Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
25  structures 320  species 1  interaction 585  sequences 8  architectures

Family: Chalcone (PF02431)

Summary: Chalcone-flavanone isomerase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Chalcone isomerase Edit Wikipedia article

chalcone isomerase
Identifiers
EC number 5.5.1.6
CAS number 9073-57-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Chalcone isomerase
PDB 1jep EBI.jpg
chalcone isomerase complexed with 4'-hydroxyflavanone
Identifiers
Symbol Chalcone
Pfam PF02431
InterPro IPR003466
SCOP 1eyp
SUPERFAMILY 1eyp

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

a chalcone \rightleftharpoons 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[edit]

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[edit]

  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[edit]

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-flavanone isomerase Provide feedback

Chalcone-flavanone isomerase is a plant enzyme responsible for the isomerisation of chalcone to naringenin, a key step in the biosynthesis of flavonoids.

Literature references

  1. Terai Y, Fujii I, Byun SH, Nakajima O, Hakamatsuka T, Ebizuka Y, Sankawa U; , Protein Expr Purif 1996;8:183-190.: Cloning of chalcone-flavanone isomerase cDNA from Pueraria lobata and its overexpression in Escherichia coli. PUBMED:8812858 EPMC:8812858

  2. Gensheimer M, Mushegian A; , Protein Sci. 2004;13:540-544.: Chalcone isomerase family and fold: no longer unique to plants. PUBMED:14718655 EPMC:14718655


External 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...

Loading domain graphics...

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...

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
(60)
Full
(585)
Representative proteomes NCBI
(589)
Meta
(20)
RP15
(78)
RP35
(167)
RP55
(221)
RP75
(257)
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, x not generated, not available.

Format an alignment

  Seed
(60)
Full
(585)
Representative proteomes NCBI
(589)
Meta
(20)
RP15
(78)
RP35
(167)
RP55
(221)
RP75
(257)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(60)
Full
(585)
Representative proteomes NCBI
(589)
Meta
(20)
RP15
(78)
RP35
(167)
RP55
(221)
RP75
(257)
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:

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 View help on the curation process

Seed source: Pfam-B_2073 (release 5.4)
Previous IDs: none
Type: Domain
Author: Mian N, Bateman A
Number in seed: 60
Number in full: 585
Average length of the domain: 182.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 69.08 %

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 23.0 23.0
Trusted cut-off 23.1 23.1
Noise cut-off 22.8 22.9
Model length: 199
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

Chalcone

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 Chalcone domain has been found. There are 25 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...