Summary: Firmicute fructose-1,6-bisphosphatase

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Wikipedia: Fructose 1,6-bisphosphatase
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Fructose 1,6-bisphosphatase Edit Wikipedia article

fructose-1,6-bisphosphatase 1

Fructose-1,6-bisphosphatase and its fructose 2,6-bisphosphate complex. Rendered from PDB 3FBP.
Identifiers
Symbol	FBP1
Alt. symbols	FBP
Entrez	2203
HUGO	3606
OMIM	229700
RefSeq	NM_000507
UniProt	P09467
Other data
EC number	3.1.3.11
Locus	Chr. 9 q22.3

Fructose-1-6-bisphosphatase

crystal structure of rabbit liver fructose-1,6-bisphosphatase at 2.3 angstrom resolution

Identifiers

Symbol

FBPase

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Firmicute fructose-1,6-bisphosphatase

Identifiers

Symbol

FBPase_2

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Fructose-1,6-bisphosphatase

crystal structure of fructose-1,6-bisphosphatase

Identifiers

Symbol

FBPase_3

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Fructose bisphosphatase (EC 3.1.3.11) is an enzyme that converts fructose-1,6-bisphosphate to fructose 6-phosphate in gluconeogenesis and the Calvin cycle which are both anabolic pathways. Fructose bisphosphatase catalyses the reverse of the reaction which is catalysed by phosphofructokinase in glycolysis.^[1]^[2] These enzymes only catalyse the reaction in one direction each, and are regulated by metabolites such as fructose 2,6-bisphosphate so that high activity of one of the two enzymes is accompanied by low activity of the other. More specifically, fructose 2,6-bisphosphate allosterically inhibits fructose 1,6-bisphosphatase, but activates phosphofructokinase-I. Fructose 1,6-bisphosphatase is involved in many different metabolic pathways and found in most organisms. FBPase requires metal ions for catalysis (Mg²⁺ and Mn²⁺ being preferred) and the enzyme is potently inhibited by Li⁺.

The fold of fructose-1,6-bisphosphatase from pig was noted to be identical to that of inositol-1-phosphatase (IMPase).^[3] Inositol polyphosphate 1-phosphatase (IPPase), IMPase and FBPase share a sequence motif (Asp-Pro-Ile/Leu-Asp-Gly/Ser-Thr/Ser) which has been shown to bind metal ions and participate in catalysis. This motif is also found in the distantly-related fungal, bacterial and yeast IMPase homologues. It has been suggested that these proteins define an ancient structurally conserved family involved in diverse metabolic pathways, including inositol signalling, gluconeogenesis, sulphate assimilation and possibly quinone metabolism.^[4]

Three different groups of FBPases have been identified in eukaryotes and bacteria (FBPase I-III).^[5] None of these groups have been found in archaea so far, though a new group of FBPases (FBPase IV) which also show inositol monophosphatase activity has recently been identified in archaea.^[6]

A new group of FBPases (FBPase V) is found in thermophilic archaea and the hyperthermophilic bacterium Aquifex aeolicus.^[7] The characterised members of this group show strict substrate specificity for FBP and are suggested to be the true FBPase in these organisms.^[7]^[8] A structural study suggests that FBPase V has a novel fold for a sugar phosphatase, forming a four-layer alpha-beta-beta-alpha sandwich, unlike the more usual five-layered alpha-beta-alpha-beta-alpha arrangement.^[8] The arrangement of the catalytic side chains and metal ligands was found to be consistent with the three-metal ion assisted catalysis mechanism proposed for other FBPases.

The fructose 1,6-bisphosphatases found within the Firmicutes (low GC Gram-positive bacteria) do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited by AMP, though this can be overcome by phosphoenolpyruvate, and is dependent on Mn(2+).^[9]^[10] Mutants lacking this enzyme are apparently still able to grow on gluconeogenic growth substrates such as malate and glycerol.

[edit] Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles. ^{[Â§ 1]}

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Glycolysis and Gluconeogenesis edit

^ The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". http://www.wikipathways.org/index.php/Pathway:WP534.

[edit] See also

[edit] References

^ Marcus F, Harrsch PB (May 1990). "Amino acid sequence of spinach chloroplast fructose-1,6-bisphosphatase". Arch. Biochem. Biophys. 279 (1): 151â7. doi:10.1016/0003-9861(90)90475-E. PMID 2159755.
^ Marcus F, Gontero B, Harrsch PB, Rittenhouse J (March 1986). "Amino acid sequence homology among fructose-1,6-bisphosphatases". Biochem. Biophys. Res. Commun. 135 (2): 374â81. doi:10.1016/0006-291X(86)90005-7. PMID 3008716.
^ Zhang Y, Liang JY, Lipscomb WN (February 1993). "Structural similarities between fructose-1,6-bisphosphatase and inositol monophosphatase". Biochem. Biophys. Res. Commun. 190 (3): 1080â3. doi:10.1006/bbrc.1993.1159. PMID 8382485.
^ York JD, Ponder JW, Majerus PW (May 1995). "Definition of a metal-dependent/Li(+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure". Proc. Natl. Acad. Sci. U.S.A. 92 (11): 5149â53. doi:10.1073/pnas.92.11.5149. PMC 41866. PMID 7761465. //www.ncbi.nlm.nih.gov/pmc/articles/PMC41866/.
^ Donahue JL, Bownas JL, Niehaus WG, Larson TJ (October 2000). "Purification and characterization of glpX-encoded fructose 1, 6-bisphosphatase, a new enzyme of the glycerol 3-phosphate regulon of Escherichia coli". J. Bacteriol. 182 (19): 5624â7. PMC 111013. PMID 10986273. //www.ncbi.nlm.nih.gov/pmc/articles/PMC111013/.
^ Stec B, Yang H, Johnson KA, Chen L, Roberts MF (November 2000). "MJ0109 is an enzyme that is both an inositol monophosphatase and the 'missing' archaeal fructose-1,6-bisphosphatase". Nat. Struct. Biol. 7 (11): 1046â50. doi:10.1038/80968. PMID 11062561.
^ ^a ^b Rashid N, Imanaka H, Kanai T, Fukui T, Atomi H, Imanaka T (August 2002). "A novel candidate for the true fructose-1,6-bisphosphatase in archaea". J. Biol. Chem. 277 (34): 30649â55. doi:10.1074/jbc.M202868200. PMID 12065581.
^ ^a ^b Nishimasu H, Fushinobu S, Shoun H, Wakagi T (June 2004). "The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea". Structure 12 (6): 949â59. doi:10.1016/j.str.2004.03.026. PMID 15274916.
^ Fujita Y, Freese E (June 1979). "Purification and properties of fructose-1,6-bisphosphatase of Bacillus subtilis". J. Biol. Chem. 254 (12): 5340â9. PMID 221467.
^ Fujita Y, Yoshida K, Miwa Y, Yanai N, Nagakawa E, Kasahara Y (August 1998). "Identification and expression of the Bacillus subtilis fructose-1, 6-bisphosphatase gene (fbp)". J. Bacteriol. 180 (16): 4309â13. PMC 107433. PMID 9696785. //www.ncbi.nlm.nih.gov/pmc/articles/PMC107433/.

[edit] Further reading

Berg, Jeremy Mark; John L. Tymoczko, Lubert Stryer (2002). "Glycolysis and Gluconeogenesis". In Susan Moran (ed.). Biochemistry (5th Edition ed.). 41 Madison Avenue, New York, New York: W. H. Freeman and Company. ISBN 0-7167-3051-0. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=books&doptcmdl=GenBookHL&term=fructose+bisphosphatase+AND+stryer%5Bbook%5D+AND+216199%5Buid%5D&rid=stryer.section.2281#2284.

[edit] External links

Fructose-1,6-Biphosphatase at the US National Library of Medicine Medical Subject Headings (MeSH)

This article incorporates text from the public domain Pfam and InterPro IPR000146

This article incorporates text from the public domain Pfam and InterPro IPR009164

This article incorporates text from the public domain Pfam and InterPro IPR002803

Hydrolase: esterases (EC 3.1)

3.1.1: Carboxylic ester hydrolases

Lipase

Phospholipase
- A1
- A2
- B

3.1.2: Thioesterase

3.1.3: Phosphatase

Alkaline phosphatase
- ALPI
- ALPL
- ALPP
Acid phosphatase (Prostatic)/Tartrate-resistant acid phosphatase/Purple acid phosphatases
Nucleotidase
Glucose 6-phosphatase
Fructose 1,6-bisphosphatase
- Calcineurin
Phosphoprotein phosphatase
- PP2A
OCRL
Pyruvate dehydrogenase phosphatase
Fructose 6-P,2-kinase:fructose 2,6-bisphosphatase
PTEN
Phytase
Inositol-phosphate phosphatase
- IMPA1

3.1.4: Phosphodiesterase

3.1.6: Sulfatase

Nuclease (includes
deoxyribonuclease and
ribonuclease)

3.1.11-16: Exonuclease

Exodeoxyribonuclease	RecBCD

Exoribonuclease	Oligonucleotidase

3.1.21-31: Endonuclease

Endodeoxyribonuclease	Deoxyribonuclease I Deoxyribonuclease II Deoxyribonuclease IV Restriction enzyme UvrABC endonuclease

