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144  structures 6154  species 0  interactions 7124  sequences 24  architectures

Family: DXP_redisom_C (PF08436)

Summary: 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain

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 "DXP reductoisomerase". More...

DXP reductoisomerase Edit Wikipedia article

DXP reductoisomerase is an enzyme which converts 2-C-methyl-D-erythritol 4-phosphate into 1-deoxy-D-xylulose 5-phosphate.

It is classified under EC 1.1.1.267.

It is part of the non-mevalonate pathway, and it is inhibited by fosmidomycin.

External links

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.

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

  1. 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.

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 18 members:

AcetDehyd-dimer Asp_DH_C Biliv-reduc_cat DapB_C DAPDH_C DXP_redisom_C G6PD_C GFO_IDH_MocA_C GFO_IDH_MocA_C2 Gp_dh_C Homoserine_dh Inos-1-P_synth OpcA_G6PD_C ox_reductase_C Oxidoreduct_C OxRdtase_C Sacchrp_dh_C Semialdhyde_dhC

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(457)
Full
(7124)
Representative proteomes UniProt
(35884)
RP15
(1053)
RP35
(3688)
RP55
(7413)
RP75
(12442)
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PP/heatmap 1            

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(457)
Full
(7124)
Representative proteomes UniProt
(35884)
RP15
(1053)
RP35
(3688)
RP55
(7413)
RP75
(12442)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(457)
Full
(7124)
Representative proteomes UniProt
(35884)
RP15
(1053)
RP35
(3688)
RP55
(7413)
RP75
(12442)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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 View help on the curation process

Seed source: Pfam-B_445 (release 18.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wuster A
Number in seed: 457
Number in full: 7124
Average length of the domain: 85.1 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 21.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.2 26.0
Noise cut-off 24.8 25.2
Model length: 84
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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...

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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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GJN7 View 3D Structure Click here
A0A144A2T4 View 3D Structure Click here
A0A1D6FCR1 View 3D Structure Click here
A0A1D6MNI9 View 3D Structure Click here
A0JUS3 View 3D Structure Click here
A0KHG9 View 3D Structure Click here
A0Q0R4 View 3D Structure Click here
A0QVH7 View 3D Structure Click here
A1AQN8 View 3D Structure Click here
A1AV71 View 3D Structure Click here
A1B969 View 3D Structure Click here
A1BJT7 View 3D Structure Click here
A1R4Z8 View 3D Structure Click here
A1S4P6 View 3D Structure Click here
A1SYV7 View 3D Structure Click here
A3DE52 View 3D Structure Click here
A3MZC4 View 3D Structure Click here
A3QG97 View 3D Structure Click here
A4G4S7 View 3D Structure Click here
A4J5Y5 View 3D Structure Click here
A4SCF3 View 3D Structure Click here
A4VJS7 View 3D Structure Click here
A4XWT5 View 3D Structure Click here
A4YVG0 View 3D Structure Click here
A5D2U3 View 3D Structure Click here
A5G7W2 View 3D Structure Click here
A5I4K2 View 3D Structure Click here
A5N834 View 3D Structure Click here
A6L0W8 View 3D Structure Click here
A7H0K4 View 3D Structure Click here
A7HLL7 View 3D Structure Click here
A7HZP3 View 3D Structure Click here
A8F4Z0 View 3D Structure Click here
A8FDB9 View 3D Structure Click here
A8H6L0 View 3D Structure Click here
A8MHH5 View 3D Structure Click here
A8ZTM6 View 3D Structure Click here
A9AIM0 View 3D Structure Click here
A9INU2 View 3D Structure Click here
A9KMX2 View 3D Structure Click here