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108  structures 4320  species 1  interaction 8372  sequences 13  architectures

Family: Asp_Glu_race (PF01177)

Summary: Asp/Glu/Hydantoin racemase

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

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.

Asp/Glu/Hydantoin racemase Provide feedback

This family contains aspartate racemase, maleate isomerases EC:5.2.1.1 [1] glutamate racemase, hydantoin racemase and arylmalonate decarboxylase EC:4.1.1.76 [2].

Literature references

  1. Fisch F, Fleites CM, Delenne M, Baudendistel N, Hauer B, Turkenburg JP, Hart S, Bruce NC, Grogan G;, J Am Chem Soc. 2010;132:11455-11457.: A Covalent Succinylcysteine-like Intermediate in the Enzyme-Catalyzed Transformation of Maleate to Fumarate by Maleate Isomerase. PUBMED:20677745 EPMC:20677745

  2. Okrasa K, Levy C, Hauer B, Baudendistel N, Leys D, Micklefield J;, Chemistry. 2008;14:6609-6613.: Structure and mechanism of an unusual malonate decarboxylase and related racemases. PUBMED:18576402 EPMC:18576402


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015942

This entry represents a group of related proteins that includes aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase.

Aspartate racemase (EC) and glutamate racemase (EC) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity [PUBMED:8385993]. Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S. In addition to characterised aspartate and glutamate racemases, this family also includes a hypothetical protein from Erwinia carotovora and one from Escherichia coli (ygeA).

Two conserved cysteines are present in the sequence of these enzymes. They are expected to play a role in catalytic activity by acting as bases in proton abstraction from the substrate.

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 contains the following 3 members:

AroM Asp_Glu_race Asp_Glu_race_2

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
(177)
Full
(8372)
Representative proteomes NCBI
(6434)
Meta
(2979)
RP15
(548)
RP35
(1190)
RP55
(1650)
RP75
(2004)
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PP/heatmap 1   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
(177)
Full
(8372)
Representative proteomes NCBI
(6434)
Meta
(2979)
RP15
(548)
RP35
(1190)
RP55
(1650)
RP75
(2004)
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
(177)
Full
(8372)
Representative proteomes NCBI
(6434)
Meta
(2979)
RP15
(548)
RP35
(1190)
RP55
(1650)
RP75
(2004)
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: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 177
Number in full: 8372
Average length of the domain: 210.50 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 83.24 %

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 27.7 27.7
Trusted cut-off 27.7 27.7
Noise cut-off 27.6 27.6
Model length: 216
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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...

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

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Interactions

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

Asp_Glu_race

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 Asp_Glu_race domain has been found. There are 108 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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