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13  structures 1790  species 0  interactions 2306  sequences 3  architectures

Family: FBPase_glpX (PF03320)

Summary: Bacterial fructose-1,6-bisphosphatase, glpX-encoded

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Bacterial fructose-1,6-bisphosphatase, glpX-encoded Provide feedback

No Pfam abstract.

Literature references

  1. Donahue JL, Bownas JL, Niehaus WG, Larson TJ; , J Bacteriol 2000;182:5624-5627.: Purification and characterization of glpX-encoded fructose 1, 6-bisphosphatase, a new enzyme of the glycerol 3-phosphate regulon of Escherichia coli. PUBMED:10986273 EPMC:10986273


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004464

Gluconeogenesis is an important metabolic pathway, which produces glucose from noncarbohydrate precursors such as organic acids, fatty acids, amino acids, or glycerol. Fructose-1,6-bisphosphatase, a key enzyme of gluconeogenesis, is found in all organisms, and five different classes of these enzymes have been identified.

This entry represents the class 2 fructose-1,6-bisphosphatases, which include GlpX and YggF of Escherichia coli (strain K12), which show different catalytic properties. The crystal structure of GlpX has been determined in a free state and in the complex with a substrate (fructose 1,6-bisphosphate) or inhibitor (phosphate). The crystal structure of the ligand-free GlpX revealed a compact, globular shape with two alpha/beta-sandwich domains. The core fold of GlpX is structurally similar to that of Li+-sensitive phosphatases suggesting that they have a common evolutionary origin and catalytic mechanism. The structure of the GlpX complex with fructose 1,6-bisphosphate revealed that the active site is located between two domains and accommodates several conserved residues coordinating two metal ions and the substrate. A third metal ion is bound to phosphate 6 of the substrate. Inorganic phosphate strongly inhibited activity of both GlpX and YggF, and the crystal structure of the GlpX complex with phosphate demonstrated that the inhibitor molecule binds to the active site. Alanine replacement mutagenesis of GlpX identifies 12 conserved residues important for activity and suggested that Thr(90) is the primary catalytic residue [PUBMED:19073594].

A number of the proteins in this entry, particularly those from algae are bi functional and can catalyzes the hydrolysis of fructose 1,6-bisphosphate and sedoheptulose 1,7-bisphosphate to fructose 6-phosphate and sedoheptulose 7-phosphate, respectively.

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 Phospoesterase (CL0171), which contains the following 3 members:

FBPase FBPase_glpX Inositol_P

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
(111)
Full
(2306)
Representative proteomes NCBI
(1381)
Meta
(1900)
RP15
(146)
RP35
(291)
RP55
(369)
RP75
(437)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(111)
Full
(2306)
Representative proteomes NCBI
(1381)
Meta
(1900)
RP15
(146)
RP35
(291)
RP55
(369)
RP75
(437)
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
(111)
Full
(2306)
Representative proteomes NCBI
(1381)
Meta
(1900)
RP15
(146)
RP35
(291)
RP55
(369)
RP75
(437)
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.

Pfam alignments:

HMM logo

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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_3515 (release 6.5)
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 111
Number in full: 2306
Average length of the domain: 308.20 aa
Average identity of full alignment: 54 %
Average coverage of the sequence by the domain: 95.06 %

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 20.5 20.5
Trusted cut-off 20.6 20.9
Noise cut-off 19.5 20.3
Model length: 309
Family (HMM) version: 8
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 FBPase_glpX domain has been found. There are 13 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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