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21  structures 1018  species 4  interactions 1389  sequences 6  architectures

# Summary: L-fucose isomerase, C-terminal domain

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

# L-fucose isomerase

L-fucose isomerase
Identifiers
EC number5.3.1.25
CAS number60063-83-4
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structures
Gene Ontology
L-fucose isomerase, first N-terminal domain
l-fucose isomerase from escherichia coli
Identifiers
SymbolFucose_iso_N1
PfamPF07881
InterProIPR012888
SCOPe1fui / SUPFAM
L-fucose isomerase, second N-terminal domain
l-fucose isomerase from escherichia coli
Identifiers
SymbolFucose_iso_N2
PfamPF07882
InterProIPR012889
SCOPe1fui / SUPFAM
L-fucose isomerase, C-terminal domain
l-fucose isomerase from escherichia coli
Identifiers
SymbolFucose_iso_C
PfamPF02952
Pfam clanCL0393
InterProIPR015888
SCOPe1fui / SUPFAM

In enzymology, a L-fucose isomerase (EC 5.3.1.25) is an enzyme that catalyzes the chemical reaction

L-fucose ${\displaystyle \rightleftharpoons }$ L-fuculose

Hence, this enzyme has one substrate, L-fucose, and one product, L-fuculose.

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-fucose aldose-ketose-isomerase. This enzyme participates in fructose and mannose metabolism.

The enzyme is a hexamer, forming the largest structurally known ketol isomerase, and has no sequence or structural similarity with other ketol isomerases. The structure was determined by X-ray crystallography at 2.5 Angstrom resolution.[1] Each subunit of the hexameric enzyme is wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues.[1]

## References

1. ^ a b Seemann JE, Schulz GE (October 1997). "Structure and mechanism of L-fucose isomerase from Escherichia coli". J. Mol. Biol. 273 (1): 256â€“68. doi:10.1006/jmbi.1997.1280. PMID 9367760.

This article incorporates text from the public domain Pfam and InterPro: IPR015888
This article incorporates text from the public domain Pfam and InterPro: IPR012889
This article incorporates text from the public domain Pfam and InterPro: IPR012888

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-fucose isomerase, C-terminal domain

No Pfam abstract.

## Literature references

1. Seemann JE, Schulz GE; , J Mol Biol 1997;273:256-268.: Structure and mechanism of L-fucose isomerase from Escherichia coli. PUBMED:9367760 EPMC:9367760

This tab holds annotation information from the InterPro database.

# InterPro entry IPR015888

L-fucose isomerase (EC) converts the aldose L-fucose into the corresponding ketose L-fuculose during the first step in fucose metabolism using Mn2+ as a cofactor. The enzyme is a hexamer, forming the largest structurally known ketol isomerase, and has no sequence or structural similarity with other ketol isomerases. The structure was determined by X-ray crystallography at 2.5 A resolution [PUBMED:9367760].

This entry represents the C-terminal domain of L-fucose isomerase.

### 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...

# Pfam Clan

This family is a member of clan FucI-AraA_C (CL0393), which has the following description:

The enzymes in this superfamily function as a hexamer, which is the largest structurally known ketol isomerase, that has no sequence or structural similarity to other ketol isomerases.

The clan contains the following 2 members:

Fucose_iso_C

# 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, the UniProtKB sequence database, 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
(24)
Full
(1389)
Representative proteomes UniProt
(6665)
NCBI
(9483)
Meta
(82)
RP15
(190)
RP35
(780)
RP55
(1378)
RP75
(2362)
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HTML View  View
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
(24)
Full
(1389)
Representative proteomes UniProt
(6665)
NCBI
(9483)
Meta
(82)
RP15
(190)
RP35
(780)
RP55
(1378)
RP75
(2362)
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
(24)
Full
(1389)
Representative proteomes UniProt
(6665)
NCBI
(9483)
Meta
(82)
RP15
(190)
RP35
(780)
RP55
(1378)
RP75
(2362)

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: Pfam-B_9303 (Release 8.0) Previous IDs: fucose_iso_C; Type: Domain Sequence Ontology: SO:0000417 Author: Griffiths-Jones SR Number in seed: 24 Number in full: 1389 Average length of the domain: 140.50 aa Average identity of full alignment: 27 % Average coverage of the sequence by the domain: 27.18 %

## HMM information

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.3 29.3
Trusted cut-off 29.3 29.3
Noise cut-off 29.2 29.2
Model length: 143
Family (HMM) version: 18

# Species distribution

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# Interactions

There are 4 interactions for this family. More...

# 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 Fucose_iso_C domain has been found. There are 21 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.