Summary: UDP-N-acetylglucosamine 2-epimerase

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Wikipedia: UDP-N-acetylglucosamine 2-epimerase
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This is the Wikipedia entry entitled "UDP-N-acetylglucosamine 2-epimerase". More...

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UDP-N-acetylglucosamine 2-epimerase Edit Wikipedia article

UDP-N-acetylglucosamine 2-epimerase

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Databases

PDB structures

AmiGO / EGO

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PubMed	articles
NCBI	proteins

UDP-N-acetylglucosamine 2-epimerase

crystal structure of udp-n-acetylglucosamine_2 epimerase

Identifiers

Symbol

Epimerase_2

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

In enzymology, an UDP-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) is an enzyme that catalyzes the chemical reaction

UDP-N-acetyl-D-glucosamine $\rightleftharpoons$ UDP-N-acetyl-D-mannosamine

Hence, this enzyme has one substrate, UDP-N-acetyl-D-glucosamine, and one product, UDP-N-acetyl-D-mannosamine.

This enzyme belongs to the family of isomerases, specifically those racemases and epimerases acting on carbohydrates and derivatives. The systematic name of this enzyme class is UDP-N-acetyl-D-glucosamine 2-epimerase. Other names in common use include UDP-N-acetylglucosamine 2'-epimerase, uridine diphosphoacetylglucosamine 2'-epimerase, uridine diphospho-N-acetylglucosamine 2'-epimerase, and uridine diphosphate-N-acetylglucosamine-2'-epimerase. This enzyme participates in aminosugars metabolism.

In microorganisms this epimerase is involved in the synthesis of the capsule precursor UDP-ManNAcA.^[1]^[2] Some of these enzymes are bifunctional. The UDP-N-acetylglucosamine 2-epimerase from rat liver displays both epimerase and kinase activity.^[3]

[edit] Structural studies

As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes 1F6D, 1O6C, 1V4V, and 1VGV.

[edit] References

^ Swartley JS, Liu LJ, Miller YK, Martin LE, Edupuganti S, Stephens DS (March 1998). "Characterization of the Gene Cassette Required for Biosynthesis of the (α1→6)-Linked N-Acetyl-d-Mannosamine-1-Phosphate Capsule of Serogroup A Neisseria meningitidis". J. Bacteriol. 180 (6): 1533–9. PMC 107054. PMID 9515923. //www.ncbi.nlm.nih.gov/pmc/articles/PMC107054/.
^ Kiser KB, Lee JC (January 1998). "Staphylococcus aureus cap5O and cap5P Genes Functionally Complement Mutations Affecting Enterobacterial Common-Antigen Biosynthesis in Escherichia coli". J. Bacteriol. 180 (2): 403–6. PMC 106897. PMID 9440531. //www.ncbi.nlm.nih.gov/pmc/articles/PMC106897/.
^ Stasche R, Hinderlich S, Weise C, Effertz K, Lucka L, Moormann P, Reutter W (September 1997). "A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Molecular cloning and functional expression of UDP-N-acetyl-glucosamine 2-epimerase/N-acetylmannosamine kinase". J. Biol. Chem. 272 (39): 24319–24. doi:10.1074/jbc.272.39.24319. PMID 9305888.

[edit] Further reading

Kikuchi K, Tsuiki S (1973). "Purification and properties of UDP-N-acetylglucosamine 2'-epimerase from rat liver". Biochim. Biophys. Acta. 327 (1): 193–206. PMID 4770741.

This article incorporates text from the public domain Pfam and InterPro IPR003331

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UDP-N-acetylglucosamine 2-epimerase Provide feedback

This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyses the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional such as O35826 and Q9Z0P6 in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of O35826 is the kinase domain [3].

