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166  structures 4614  species 0  interactions 9345  sequences 68  architectures

Family: Lyase_aromatic (PF00221)

Summary: Aromatic amino acid lyase

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Aromatic amino acid lyase Provide feedback

This family includes proteins with phenylalanine ammonia-lyase, EC:4.3.1.24, histidine ammonia-lyase, EC:4.3.1.3, and tyrosine aminomutase, EC:5.4.3.6, activities [1-3].

Literature references

  1. Appert C, Logemann E, Hahlbrock K, Schmid J, Amrhein N;, Eur J Biochem. 1994;225:491-499.: Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). PUBMED:7925471 EPMC:7925471

  2. Schwede TF, Retey J, Schulz GE;, Biochemistry. 1999;38:5355-5361.: Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. PUBMED:10220322 EPMC:10220322

  3. Rachid S, Krug D, Kunze B, Kochems I, Scharfe M, Zabriskie TM, Blocker H, Muller R;, Chem Biol. 2006;13:667-681.: Molecular and biochemical studies of chondramide formation-highly cytotoxic natural products from Chondromyces crocatus Cm c5. PUBMED:16793524 EPMC:16793524


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001106

PAL and HAL are members of the Lyase class I_like superfamily of enzymes that, catalyze similar beta-elimination reactions and are active as homotetramers. Both PAL and HAL contain a catalytic Ala-Ser-Gly triad that is post-translationally cyclised [ PUBMED:16478474 ]. PAL is a key biosynthetic catalyst in phenylpropanoid assembly in plants and fungi, and is involved in the biosynthesis of a wide variety of secondary metabolites such as flavanoids, furanocoumarin phytoalexins and cell wall components. These compounds are important for normal growth and in responses to environmental stress. HAL catalyses the first step in histidine degradation, the removal of an ammonia group from histidine to produce urocanic acid. The core domain in PAL and HAL share about 30% sequence identity, with PAL containing an additional approximately 160 residues extending from the common fold [ PUBMED:15350127 ]. Tyrosine 2,3-aminomutase has aminomutase activity and, to a much lesser extent, ammonia-lyase activity [ PUBMED:19222035 ].

This family includes phenylalanine ammonia-lyase, (PAL; EC ), histidine ammonia-lyase, (HAL; EC ), and tyrosine aminomutase, ( EC ) [ PUBMED:7925471 , PUBMED:10220322 , PUBMED:16793524 ].

PAL is being explored as enzyme substitution therapy for Phenylketonuria (PKU), a disorder which involves an inability to metabolize phenylalanine. HAL failure in humans results in the disease histidinemia [ PUBMED:11578924 , PUBMED:12502351 , PUBMED:12667480 , PUBMED:11895450 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 and the UniProtKB 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
(419)
Full
(9345)
Representative proteomes UniProt
(40395)
RP15
(1136)
RP35
(4019)
RP55
(8841)
RP75
(15741)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(419)
Full
(9345)
Representative proteomes UniProt
(40395)
RP15
(1136)
RP35
(4019)
RP55
(8841)
RP75
(15741)
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
(419)
Full
(9345)
Representative proteomes UniProt
(40395)
RP15
(1136)
RP35
(4019)
RP55
(8841)
RP75
(15741)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Prosite
Previous IDs: PAL;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Eberhardt R
Number in seed: 419
Number in full: 9345
Average length of the domain: 428.90 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 80.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.3 27.3
Trusted cut-off 27.3 27.6
Noise cut-off 27.2 27.2
Model length: 463
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 Lyase_aromatic domain has been found. There are 166 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0VM80 View 3D Structure Click here
A0A0P0YAL3 View 3D Structure Click here
A0A0R0KUR1 View 3D Structure Click here
A0A0R4J2S3 View 3D Structure Click here
A0A1D6E5Y8 View 3D Structure Click here
A0A1D6E5Y9 View 3D Structure Click here
A0A1D6FET9 View 3D Structure Click here
A0A1D6FUK0 View 3D Structure Click here
A0A1D6HDL5 View 3D Structure Click here
A0A1D6HDL9 View 3D Structure Click here
A0A1D6I6Y6 View 3D Structure Click here
A0A1D6JJB6 View 3D Structure Click here
A0A1D6K1R9 View 3D Structure Click here
A0A1D6KXF9 View 3D Structure Click here
A0A1D6LIU0 View 3D Structure Click here
A0A1D6MW96 View 3D Structure Click here
A0A1D6N513 View 3D Structure Click here
A0A1D6Q5B1 View 3D Structure Click here
A0A1D6Q5B7 View 3D Structure Click here
A0A1D6QQZ2 View 3D Structure Click here
A4FUP1 View 3D Structure Click here
B4FW68 View 3D Structure Click here
B8A046 View 3D Structure Click here
C0HJ40 View 3D Structure Click here
C0PL14 View 3D Structure Click here
I1JPN0 View 3D Structure Click here
I1KQ70 View 3D Structure Click here
I1L905 View 3D Structure Click here
I1LZ94 View 3D Structure Click here
I1NA96 View 3D Structure Click here
K7KRK6 View 3D Structure Click here
K7LKL7 View 3D Structure Click here
K7N485 View 3D Structure Click here
P14717 View 3D Structure Click here
P21213 View 3D Structure Click here
P27991 View 3D Structure Click here
P35492 View 3D Structure Click here
P35510 View 3D Structure Click here
P42357 View 3D Structure Click here
P45724 View 3D Structure Click here