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11  structures 5577  species 1  interaction 5653  sequences 2  architectures

Family: Chor_lyase (PF04345)

Summary: Chorismate lyase

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This is the Wikipedia entry entitled "Chorismate lyase". More...

Chorismate lyase Edit Wikipedia article

In enzymology, a chorismate lyase (EC 4.1.3.40) is an enzyme that catalyzes the chemical reaction

Chorismate lyase
Identifiers
EC number 4.1.3.40
CAS number 157482-18-3
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
chorismate \rightleftharpoons 4-hydroxybenzoate + pyruvate
The chorismate pyruvate lyase (CPL) catalyzed reaction.

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.[2] Its activity does not require metal cofactors.[3]

Activity[1]

Chorismate lyase
PDB 1tt8 EBI.jpg
chorismate lyase with product, 1.0 a resolution
Identifiers
Symbol Chor_lyase
Pfam PF04345
Pfam clan CL0122
InterPro IPR007440
SCOP 1jd3
SUPERFAMILY 1jd3

Catayltic activity

  • Chorismate = 4HB + pyruvate[4]
  • This enzyme has an optimum pH at 7.5

Enzymatic activity

Inhibited by:

  • Vanillate
  • 4-hydroxybenzaldehyde
  • 3-carboxylmethylaminmethyl-4-hydroxybenzoic acid
  • 4HB - ubiC is inhibited by the product of the reaction, which scientists believe serves as a control mechanism for the pathway

Pathway

The pathway used is called the ubiquinone biosynthesis pathway, it catalyzes the first step in the biosynthesis of ubiquinone in E. coli. Ubiquinone is a lipid-soluble electron-transporting coenzyme. They are essential electron carriers in prokaryotes and are essential in aerobic organisms to achieve ATP.[1]

Nomenclature[1]

There are several different names for chorismate lyase. it is also called chorismate pyruvate lyase (4-hydroxybenzoate-forming) and it is also abbreviated several different ways: CPL, CL, and ubiC. It is sometimes referred to as ubiC, because that is the gene name. This enzyme belongs to the class Lyases; more specifically the ox-acid-lyase or the carbon-carbon-lyases.

    • taxonomic lineage: bacteria → proteobacteria → gammaproteobacteria → enterobacteriales → enterobacteriaceae → escherichia → escherichia coli

Structure[1]

This enzyme is a monomer. Its secondary structure contains helixes, turns, and beta strands.

  • It has a mass of 18,777 daltons
  • Its sequence is 165 amino acids long

Binding Sites

  • position: 35(M)
  • position: 77(R)
  • position: 115(L)

Mutagenesis[1]

  • position: 91- G → A; increases product inhibition by 40%. No effect on substrate affinity.
  • position: 156 - E → K; loss of activity

References

  1. ^ a b c d e f g h "http://www.uniprot.org/uniprot/P26602#structure". 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/enzymes/GetPage.pl?ec_number=4.1.3.40". 

Further reading

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


Internal database links

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...

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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

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...

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  Seed
(3)
Full
(5653)
Representative proteomes NCBI
(1784)
Meta
(245)
RP15
(25)
RP35
(89)
RP55
(165)
RP75
(282)
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  Seed
(3)
Full
(5653)
Representative proteomes NCBI
(1784)
Meta
(245)
RP15
(25)
RP35
(89)
RP55
(165)
RP75
(282)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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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

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Seed source: COG3161
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 3
Number in full: 5653
Average length of the domain: 158.50 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 93.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -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 20.9 20.8
Model length: 168
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Chor_lyase

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 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.

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