Literature references

Swartley JS, Liu LJ, Miller YK, Martin LE, Edupuganti S, Stephens DS; , J Bacteriol. 1998;180:1533-1539.: Characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked N-acetyl-D-mannosamine-1-phosphate capsule of serogroup A Neisseria meningitidis. PUBMED:9515923 EPMC:9515923
Kiser KB, Lee JC; , J Bacteriol 1998;180:403-406.: Staphylococcus aureus cap5O and cap5P genes functionally complement mutations affecting enterobacterial common-antigen biosynthesis in Escherichia coli. PUBMED:9440531 EPMC:9440531
Stasche R, Hinderlich S, Weise C, Effertz K, Lucka L, Moormann P, Reutter W; , J Biol Chem 1997;272:24319-24324.: A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Molecular cloning and functional expression of UDP-N-acetyl-glucosamine 2-epimerase/N-acetylmannosamine kinase. PUBMED:9305888 EPMC:9305888

External database links

PANDIT:	PF02350
Pseudofam:	PF02350
SCOP:	1f6d
SYSTERS:	Epimerase_2

This tab holds annotation information from the InterPro database.

InterPro entry IPR003331

UDP-N-acetylglucosamine 2-epimerase EC catalyses the production of UDP-ManNAc from UDP-GlcNAc. Some of the enzymes is this family are bifunctional. In microorganisms the epimerase is involved in in the synthesis of the capsule precursor UDP-ManNAcA [PUBMED:9515923, PUBMED:9440531]. The protein from rat liver displays both epimerase and kinase activity [PUBMED:9305888].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)
Biological process	lipopolysaccharide biosynthetic process (GO:0009103)
Biological process	UDP-N-acetylglucosamine metabolic process (GO:0006047)

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 GT-B (CL0113), which contains the following 35 members:

Alg14 Capsule_synth DUF1205 DUF1972 DUF3492 DUF354 Epimerase_2 Glyco_tran_28_C Glyco_trans_1_2 Glyco_trans_1_3 Glyco_trans_1_4 Glyco_trans_4_2 Glyco_trans_4_3 Glyco_trans_4_4 Glyco_transf_20 Glyco_transf_28 Glyco_transf_4 Glyco_transf_41 Glyco_transf_5 Glyco_transf_56 Glyco_transf_9 Glyco_transf_90 Glycogen_syn Glycos_transf_1 Glycos_transf_N Glyphos_transf LpxB MGDG_synth Mito_fiss_Elm1 Phosphorylase PIGA PS_pyruv_trans SUA5 Sucrose_synth UDPGT

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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 (187)	Full (4483)	Representative proteomes				NCBI (3343)	Meta (2891)
	Seed (187)	Full (4483)	RP15 (306)	RP35 (604)	RP55 (780)	RP75 (922)	NCBI (3343)	Meta (2891)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (187)	Full (4483)	Representative proteomes				NCBI (3343)	Meta (2891)
	Seed (187)	Full (4483)	RP15 (306)	RP35 (604)	RP55 (780)	RP75 (922)	NCBI (3343)	Meta (2891)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (187)	Full (4483)	Representative proteomes				NCBI (3343)	Meta (2891)
	Seed (187)	Full (4483)	RP15 (306)	RP35 (604)	RP55 (780)	RP75 (922)	NCBI (3343)	Meta (2891)
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.

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

Seed source:

Pfam-B_888 (release 5.2) & Pfam-B_4862 (Release 7.5)

Previous IDs:

none

Type:

Family

Author:

Bashton M, Bateman A

Number in seed:

187

Number in full:

4483

Average length of the domain:

333.90 aa

Average identity of full alignment:

34 %

Average coverage of the sequence by the domain:

89.01 %

HMM information

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	22.8	22.8
Trusted cut-off	22.8	22.8
Noise cut-off	22.7	22.7

Model length:

346

Family (HMM) version:

14

Download:

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Species distribution

Sunburst
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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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order
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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

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

Epimerase_2

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 Epimerase_2 domain has been found. There are 20 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Epimerase_2 (PF02350)

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Summary: UDP-N-acetylglucosamine 2-epimerase

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UDP-N-acetylglucosamine 2-epimerase Edit Wikipedia article

[edit] Structural studies

[edit] References

[edit] Further reading

UDP-N-acetylglucosamine 2-epimerase Provide feedback

Literature references

External database links

InterPro entry IPR003331

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

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External links

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Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

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Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

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Selected sequences

Species trees

Interactive tree

Interactions

Structures