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140  structures 6049  species 5  interactions 6191  sequences 13  architectures

Family: DXP_redisom_C (PF08436)

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
PDB 1q0q EBI.jpg
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
SCOP 1onn
SUPERFAMILY 1onn
DXP reductoisomerase
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

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 can be 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

External links

This article incorporates text from the public domain Pfam and InterPro IPR013512 This article incorporates text from the public domain Pfam and InterPro IPR013644


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 15 members:

AcetDehyd-dimer Biliv-reduc_cat DapB_C DAPDH_C DUF108 DXP_redisom_C G6PD_C GFO_IDH_MocA_C Gp_dh_C Homoserine_dh Inos-1-P_synth ox_reductase_C Oxidoreduct_C Sacchrp_dh_C Semialdhyde_dhC

Alignments

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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
(551)
Full
(6191)
Representative proteomes UniProt
(18808)
NCBI
(25293)
Meta
(1713)
RP15
(1603)
RP35
(4220)
RP55
(6305)
RP75
(8934)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(551)
Full
(6191)
Representative proteomes UniProt
(18808)
NCBI
(25293)
Meta
(1713)
RP15
(1603)
RP35
(4220)
RP55
(6305)
RP75
(8934)
Alignment:
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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
(551)
Full
(6191)
Representative proteomes UniProt
(18808)
NCBI
(25293)
Meta
(1713)
RP15
(1603)
RP35
(4220)
RP55
(6305)
RP75
(8934)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

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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.

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: 551
Number in full: 6191
Average length of the domain: 85.40 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 21.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.4 23.4
Trusted cut-off 23.4 23.8
Noise cut-off 22.2 23.3
Model length: 84
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Interactions

There are 5 interactions for this family. More...

DXP_reductoisom DXPR_C DXP_reductoisom DXPR_C DXP_redisom_C

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 140 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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