Summary: Transaldolase

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Wikipedia: Transaldolase
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Transaldolase Edit Wikipedia article

It has been suggested that Transaldolase B be merged into this article or section. (Discuss) Proposed since September 2010.

Transaldolase

Identifiers

Databases

PDB structures

AmiGO / EGO

Search
PMC	articles
PubMed	articles
NCBI	proteins

Transaldolase

Crystallographic structure of human transaldolase.^[1]^[2]

Identifiers

Symbol

Transaldolase

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

Transaldolase
Identifiers
Symbol	TALDO1
Entrez	6888
HUGO	11559
OMIM	602063
RefSeq	NM_006755
UniProt	P37837
Other data
EC number	2.2.1.2
Locus	Chr. 11 p15.5-15.4

Transaldolase is an enzyme (EC 2.2.1.2) of the non-oxidative phase of the pentose phosphate pathway. In humans, transaldolase is encoded by the TALDO1 gene.^[3]^[4]

The following chemical reaction is catalyzed by transaldolase:

sedoheptulose 7-phosphate + glyceraldehyde 3-phosphate $\rightleftharpoons$ erythrose 4-phosphate + fructose 6-phosphate

[edit] Clinical significance

The pentose phosphate pathway has two metabolic functions: (1) generation of nicotinamide adenine dinucleotide phosphate (reduced NADPH), for reductive biosynthesis, and (2) formation of ribose which is an essential component of ATP, DNA, and RNA. Transaldolase links the pentose phosphate pathway to glycolysis. In patients with deficiency of transaldolase, there's an accumulation of erythritol (from erythrose 4-phosphate), D-arabitol, and ribitol.^[5]^[6]

The deletion in 3 base pairs in the TALDO1 gene results in the absence of serine at position 171 of the transaldolase protein, which is part of a highly conserved region suggesting that the mutation causes the transaldolase deficiency that is found in erythrocytes and lymphoblasts.^[5] The deletion of this amino acid can lead to liver cirrhosis and hepatosplenomegaly (enlarged spleen and liver) during early infancy. Transaldolase is also a target of autoimmunity in patients with multiple sclerosis.^[7]

[edit] Structure

Active site of the transaldolase enzyme highlighting the key amino acid residues (Asp-27, Glu-106, and Lys-142) involved in catalysis.^[1]

Transaldolase is a single domain composed of 337 amino acids. The core structure is an α/β barrel, similar to other class I aldolases, made up of eight parallel β-sheets and seven α-helices. There are also seven additional α-helices that are not part of the barrel. Hydrophobic amino acids are located between the β-sheets in the barrel and the surrounding α-helices to contribute to packing, such as the area containing Leu-168, Phe-170, Phe-189, Gly-311, and Phe-315. In the crystal, human transaldolase forms a dimer, with the two subunits connected by 18 residues in each subunit. See mechanism to the left for details.

The active site, located in the center of the barrel, contains three key residues: lysine-142, glutamate-106, and aspartate-27. The lysine holds the sugar in place while the glutamate and aspartate act as proton donors and acceptors.^[1]

[edit] Mechanism of catalysis

The residue of lysine-142 in the active site of transaldolase forms a Schiff base with the keto group in sedoheptulose-7-phosphate after deprotonation by another active site residue, glutamate-106. The reaction mechanism is similar to the reverse reaction catalyzed by aldolase: the bond joining carbons 3 and 4 is broken, leaving dihydroxyacetone joined to the enzyme via a Schiff base. This cleavage reaction generates the unusual aldose sugar erythrose-4-phosphate. Then transaldolase catalyzes the condensation of glyceraldehyde-3-phosphate with the Schiff base of dihydroxyacetone, yielding enzyme bound fructose 6-phosphate. Hydrolysis of the Schiff base liberates free fructose 6-phosphate, one of the products of the pentose phosphate pathway.

Reaction scheme for the conversion of sedoheptulose-7-phosphate to fructose-6-phosphate.^[8]

The pentose phosphate pathway adapted from (Verhoeven, 2001)^[5]

