Summary: dTDP-4-dehydrorhamnose 3,5-epimerase
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DTDP-4-dehydrorhamnose 3,5-epimerase Edit Wikipedia article
rmlc p aeruginosa with dtdp-rhamnose
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
- dTDP-4-dehydro-6-deoxy-D-glucose 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.
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.
- 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.
- 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.
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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 184.108.40.206.
Internal database links
|Similarity to PfamA using HHSearch:||FdtA|
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||dTDP-4-dehydrorhamnose 3,5-epimerase activity (GO:0008830)|
|Biological process||lipopolysaccharide biosynthetic process (GO:0009103)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This clan represents the conserved barrel domain of the 'cupin' superfamily  ('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:2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pfam-B_540 (release 3.0)|
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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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