is thought to be involved in the assembly of the tetrameric enzyme.^[7]

Between prokaryotes and eukaryotes, a difference in ICL structure is the addition of approximately 100 amino acids near the center of the eukaryotic enzyme. In eukaryotes, the additional amino acids are thought to function in the localization of ICL to single-membrane-bound organelles called glyoxysomes.^[4]^[8] These additional amino acids account for the difference in molecular mass: the prokaryotic ICL is 48kDa, while the eukaryotic ICL is 67 kDa.^[4] Only one cysteine residue is conserved between the sequences of the fungal, plant and bacterial enzymes; it is located in the middle of a conserved hexapeptide.

[edit] Biological Function

The ICL enzyme has been found to be functional in various archaea, bacteria, protists, plants, fungi, and nematodes.^[9] Although the gene has been found in genomes of nematodes and cnidaria, it has not been found in the genomes of placental mammals.^[9]

By diverting isocitrate from the TCA cycle, the actions of ICL and malate synthase in the glyoxylate cycle result in the net assimilation of carbon from 2-carbon compounds.^[10] Thus, while the TCA cycle yields no net carbon assimilation, the glyoxylate cycle generates intermediates that can be used to synthesize glucose (via gluconeogenesis), and other biosynthetic products. As a result, organisms that use ICL and malate synthase are able to synthesize glucose and metabolic intermediates from acetyl-CoA derived from acetate or from the degradation of ethanol, fatty acids or poly-Î²-hydroxybutyrate.^[4]

This function is especially important for higher plants which use oilseeds. In these germinating seeds, the breakdown of oils generates acetyl-CoA. This serves as a substrate for the glyoxylate cycle, which generates other cyclic intermediates and serves as a primary nutrient source prior to the production of sugars from photosynthesis.^[8]

[edit] Disease Relevance

ICL has found to be important in human, animal, and plant pathogenesis.^[4] For several agricultural crops including cereals, cucumbers, and melons, increased expression of the gene encoding ICL is important for fungal virulence.^[4] For instance, increased gene expression of icl1 has been seen in the fungus Leptosphaeria maculans upon infection of canola. Inactivation of the icl1 gene leads to reduced pathogenicity of the fungus, which is thought to be a result of the inability of the fungus to use carbon sources provided by the plant.^[11]

Additionally, upregulation of the glyoxylate cycle has been seen for pathogens that attack humans. This is the case for fungi such as Candida albicans, which inhabits the skin, mouth, GI tract, gut and vagina of mammals and can lead to systemic infections of immunocompromised patients; as well as for the bacterium Mycobacterium tuberculosis, the major causative agent of tuberculosis.^[12]^[13] In this latter case, ICL has been found to be essential for survival in the host.^[14]

Because of its use by pathogenic fungi and bacteria, specific inhibitors are being sought for ICL and malate synthase.^[4] Although some inhibitors have already been identified, including itaconate, itaconic anhydride, bromopyruvate, nitropropionate, oxalate and malate, these are non-specific and would also inhibit other enzymes essential for host function.^[4] More research is needed to identify inhibitors that selectively target enzymes in the glyoxylate cycle.

