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0  structures 863  species 0  interactions 1209  sequences 7  architectures

Family: Chalcone_3 (PF16036)

Summary: Chalcone isomerase-like

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This is the Wikipedia entry entitled "Chalcone isomerase". More...

Chalcone isomerase Edit Wikipedia article

chalcone isomerase
Identifiers
EC number5.5.1.6
CAS number9073-57-8
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Chalcone isomerase
PDB 1jep EBI.jpg
chalcone isomerase complexed with 4'-hydroxyflavanone
Identifiers
SymbolChalcone
PfamPF02431
InterProIPR003466
SCOPe1eyp / SUPFAM

In enzymology, a chalcone isomerase (EC 5.5.1.6) is an enzyme that catalyzes the chemical reaction

a chalcone a flavanone

Hence, this enzyme has one substrate, a chalcone, and one product, a flavanone.

This enzyme belongs to the family of isomerases, specifically the class of intramolecular lyases. The systematic name of this enzyme class is flavanone lyase (decyclizing). This enzyme is also called chalcone-flavanone isomerase. This enzyme participates in flavonoid biosynthesis.

The Petunia hybrida (Petunia) genome contains two genes coding for very similar enzymes, ChiA and ChiB, but only the first seems to encode a functional chalcone isomerase.

Structural studies

As of late 2007, 7 structures have been solved for this class of enzymes, with PDB accession codes 1EYP, 1EYQ, 1FM7, 1FM8, 1JEP, 1JX0, and 1JX1.

Chalcone isomerase has a core 2-layer alpha/beta structure consisting of beta(3)-alpha(2)-beta-alpha(2)-beta(3).[1]

References

  1. ^ Jez JM, Bowman ME, Dixon RA, Noel JP (September 2000). "Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase". Nat. Struct. Biol. 7 (9): 786–91. doi:10.1038/79025. PMID 10966651.

Further reading

This article incorporates text from the public domain Pfam and InterPro: IPR003466


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.

Chalcone isomerase-like Provide feedback

Chalcone_3 is a family of largely bacterial members.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016087

Chalcone isomerase (EC; also known as chalcone-flavanone isomerase) is a plant enzyme responsible for the isomerisation of chalcone to naringenin, a key step in the biosynthesis of flavonoids. The Petunia hybrida (Petunia) genome contains two genes coding for very similar enzymes, ChiA and ChiB, but only the first seems to encode a functional chalcone isomerase. Chalcone isomerase has a core 2-layer alpha/beta structure consisting of beta(3)-alpha(2)-beta-alpha(2)-beta(3) [PUBMED:10966651].

This entry represents chalcone isomerases and enzymes with a common structure.

Gene Ontology

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

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 Chalcone-like (CL0560), which has the following description:

This superfamily is characterised by a fold that is conserved across plants, bacteria and fungi. However, possible key residues necessary for binding naringenin, 4',5,7-trihydroxyflavanone, are not conserved beyond plants.

The clan contains the following 3 members:

Chalcone Chalcone_2 Chalcone_3

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(54)
Full
(1209)
Representative proteomes UniProt
(5795)
NCBI
(9167)
Meta
(204)
RP15
(190)
RP35
(625)
RP55
(1239)
RP75
(2125)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(54)
Full
(1209)
Representative proteomes UniProt
(5795)
NCBI
(9167)
Meta
(204)
RP15
(190)
RP35
(625)
RP55
(1239)
RP75
(2125)
Alignment:
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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
(54)
Full
(1209)
Representative proteomes UniProt
(5795)
NCBI
(9167)
Meta
(204)
RP15
(190)
RP35
(625)
RP55
(1239)
RP75
(2125)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

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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: Jackhmmer:E6XGV6
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 54
Number in full: 1209
Average length of the domain: 157.10 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 79.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 165
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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