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99  structures 1661  species 0  interactions 2280  sequences 3  architectures

# Summary: L-arabinose isomerase

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This is the Wikipedia entry entitled "L-arabinose isomerase". More...

# L-arabinose isomerase

L-arabinose isomerase
L-arabinose isomerase hexamer, Geobacillus kaustophilus
Identifiers
EC number5.3.1.4
CAS number9023-80-7
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structures
Gene Ontology
Arabinose isomerase
crystal structure of l-arabinose isomerase from e.coli
Identifiers
SymbolArabinose_Isome
PfamPF02610
InterProIPR003762

In enzymology, a L-arabinose isomerase (EC 5.3.1.4) is an enzyme that catalyzes the chemical reaction

L-arabinose ${\displaystyle \rightleftharpoons }$ L-ribulose

Hence, this enzyme has one substrate, L-arabinose, and one product, L-ribulose.

This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The systematic name of this enzyme class is L-arabinose aldose-ketose-isomerase. This enzyme participates in pentose and glucuronate interconversions.

This enzyme catalyses the conversion of L-arabinose to L-ribulose as the first step in the pathway of L-arabinose utilization as a carbon source.[1]

## Structural studies

As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 2AJT and 2HXG.

## References

1. ^ Sa-Nogueira I, Nogueira TV, Soares S, de Lencastre H (March 1997). "The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression". Microbiology. 143 (3): 957â€“69. doi:10.1099/00221287-143-3-957. PMID 9084180.

• HEATH EC, HORECKER BL, SMYRNIOTIS PZ, TAKAGI Y (1958). "Pentose fermentation by Lactobacillus plantarum. II. L-arabinose isomerase". J. Biol. Chem. 231 (2): 1031â€“7. PMID 13539034.
• Nakamatu T, Yamanaka K (1969). "Crystallization and properties of L-arabinose isomerase from Lactobacillus gayonii". Biochim. Biophys. Acta. 178 (1): 156â€“65. doi:10.1016/0005-2744(69)90142-9. PMID 5773448.
This article incorporates text from the public domain Pfam and InterPro: IPR003762

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.

# L-arabinose isomerase

This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme [1].

## Literature references

1. Sa-Nogueira I, Nogueira TV, Soares S, de Lencastre H; , Microbiology 1997;143:957-969.: The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. PUBMED:9084180 EPMC:9084180

This tab holds annotation information from the InterPro database.

# InterPro entry IPR003762

The Escherichia coli araBAD operon consists of three genes encoding three enzymes that convert L-arabinose to D-xylulose-5 phosphate. L-arabinose isomerase (AraA) EC catalyses the conversion of L-arabinose to L-ribulose as the first step in the pathway of L-arabinose utilization as a carbon source [ PUBMED:9084180 ].

### 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...

# 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...

## 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
(125)
Full
(2280)
Representative proteomes UniProt
(10667)
RP15
(188)
RP35
(1065)
RP55
(2434)
RP75
(4312)
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PP/heatmap 1 View

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

Key: available, not generated, not available.

## Format an alignment

Seed
(125)
Full
(2280)
Representative proteomes UniProt
(10667)
RP15
(188)
RP35
(1065)
RP55
(2434)
RP75
(4312)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(125)
Full
(2280)
Representative proteomes UniProt
(10667)
RP15
(188)
RP35
(1065)
RP55
(2434)
RP75
(4312)

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.

# 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

 Seed source: COG2160 Previous IDs: none Type: Family Sequence Ontology: SO:0100021 Author: Bashton M , Bateman A Number in seed: 125 Number in full: 2280 Average length of the domain: 340.80 aa Average identity of full alignment: 39 % Average coverage of the sequence by the domain: 69.80 %

## HMM information

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 29.4 29.4
Trusted cut-off 29.4 29.4
Noise cut-off 29.1 29.1
Model length: 356
Family (HMM) version: 18

# Species distribution

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### Colour assignments

 Archea Eukaryota Bacteria Other sequences Viruses Unclassified Viroids Unclassified sequence

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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 Arabinose_Isome domain has been found. There are 99 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.