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55  structures 2817  species 1  interaction 3552  sequences 9  architectures

Family: dTDP_sugar_isom (PF00908)

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

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

DTDP-4-dehydrorhamnose 3,5-epimerase Edit Wikipedia article

dTDP-4-dehydrorhamnose 3,5-epimerase
PDB 2ixh EBI.jpg
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[edit]

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[edit]

  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[edit]

  • 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


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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 Provide feedback

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.

Internal database links

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

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Domain organisation

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Alignments

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  Seed
(19)
Full
(3552)
Representative proteomes NCBI
(2953)
Meta
(1971)
RP15
(286)
RP35
(589)
RP55
(765)
RP75
(902)
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Format an alignment

  Seed
(19)
Full
(3552)
Representative proteomes NCBI
(2953)
Meta
(1971)
RP15
(286)
RP35
(589)
RP55
(765)
RP75
(902)
Alignment:
Format:
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Sequence:
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  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.

Pfam alignments:

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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.

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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.

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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 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 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
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Species distribution

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Interactions

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

dTDP_sugar_isom

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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