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50  structures 4642  species 1  interaction 6022  sequences 17  architectures

Family: Ribul_P_3_epim (PF00834)

Summary: Ribulose-phosphate 3 epimerase family

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This is the Wikipedia entry entitled "Ribulose-phosphate 3-epimerase". More...

Ribulose-phosphate 3-epimerase Edit Wikipedia article

ribulose-phosphate 3-epimerase
EC number
CAS number 9024-20-8
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Ribulose-phosphate 3 epimerase family
Symbol Ribul_P_3_epim
Pfam PF00834
InterPro IPR000056
SCOP 1rpx

In enzymology, a ribulose-phosphate 3-epimerase (EC (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle.

D-ribulose 5-phosphate \rightleftharpoons D-xylulose 5-phosphate

Hence, this enzyme has one substrate, D-ribulose 5-phosphate, and one product, D-xylulose 5-phosphate.

This enzyme belongs to the family of isomerases, specifically those racemases and epimerases acting on carbohydrates and derivatives.

In Alcaligenes eutrophus two copies of the gene coding for PPE are known,[1] one is chromosomally encoded P40117, the other one is on a plasmid Q04539. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.

The systematic name of this enzyme class is D-ribulose-5-phosphate 3-epimerase. Other names in common use include phosphoribulose epimerase, erythrose-4-phosphate isomerase, phosphoketopentose 3-epimerase, xylulose phosphate 3-epimerase, phosphoketopentose epimerase, ribulose 5-phosphate 3-epimerase, D-ribulose phosphate-3-epimerase, D-ribulose 5-phosphate epimerase, D-ribulose-5-P 3-epimerase, D-xylulose-5-phosphate 3-epimerase, and pentose-5-phosphate 3-epimerase.

This enzyme participates in 3 metabolic pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and carbon fixation.

Structural studies[edit]

As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes 1H1Y, 1H1Z, 1RPX, and 1TQJ.

Human proteins containing this domain[edit]

RPE (gene);


  • Ashwell G and Hickman J (1957). "Enzymatic formation of xylulose 5-phosphate from ribose 5-phosphate in spleen". J. Biol. Chem. 226 (1): 65–76. PMID 13428737. 
  • DICKENS F, WILLIAMSON DH (1956). "Pentose phosphate isomerase and epimerase from animal tissues". Biochem. J. 64 (3): 567–78. PMC 1199776. PMID 13373810. 
  • Hurwitz J and Horecker BL (1956). "The purification of phosphoketopentoepimerase from Lactobacillus pentosus and the preparation of xylulose 5-phosphate". J. Biol. Chem. 223 (2): 993–1008. PMID 13385247. 
  • Stumpf PK and Horecker BL (1956). "The roole of xylulose 5-phosphate in xylose metabolism of Lactobacillus pentosus". J. Biol. Chem. 218: 753–768. 
  • Terada T, Mukae H, Ohashi K, Hosomi S, Mizoguchi T, Uehara K (1985). "Characterization of an enzyme which catalyzes isomerization and epimerization of D-erythrose 4-phosphate". Eur. J. Biochem. 148 (2): 345–51. doi:10.1111/j.1432-1033.1985.tb08845.x. PMID 3987693. 

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.

Ribulose-phosphate 3 epimerase family Provide feedback

This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000056

Ribulose-phosphate 3-epimerase (EC) (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Ralstonia eutropha (Alcaligenes eutrophus) two copies of the gene coding for PPE are known [PUBMED:1429456], one is chromosomally encoded SWISSPROT, the other one is on a plasmid SWISSPROT. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure. This family also includes other enzymes from the ribulose-phosphate 3-epimerase family, like D-allulose-6-phosphate 3-epimerase and other putative pentose-5-phosphate 3-epimerases. D-allulose-6-phosphate 3-epimerase catalyses the reversible epimerization of D-allulose 6-phosphate to D-fructose 6-phosphate, but it can also catalyse with lower efficiency the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate [PUBMED:18700786].

Gene Ontology

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Domain organisation

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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Curation and family details

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Seed source: Pfam-B_1291 (release 2.1)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 13
Number in full: 6022
Average length of the domain: 198.40 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 88.92 %

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 20.6 20.6
Trusted cut-off 20.6 20.7
Noise cut-off 20.5 20.3
Model length: 201
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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



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 Ribul_P_3_epim domain has been found. There are 50 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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