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.
11  structures 1158  species 1  interaction 1188  sequences 2  architectures

Family: Chor_lyase (PF04345)

Summary: Chorismate lyase

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 "Chorismate lyase". More...

Chorismate lyase Edit Wikipedia article

Chorismate lyase
EC number
CAS number 157482-18-3
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Chorismate lyase
PDB 1tt8 EBI.jpg
chorismate lyase with product, 1.0 a resolution
Symbol Chor_lyase
Pfam PF04345
Pfam clan CL0122
InterPro IPR007440
SCOP 1jd3

In enzymology, a chorismate lyase (EC is an enzyme that catalyzes the chemical reaction

chorismate \rightleftharpoons 4-hydroxybenzoate + pyruvate

Hence, this enzyme has one substrate, chorismate, and two products, 4-hydroxybenzoate and pyruvate.

This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is chorismate pyruvate-lyase (4-hydroxybenzoate-forming). Other names in common use include CL, CPL, and UbiC.

This enzyme catalyses the first step in ubiquinone biosynthesis, the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate in Escherichia coli and other Gram-negative bacteria.[1] Its activity does not require metal cofactors.[2]


  1. ^ Nichols BP, Green JM (August 1992). "Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase". J. Bacteriol. 174 (16): 5309–16. PMC 206367. PMID 1644758. 
  2. ^ Siebert M, Severin K, Heide L (April 1994). "Formation of 4-hydroxybenzoate in Escherichia coli: characterization of the ubiC gene and its encoded enzyme chorismate pyruvate-lyase". Microbiology (Reading, Engl.) 140 (4): 897–904. doi:10.1099/00221287-140-4-897. PMID 8012607. 

Further reading[edit]

This article incorporates text from the public domain Pfam and InterPro IPR007440

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.

Chorismate lyase Provide feedback

Chorismate lyase catalyses the first step in ubiquinone synthesis, i.e. the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate.

Literature references

  1. Gallagher DT, Mayhew M, Holden MJ, Howard A, Kim KJ, Vilker VL; , Proteins 2001;44:304-311.: The crystal structure of chorismate lyase shows a new fold and a tightly retained product. PUBMED:11455603 EPMC:11455603

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007440

Chorismate--pyruvate lyase catalyses the first step in ubiquinone synthesis, the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate in Escherichia coli and other Gram-negative bacteria [PUBMED:1644758]. The yeast Saccharomyces cerevisiae can synthesize ubiquinone from either chorismate or tyrosine [PUBMED:11583838], however this enzyme is found only in bacteria. Its activity does not require metal cofactors [PUBMED:8012607].

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...

Pfam Clan

This family is a member of clan UTRA (CL0122), which has the following description:

This clan includes chorismate lyase as well as the UTRA domain

The clan contains the following 4 members:

Chor_lyase DUF98 PPO1_KFDV UTRA


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.

Representative proteomes NCBI
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

Representative proteomes NCBI

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.

Representative proteomes NCBI
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...


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: COG3161
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 3
Number in full: 1188
Average length of the domain: 159.80 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 92.75 %

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 21.0 21.0
Trusted cut-off 21.3 21.0
Noise cut-off 20.8 20.8
Model length: 168
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls


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


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


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.


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



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 Chor_lyase domain has been found. There are 11 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...