[edit] See also

[edit] References

^ Britton, KL; Abeysinghe IS, Baker PJ, Barynin V, Diehl P, Langridge SJ, McFadden BA, Sedelnikova SE, Stillman TJ, Weeradechapon K, Rice DW (Sep 2001). "The structure and domain organization of Escherichia coli isocitrate lyase". Acta Crystallogr D 57 (9): 1209â1218. doi:10.1107/S0907444901008642. PMID 11526312.
^ Beeching JR (1989). "High sequence conservation between isocitrate lyase from Escherichia coli and Ricinus communis". Protein Seq. Data Anal. 2 (6): 463â466. PMID 2696959.
^ Tanaka A, Atomi H, Ueda M, Hikida M, Hishida T, Teranishi Y (1990). "Peroxisomal isocitrate lyase of the n-alkane-assimilating yeast Candida tropicalis: gene analysis and characterization". J. Biochem. 107 (2): 262â266. PMID 2361956.
^ ^a ^b ^c ^d ^e ^f ^g ^h ⁱ Dunn, MF; Ramirez-Trujill JA, Hernandez-Lucas I (Oct 2009). "Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis". Microbiology 155 (10): 3166â3175. doi:10.1099/mic.0.030858-0. PMID 19684068.
^ Garrett R and Grisham CN (2008). Biochemistry. Brooks Cole. pp. 588. ISBN 978-0-495-10935-8.
^ ^a ^b Cozzone, AJ (1998). "Regulation of acetate metabolism by protein phosphorylation in enteric bacteria". Annu. Rev. Microbiol. 52: 127â164. doi:10.1146/annurev.micro.52.1.127. PMID 9891796.
^ Rehman, A; McFadden BA (Jul 1997). "Lysine 194 is functional in isocitrate lyase from Escherichia coli". Curr. Microbiol. 35 (1): 14â17. doi:10.1007/s002849900203. PMID 9175553.
^ ^a ^b Eastmond, PJ; Graham IA (Feb 2001). "Re-examining the role of the glyoxylate cycle in oilseeds". Trends Plant Sci 6 (2): 72â78. doi:10.1016/S1360-1385(00)01835-5. PMID 11173291.
^ ^a ^b Kondrashov, FA; Koonin EV, Morgunov IG, Finogenova TV, Kondrashova MN (23). "Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation". Biol Direct 1 (31): 31. doi:10.1186/1745-6150-1-31. PMC 1630690. PMID 17059607. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1630690/.
^ Kornberg, HL; Krebs HA (18). "Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle". Nature 179 (4568): 988â991. doi:10.1038/179988a0. PMID 13430766.
^ Idnurm, A; Howlett BJ (Oct 2002). "Isocitrate lyase is essential for pathogenicity of the fungus Leptosphaeria maculans to canola (Brassica napus)". Eukaryot Cell 1 (5): 719â724. doi:10.1128/EC.1.5.719-724.2002. PMC 126752. PMID 12455691. //www.ncbi.nlm.nih.gov/pmc/articles/PMC126752/.
^ Lorenz, MC; Bender JA (Oct 2004). "Fink GR". Eukaryot Cell 3 (5): 1076â1087. doi:10.1128/EC.3.5.1076-1087.2004. PMC 522606. PMID 15470236. //www.ncbi.nlm.nih.gov/pmc/articles/PMC522606/.
^ Srivastava, V; Jain A, Srivastava BS, Srivastava R (May 2008). "Selection of genes of Mycobacterium tuberculosis upregulated during residence in lungs of infected mice". Tuberculosis (Edinb) 88 (3): 171â177. doi:10.1016/j.tube.2007.10.002. PMID 18054522.
^ MuÃ±oz-ElÃas, EJ; McKinney JD (Jun 2005). "Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence". Nat Med 11 (6): 638â644. doi:10.1038/nm1252. PMC 1464426. PMID 15895072. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1464426/.

[edit] Further reading

McFadden BA and Howes WV (1963). "Crystallisation and some properties of isocitrate lyase from Pseudomonas indigofera". J. Biol. Chem. 238: 1737â1742.
Shiio I, Shiio T and McFadden BA (1965). "Isocitrate lyase from Pseudomonas indigofera. I. Preparation, amino acid composition and molecular weight". Biochim. Biophys. Acta 96: 114â22. PMID 14285253.
VICKERY HB (1962). "A suggested new nomenclature for the isomers of isocitric acid". J. Biol. Chem. 237: 1739â41. PMID 13925783.

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Isocitrate lyase family Edit Wikipedia article

Isocitrate lyase family

Identifiers

Symbol

ICL

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

Isocitrate lyase family is a family of evolutionarily related proteins.

Isocitrate lyase (EC 4.1.3.1)^[1]^[2] is an enzyme that catalyzes the conversion of isocitrate to succinate and glyoxylate. This is the first step in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. A cysteine, a histidine and a glutamate or aspartate have been found to be important for the enzyme's catalytic activity. Only one cysteine residue is conserved between the sequences of the fungal, plant and bacterial enzymes; it is located in the middle of a conserved hexapeptide.