[edit] See also

Transaldolase deficiency

[edit] References

^ ^a ^b ^c PDB 1F05; Thorell S, Gergely P, Banki K, Perl A, Schneider G (June 2000). "The three-dimensional structure of human transaldolase". FEBS Lett. 475 (3): 205–8. doi:10.1016/S0014-5793(00)01658-6. PMID 10869557.
^ Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera–a visualization system for exploratory research and analysis". J Comput Chem 25 (13): 1605–12. doi:10.1002/jcc.20084. PMID 15264254.
^ "Entrez Gene: transaldolase 1". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6888.
^ Banki K, Eddy RL, Shows TB, Halladay DL, Bullrich F, Croce CM, Jurecic V, Baldini A, Perl A (October 1997). "The human transaldolase gene (TALDO1) is located on chromosome 11 at p15.4-p15.5". Genomics 45 (1): 233–8. doi:10.1006/geno.1997.4932. PMID 9339383.
^ ^a ^b ^c Verhoeven NM, Huck JH, Roos B, Struys EA, Salomons GS, Douwes AC, van der Knaap MS, Jakobs C (May 2001). "Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway". Am. J. Hum. Genet. 68 (5): 1086–92. doi:10.1086/320108. PMC 1226089. PMID 11283793. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1226089/.
^ Perl A (June 2007). "The pathogenesis of transaldolase deficiency". IUBMB Life 59 (6): 365–73. doi:10.1080/15216540701387188. PMID 17613166.
^ Niland B, Perl A (2004). "Evaluation of autoimmunity to transaldolase in multiple sclerosis". Methods Mol. Med. 102: 155–71. doi:10.1385/1-59259-805-6:155. PMID 15286385.
^ Jia J, Schörken U, Lindqvist Y, Sprenger GA, Schneider G (January 1997). "Crystal structure of the reduced Schiff-base intermediate complex of transaldolase B from Escherichia coli: mechanistic implications for class I aldolases". Protein Sci. 6 (1): 119–24. doi:10.1002/pro.5560060113. PMC 2143518. PMID 9007983. http://www.proteinscience.org/cgi/content/abstract/6/1/119.

[edit] External links

Transaldolase at the US National Library of Medicine Medical Subject Headings (MeSH)

Transferases: aldehyde-ketone (EC 2.2)

2.2.1

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 · pentose phosphate pathway enzymes

oxidative

nonoxidative

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)

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Transaldolase Provide feedback

No Pfam abstract.

Literature references

Choi KH, Shi J, Hopkins CE, Tolan DR, Allen KN; , Biochemistry 2001;40:13868-13875.: Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate. PUBMED:11705376 EPMC:11705376
Schorken U, Thorell S, Schurmann M, Jia J, Sprenger GA, Schneider G; , Eur J Biochem 2001;268:2408-2415.: Identification of catalytically important residues in the active site of Escherichia coli transaldolase. PUBMED:11298760 EPMC:11298760
Thorell S, Gergely P Jr, Banki K, Perl A, Schneider G , FEBS Lett 2000;475:205-208.: The three-dimensional structure of human transaldolase. PUBMED:10869557 EPMC:10869557

External database links

HOMSTRAD:	Transaldolase
PANDIT:	PF00923
PROSITE:	PDOC00741
Pseudofam:	PF00923
SCOP:	1ucw
SYSTERS:	Transaldolase

This tab holds annotation information from the InterPro database.

InterPro entry IPR001585

Transaldolase (EC) catalyses the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. This enzyme, together with transketolase, provides a link between the glycolytic and pentose-phosphate pathways. Transaldolase is an enzyme of about 34 kDa whose sequence has been well conserved throughout evolution. A lysine has been implicated [PUBMED:8109173] in the catalytic mechanism of the enzyme; it acts as a nucleophilic group that attacks the carbonyl group of fructose-6-phosphate.

Gene Ontology

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

Biological process

carbohydrate metabolic process (GO:0005975)

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 TIM_barrel (CL0036), which contains the following 57 members:

Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH iPGM_N MtrH NanE NAPRTase NeuB NMO OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PhosphMutase PRAI Pterin_bind QRPTase_C Racemase_4 RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiG TIM TIM-br_sig_trns TMP-TENI Transaldolase Trp_syntA UvdE UxuA

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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HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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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 (131)	Full (6718)	Representative proteomes				NCBI (4243)	Meta (3165)
	Seed (131)	Full (6718)	RP15 (481)	RP35 (911)	RP55 (1226)	RP75 (1447)	NCBI (4243)	Meta (3165)
Jalview	View	View	View	View	View	View	View	View
HTML	View		View	View	View	View
PP/heatmap	₁		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 (131)	Full (6718)	Representative proteomes				NCBI (4243)	Meta (3165)
	Seed (131)	Full (6718)	RP15 (481)	RP35 (911)	RP55 (1226)	RP75 (1447)	NCBI (4243)	Meta (3165)
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 (131)	Full (6718)	Representative proteomes				NCBI (4243)	Meta (3165)
	Seed (131)	Full (6718)	RP15 (481)	RP35 (911)	RP55 (1226)	RP75 (1447)	NCBI (4243)	Meta (3165)
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_787 (release 3.0)

Previous IDs:

none

Type:

Family

Author:

Bateman A, Griffiths-Jones SR

Number in seed:

131

Number in full:

6718

Average length of the domain:

256.10 aa

Average identity of full alignment:

30 %

Average coverage of the sequence by the domain:

91.25 %

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	20.9	20.9
Trusted cut-off	22.8	22.2
Noise cut-off	20.2	20.0

Model length:

287

Family (HMM) version:

14

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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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

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

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.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

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.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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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.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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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.

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Interactions

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

Transaldolase

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 Transaldolase domain has been found. There are 128 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Transaldolase (PF00923)

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Summary: Transaldolase

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Transaldolase Edit Wikipedia article

Contents

[edit] Clinical significance

[edit] Structure

[edit] Mechanism of catalysis

[edit] See also

[edit] References

[edit] External links

Transaldolase Provide feedback

Literature references

External database links

InterPro entry IPR001585

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures