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55  structures 2817  species 1  interaction 3552  sequences 9  architectures

# Summary: dTDP-4-dehydrorhamnose 3,5-epimerase

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

This is the Wikipedia entry entitled "DTDP-4-dehydrorhamnose 3,5-epimerase". More...

# DTDP-4-dehydrorhamnose 3,5-epimerase

dTDP-4-dehydrorhamnose 3,5-epimerase

rmlc p aeruginosa with dtdp-rhamnose
Identifiers
Symbol dTDP_sugar_isom
Pfam PF00908
Pfam clan CL0029
InterPro IPR000888
SCOP 1epz
SUPERFAMILY 1epz
dTDP-4-dehydrorhamnose 3,5-epimerase
Identifiers
EC number 5.1.3.13
CAS number 37318-39-1
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

In enzymology, a dTDP-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) is an enzyme that catalyzes the chemical reaction

dTDP-4-dehydro-6-deoxy-D-glucose $\rightleftharpoons$ dTDP-4-dehydro-6-deoxy-L-mannose

Hence, this enzyme has one substrate, dTDP-4-dehydro-6-deoxy-D-glucose, and one product, dTDP-4-dehydro-6-deoxy-L-mannose.

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 dTDP-4-dehydro-6-deoxy-D-glucose 3,5-epimerase. Other names in common use include dTDP-L-rhamnose synthetase, dTDP-L-rhamnose synthetase, thymidine diphospho-4-ketorhamnose 3,5-epimerase, TDP-4-ketorhamnose 3,5-epimerase, dTDP-4-dehydro-6-deoxy-D-glucose 3,5-epimerase, and TDP-4-keto-L-rhamnose-3,5-epimerase. This enzyme participates in 3 metabolic pathways: nucleotide sugars metabolism, streptomycin biosynthesis, and polyketide sugar unit biosynthesis.

## Structural studies

The crystal structure of RmlC from Methanobacterium thermoautotrophicum was determined in the presence and absence of a substrate analogue. RmlC is a homodimer comprising a central jelly roll motif, which extends in two directions into longer beta-sheets. Binding of dTDP is stabilised by ionic interactions to the phosphate group and by a combination of ionic and hydrophobic interactions with the base. The active site, which is located in the centre of the jelly roll, is formed by residues that are conserved in all known RmlC sequence homologues. The active site is lined with a number of charged residues and a number of residues with hydrogen-bonding potentials, which together comprise a potential network for substrate binding and catalysis. The active site is also lined with aromatic residues which provide favourable environments for the base moiety of dTDP and potentially for the sugar moiety of the substrate.[1]

As of late 2007, 14 structures have been solved for this class of enzymes, with PDB accession codes 1DZR, 1DZT, 1EP0, 1EPZ, 1NXM, 1NYW, 1NZC, 1PM7, 1RTV, 1UPI, 1WLT, 2B9U, 2IXC, and 2IXL.

## References

1. ^ Christendat D, Saridakis V, Dharamsi A, Bochkarev A, Pai EF, Arrowsmith CH, Edwards AM (August 2000). "Crystal structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase from Methanobacterium thermoautotrophicum complexed with dTDP". J. Biol. Chem. 275 (32): 24608–12. doi:10.1074/jbc.C000238200. PMID 10827167.

## Further reading

• Gaugler RW, Gabriel O (1973). "Biological mechanisms involved in the formation of deoxy sugars VII. Biosynthesis of 6-deoxy-L-talose". J. Biol. Chem. 248 (17): 6041–9. PMID 4199258.
• Melo A, Glaser L (1968). "The mechanism of 6-deoxyhexose synthesis. II. Conversion of deoxythymidine diphosphate 4-keto-6-deoxy-D-glucose to deoxythymidine diphosphate L-rhamnose". J. Biol. Chem. 243 (7): 1475–8. PMID 4384782.

This article incorporates text from the public domain Pfam and InterPro IPR000888

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.

# dTDP-4-dehydrorhamnose 3,5-epimerase

This family catalyse the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13.

## External database links

This tab holds annotation information from the InterPro database.

# InterPro entry IPR000888

Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-d-hexulose 3, 5-epimerase (RmlC, EC) is involved in the biosynthesis of dTDP-l-rhamnose, which is an essential component of the bacterial cell wall, converting dTDP-4-keto-6-deoxy-D-glucose to dTDP-4-keto-L-rhamnose.

The crystal structure of RmlC from Methanobacterium thermoautotrophicum was determined in the presence and absence of a substrate analogue. RmlC is a homodimer comprising a central jelly roll motif, which extends in two directions into longer beta-sheets. Binding of dTDP is stabilised by ionic interactions to the phosphate group and by a combination of ionic and hydrophobic interactions with the base. The active site, which is located in the centre of the jelly roll, is formed by residues that are conserved in all known RmlC sequence homologues. The active site is lined with a number of charged residues and a number of residues with hydrogen-bonding potentials, which together comprise a potential network for substrate binding and catalysis. The active site is also lined with aromatic residues which provide favorable environments for the base moiety of dTDP and potentially for the sugar moiety of the substrate [PUBMED:10827167].

### 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...

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# Pfam Clan

This family is a member of clan Cupin (CL0029), which has the following description:

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

The clan contains the following 53 members:

dTDP_sugar_isom

# 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
(19)
Full
(3552)
Representative proteomes NCBI
(2953)
Meta
(1971)
RP15
(286)
RP35
(589)
RP55
(765)
RP75
(902)
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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
(19)
Full
(3552)
Representative proteomes NCBI
(2953)
Meta
(1971)
RP15
(286)
RP35
(589)
RP55
(765)
RP75
(902)
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
(19)
Full
(3552)
Representative proteomes NCBI
(2953)
Meta
(1971)
RP15
(286)
RP35
(589)
RP55
(765)
RP75
(902)
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_540 (release 3.0) Previous IDs: none Type: Domain Author: Bateman A Number in seed: 19 Number in full: 3552 Average length of the domain: 172.40 aa Average identity of full alignment: 40 % Average coverage of the sequence by the domain: 87.60 %

## 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 20.3 20.3
Trusted cut-off 20.4 20.8
Noise cut-off 20.2 20.2
Model length: 177
Family (HMM) version: 12
Download: download the raw HMM for this family

# Species distribution

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# Interactions

There is 1 interaction 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 dTDP_sugar_isom domain has been found. There are 55 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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