Other enzymes also belong to this family including carboxyvinyl-carboxyphosphonate phosphorylmutase (EC 2.7.8.23) which catalyses the conversion of 1-carboxyvinyl carboxyphosphonate to 3-(hydrohydroxyphosphoryl) pyruvate carbon dioxide, and phosphoenolpyruvate mutase (EC 5.4.2.9), which is involved in the biosynthesis of phosphinothricin tripeptide antiobiotics.

[edit] Subfamilies

[edit] References

^ Beeching JR (1989). "High sequence conservation between isocitrate lyase from Escherichia coli and Ricinus communis". Protein Seq. Data Anal. 2 (6): 463466. PMID 2696959.
^ Tanaka A, Atomi H, Ueda M, Hikida M, Hishida T, Teranishi Y (1990). "Peroxisomal isocitrate lyase of the n-alkane-assimilating yeast Candida tropicalis: gene analysis and characterization". J. Biochem. 107 (2): 262266. PMID 2361956.

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This article incorporates text from the public domain Pfam and InterPro IPR000918

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Internal database links

Similarity to PfamA using HHSearch:

PEP_mutase

External database links

HOMSTRAD:	ICL
PANDIT:	PF00463
PROSITE:	PDOC00145
Pseudofam:	PF00463
SCOP:	1f8m
SYSTERS:	ICL

This tab holds annotation information from the InterPro database.

InterPro entry IPR000918

Isocitrate lyase (EC) [PUBMED:2696959, PUBMED:2361956] is an enzyme that catalyzes the conversion of isocitrate to succinate and glyoxylate. This is the first step in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. A cysteine, a histidine and a glutamate or aspartate have been found to be important for the enzyme's catalytic activity. Only one cysteine residue is conserved between the sequences of the fungal, plant and bacterial enzymes; it is located in the middle of a conserved hexapeptide.

Other enzymes also belong to this family including carboxyvinyl-carboxyphosphonate phosphorylmutase (EC) which catalyses the conversion of 1-carboxyvinyl carboxyphosphonate to 3-(hydrohydroxyphosphoryl) pyruvate carbon dioxide, and phosphoenolpyruvate mutase (EC), which is involved in the biosynthesis of phosphinothricin tripeptide antiobiotics.

Gene Ontology

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

Molecular function	catalytic activity (GO:0003824)
Biological process	metabolic process (GO:0008152)

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 PK_TIM (CL0151), which contains the following 10 members:

C-C_Bond_Lyase HpcH_HpaI ICL Malate_synthase Pantoate_transf PEP-utilizers_C PEP_mutase PEPcase PEPcase_2 PK

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

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

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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 (7)	Full (4174)	Representative proteomes				NCBI (4424)	Meta (4281)
	Seed (7)	Full (4174)	RP15 (314)	RP35 (663)	RP55 (947)	RP75 (1148)	NCBI (4424)	Meta (4281)
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 (7)	Full (4174)	Representative proteomes				NCBI (4424)	Meta (4281)
	Seed (7)	Full (4174)	RP15 (314)	RP35 (663)	RP55 (947)	RP75 (1148)	NCBI (4424)	Meta (4281)
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 (7)	Full (4174)	Representative proteomes				NCBI (4424)	Meta (4281)
	Seed (7)	Full (4174)	RP15 (314)	RP35 (663)	RP55 (947)	RP75 (1148)	NCBI (4424)	Meta (4281)
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:

Prosite

Previous IDs:

none

Type:

Domain

Author:

Finn RD

Number in seed:

7

Number in full:

4174

Average length of the domain:

225.10 aa

Average identity of full alignment:

28 %

Average coverage of the sequence by the domain:

93.61 %

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	19.5	19.5
Trusted cut-off	19.5	19.5
Noise cut-off	19.4	19.3

Model length:

526

Family (HMM) version:

16

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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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 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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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
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

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ICL

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 ICL domain has been found. There are 69 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: ICL (PF00463)

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Summary: Isocitrate lyase family

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Contents

[edit] Mechanism

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External database links

InterPro entry IPR000918

Gene Ontology

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