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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

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 "Ribulose-phosphate 3-epimerase". More...

Ribulose-phosphate 3-epimerase Edit Wikipedia article

ribulose-phosphate 3-epimerase
Identifiers
EC number 5.1.3.1
CAS number 9024-20-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Ribulose-phosphate 3 epimerase family
Identifiers
Symbol Ribul_P_3_epim
Pfam PF00834
InterPro IPR000056
PROSITE PDOC00833
SCOP 1rpx
SUPERFAMILY 1rpx

In enzymology, a ribulose-phosphate 3-epimerase (EC 5.1.3.1) (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);

References[edit]

  • 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. 


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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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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 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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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
(13)
Full
(6022)
Representative proteomes NCBI
(4019)
Meta
(3152)
RP15
(465)
RP35
(866)
RP55
(1148)
RP75
(1359)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(13)
Full
(6022)
Representative proteomes NCBI
(4019)
Meta
(3152)
RP15
(465)
RP35
(866)
RP55
(1148)
RP75
(1359)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(13)
Full
(6022)
Representative proteomes NCBI
(4019)
Meta
(3152)
RP15
(465)
RP35
(866)
RP55
(1148)
RP75
(1359)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

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.

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_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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Interactions

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

Ribul_P_3_epim

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 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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