Summary: 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
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This is the Wikipedia entry entitled "DXP reductoisomerase". More...
DXP reductoisomerase Edit Wikipedia article
1-deoxy-D-xylulose-5-phosphate reductoisomerase | |||||||||
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![]() crystal structure of DXR in complex with the substrate 1-deoxy-D-xylulose 5-phosphate | |||||||||
Identifiers | |||||||||
Symbol | DXP_reductoisom | ||||||||
Pfam | PF02670 | ||||||||
Pfam clan | CL0063 | ||||||||
InterPro | IPR013512 | ||||||||
SCOPe | 1onn / SUPFAM | ||||||||
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DXP reductoisomerase | |||||||||
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Identifiers | |||||||||
EC number | 1.1.1.267 | ||||||||
CAS number | 210756-42-6 | ||||||||
Databases | |||||||||
IntEnz | IntEnz view | ||||||||
BRENDA | BRENDA entry | ||||||||
ExPASy | NiceZyme view | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
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DXP reductoisomerase (1-deoxy-D-xylulose 5-phosphate reductoisomerase or DXR) is an enzyme that interconverts 1-deoxy-D-xylulose 5-phosphate (DXP) and 2-C-methyl-D-erythritol 4-phosphate (MEP).[1]
It is classified under EC 1.1.1.267. It is normally abbreviated DXR, but it is sometimes named IspC, as the product of the ispC gene.
DXR is part of the MEP pathway (nonmevalonate pathway) of isoprenoid precursor biosynthesis. DXR is inhibited by fosmidomycin.
This enzyme is required for terpenoid biosynthesis in some organisms, since it is a key enzyme on the MEP pathway for the production of the isoprenoid precursors IPP and DMAPP.[1] In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the MEP pathway for isoprenoid precursor biosynthesis. The enzyme requires Mn2+, Co2+ or Mg2+ for activity, with Mn2+ being most effective.
References
- ^ a b Takahashi S, Kuzuyama T, Watanabe H, Seto H (August 1998). "A 1-deoxy-D-xylulose-5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in the non-mevalonate pathway for terpenoid biosynthesis". Proc. Natl. Acad. Sci. U.S.A. 95 (17): 9879–84. doi:10.1073/pnas.95.17.9879. PMC 21430. PMID 9707569.
External links
- DXP+reductoisomerase at the US National Library of Medicine Medical Subject Headings (MeSH)
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1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain Provide feedback
This domain is found to the C-terminus of PF02670 domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases which catalyse the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH [1].
Literature references
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Takahashi S, Kuzuyama T, Watanabe H, Seto H; , Proc Natl Acad Sci U S A 1998;95:9879-9884.: A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. PUBMED:9707569 EPMC:9707569
This tab holds annotation information from the InterPro database.
InterPro entry IPR013644
1-deoxy-D-xylulose 5-phosphate reductoisomerase synthesises 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate in a single step by intramolecular rearrangement and reduction and is responsible for terpenoid biosynthesis in some organisms [ PUBMED:9707569 ]. In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the non-mevalonate pathway for isoprenoid biosynthesis. The enzyme requires Mn2+, Co2+ or Mg2+ for activity, with the first being most effective.
This domain is found to the C terminus of INTERPRO domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | protein binding (GO:0005515) |
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 GADPH_aa-bio_dh (CL0139), which has the following description:
This clan contains the C terminal domains of dehydrogenase enzymes involved in the biosynthesis of arginine, aspartate and aspartate derived amino acids. It also contains the C terminal domain of GAPDH, a dehydrogenase involved in glycolysis and gluconeogenesis.
The clan contains the following 17 members:
AcetDehyd-dimer Biliv-reduc_cat DapB_C DAPDH_C DUF108 DXP_redisom_C G6PD_C GFO_IDH_MocA_C GFO_IDH_MocA_C2 Gp_dh_C Homoserine_dh Inos-1-P_synth ox_reductase_C Oxidoreduct_C OxRdtase_C Sacchrp_dh_C Semialdhyde_dhCAlignments
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 and the UniProtKB sequence database. More...
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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 (458) |
Full (6843) |
Representative proteomes | UniProt (33368) |
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RP15 (992) |
RP35 (3469) |
RP55 (6932) |
RP75 (11623) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (458) |
Full (6843) |
Representative proteomes | UniProt (33368) |
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RP15 (992) |
RP35 (3469) |
RP55 (6932) |
RP75 (11623) |
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Raw Stockholm | |||||||
Gzipped |
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.
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_445 (release 18.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Wuster A |
Number in seed: | 458 |
Number in full: | 6843 |
Average length of the domain: | 85.10 aa |
Average identity of full alignment: | 58 % |
Average coverage of the sequence by the domain: | 21.63 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 84 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 DXP_redisom_C domain has been found. There are 144 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.
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