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40  structures 1453  species 0  interactions 2675  sequences 8  architectures

Family: Amdase (PF17645)

Summary: Arylmalonate decarboxylase

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This is the Wikipedia entry entitled "Arylmalonate decarboxylase". More...

Arylmalonate decarboxylase Edit Wikipedia article

arylmalonate decarboxylase
Identifiers
EC number4.1.1.76
CAS number144713-36-0
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO

In enzymology, an arylmalonate decarboxylase (EC 4.1.1.76) is an enzyme that catalyzes the chemical reaction

2-aryl-2-methylmalonate 2-arylpropanoate + CO2

Hence, this enzyme has one substrate, 2-aryl-2-methylmalonate, and two products, 2-arylpropanoate and CO2.

This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 2-aryl-2-methylmalonate carboxy-lyase (2-arylpropanoate-forming). Other names in common use include AMDASE, 2-aryl-2-methylmalonate carboxy-lyase, and 2-aryl-2-methylmalonate carboxy-lyase (2-arylpropionate-forming).

Structural studies

As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2DGD.

References

  • Miyamoto K, Ohta H (1992). "Cloning and heterologous expression of a novel arylmalonate decarboxylase gene from Alcaligenes bronchisepticus KU 1201". Appl. Microbiol. Biotechnol. 38 (2): 234–8. doi:10.1007/bf00174474. PMID 1369144.


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.

Arylmalonate decarboxylase Provide feedback

This entry contains members such as the arylmalonate decarboxylases (AMDase; EC 4.1.1.76), which belong to the family of carboxy-lyases (EC 4.1). Amdases are capable of decarboxylating a range of alpha-disubstituted malonic acid derivates to enantiopure products without the need for any cofactor. AMDases are members of the widespread Asp/Glu racemase family PF01177 together with aspartate (EC 5.1.1.13) and glutamate racemases (EC 5.1.1.3), hydantoin racemases (EC 5.1.99.5) and maleate isomerases (EC 5.2.1.1) [1].

Literature references

  1. Maimanakos J, Chow J, Gassmeyer SK, Gullert S, Busch F, Kourist R, Streit WR;, Front Microbiol. 2016;7:1332.: Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families. PUBMED:27610105 EPMC:27610105


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR026286

Maleate isomerase catalyses the conversion of maleate to fumarate [ PUBMED:9345272 , PUBMED:10803955 ]. This family also includes proteins described as arylmalonate decarboxylases [ PUBMED:1369144 ].

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 Asp-glut_race (CL0399), which has the following description:

Superfamily contains aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase families from fungi, plants, bacteria and archaeal species.

The clan contains the following 5 members:

Amdase AroM Asp_Glu_race Asp_Glu_race_2 OTCace

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
(12)
Full
(2675)
Representative proteomes UniProt
(11220)
RP15
(158)
RP35
(1050)
RP55
(2740)
RP75
(5004)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(12)
Full
(2675)
Representative proteomes UniProt
(11220)
RP15
(158)
RP35
(1050)
RP55
(2740)
RP75
(5004)
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
(12)
Full
(2675)
Representative proteomes UniProt
(11220)
RP15
(158)
RP35
(1050)
RP55
(2740)
RP75
(5004)
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: Chow J
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: El-Gebali S
Number in seed: 12
Number in full: 2675
Average length of the domain: 192.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 76.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.9 25.9
Trusted cut-off 25.9 25.9
Noise cut-off 25.8 25.7
Model length: 217
Family (HMM) version: 3
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 Amdase domain has been found. There are 40 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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