Endoribonuclease	RNase III RNase H 1 2A 2B 2C RNase P RNase A 1 2 3 4/5 RNase T1 RNA-induced silencing complex

either deoxy- or ribo-	Aspergillus nuclease S1 Micrococcal nuclease

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

Metabolism: carbohydrate metabolism: glycolysis/gluconeogenesis enzymes

Glycolysis

Hexokinase (HK1, HK2, HK3, Glucokinase)â/Glucose 6-phosphataseâ Â· Glucose isomerase Â· Phosphofructokinase 1 (Liver, Muscle, Platelet)â/Fructose 1,6-bisphosphataseâ

Fructose-bisphosphate aldolase (Aldolase A, B, C) Â· Triosephosphate isomerase

Glyceraldehyde 3-phosphate dehydrogenase Â· Phosphoglycerate kinase Â· Phosphoglycerate mutase Â· Enolase Â· Pyruvate kinase (PKLR, PKM2)

Gluconeogenesis only

to oxaloacetate: Pyruvate carboxylase Â· Phosphoenolpyruvate carboxykinase

from lactate (Cori cycle): Lactate dehydrogenase

from alanine (Alanine cycle): Alanine transaminase

from glycerol: Glycerol kinase Â· Glycerol dehydrogenase

Regulatory

Fructose 6-P,2-kinase:fructose 2,6-bisphosphatase (PFKFB1, PFKFB2, PFKFB3, PFKFB4) Â· Bisphosphoglycerate mutase

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

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.

Firmicute fructose-1,6-bisphosphatase Provide feedback

This family consists of several bacterial fructose-1,6-bisphosphatase proteins ( EC:3.1.3.11) which seem to be specific to phylum Firmicutes. Fructose-1,6-bisphosphatase (FBPase) is a well known enzyme involved in gluconeogenesis [1]. This family does not seem to be structurally related to PF00316.

Literature references

Fujita Y, Yoshida K, Miwa Y, Yanai N, Nagakawa E, Kasahara Y; , J Bacteriol 1998;180:4309-4313.: Identification and expression of the Bacillus subtilis fructose-1, 6-bisphosphatase gene (fbp). PUBMED:9696785 EPMC:9696785

External database links

PANDIT:	PF06874
Pseudofam:	PF06874
SYSTERS:	FBPase_2

This tab holds annotation information from the InterPro database.

InterPro entry IPR009164

Fructose 1,6-bisphosphatase catalyses the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate [PUBMED:3008716]. This is an essential reaction in the process of gluconeogenesis, the process by which non-carbohydrate precursors are converted to glucose, and hence this enzyme is found almost universally. Enzyme activity can be regulated by a number of different mechanisms including AMP inhibition, cylic AMP-dependent phosphorylation and light-dependent-activation.

This entry represents a group of fructose 1,6-bisphosphatases found within the Firmicutes (low GC Gram-positive bacteria) which do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited by AMP, though this can be overcome by phosphoenolpyruvate, and is dependent on Mn(2+) [PUBMED:221467, PUBMED:9696785]. Mutants lacking this enzyme are apparently still able to grow on gluconeogenic growth substrates such as malate and glycerol.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)
Biological process	gluconeogenesis (GO:0006094)

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 Calcineurin (CL0163), which contains the following 8 members:

DNA_pol_E_B FBPase_2 Metallophos Metallophos_2 Metallophos_3 PGA_cap PhoD YmdB

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

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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 (33)	Full (868)	Representative proteomes				NCBI (645)	Meta (36)
	Seed (33)	Full (868)	RP15 (39)	RP35 (65)	RP55 (82)	RP75 (91)	NCBI (645)	Meta (36)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (33)	Full (868)	Representative proteomes				NCBI (645)	Meta (36)
	Seed (33)	Full (868)	RP15 (39)	RP35 (65)	RP55 (82)	RP75 (91)	NCBI (645)	Meta (36)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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 (33)	Full (868)	Representative proteomes				NCBI (645)	Meta (36)
	Seed (33)	Full (868)	RP15 (39)	RP35 (65)	RP55 (82)	RP75 (91)	NCBI (645)	Meta (36)
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

Seed source:

Pfam-B_13194 (release 10.0)

Previous IDs:

Firmicut_FBPase;

Type:

Family

Author:

Moxon SJ

Number in seed:

33

Number in full:

868

Average length of the domain:

621.00 aa

Average identity of full alignment:

51 %

Average coverage of the sequence by the domain:

98.14 %

HMM information

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	21.5	21.5
Trusted cut-off	21.6	21.5
Noise cut-off	21.2	21.4

Model length:

641

Family (HMM) version:

6

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: FBPase_2 (PF06874)

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Summary: Firmicute fructose-1,6-bisphosphatase

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Fructose 1,6-bisphosphatase Edit Wikipedia article

Contents

[edit] Interactive pathway map

[edit] See also

[edit] References

[edit] Further reading

[edit] External links

Firmicute fructose-1,6-bisphosphatase Provide feedback

Literature references

External database links

InterPro entry IPR009164

Gene Ontology

Domain organisation

Pfam Clan

Alignments

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