Summary: Triosephosphate isomerase
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This is the Wikipedia entry entitled "Triosephosphate isomerase". More...
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Triosephosphate isomerase Edit Wikipedia article
Triose-phosphate isomerase, also called TIM, is an enzyme that catalyzes the reversible isomerisation of D-glyceraldehyde 3-phosphate to dihydroxyacetone phosphate, which are triose-phosphates, hence the name of the enzyme. This reaction is a part of the glucose-metabolism. TIM was found to occur in every organsims in which TIM was looked for, including humans, chicken, the sleeping sickness parasite, and the bacterium E. coli. Furthermore TIM catalyzes this reaction so fast that it an catalytic perfect enzyme.
The three-dimensional structure (Fig. 1) contains on the outside Î±-helices, and on the inside 8 ÃŸ-sheets. This structure is called ÃŸ/Î±-barrel (called alpha-beta barrel) or also TIM-barrel, since TIM is the prototype of this structure. Figure 1 shows one subunit of the dimeric human TIM. The active site of this enzyme is in the middle of this image. The N-terminus of this protein (the beginning of the amino acid chain) is in dark blue, the C-terminus (the end) is in red).
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Triosephosphate isomerase Provide feedback
Triosephosphate isomerase ( EC:184.108.40.206) (TIM)  is the glycolytic enzyme that catalyses the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production, present in eukaryotes and prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism [2,3]. The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure . The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder .
Jogl G, Rozovsky S, McDermott AE, Tong L;, Proc Natl Acad Sci U S A. 2003;100:50-55.: Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution. PUBMED:12509510 EPMC:12509510
Nagano N, Orengo CA, Thornton JM;, J Mol Biol. 2002;321:741-765.: One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. PUBMED:12206759 EPMC:12206759
Olah J, Orosz F, Keseru GM, Kovari Z, Kovacs J, Hollan S, Ovadi J;, Biochem Soc Trans. 2002;30:30-38.: Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease. PUBMED:12023819 EPMC:12023819
Internal database links
|SCOOP:||FMN_dh His_biosynth IGPS NMO ThiG Trp_syntA|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000652
Triosephosphate isomerase ( EC ) (TIM) [ PUBMED:2204417 ] is the glycolytic enzyme that catalyses the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production. It is present in eukaryotes as well as in prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism [ PUBMED:2005961 , PUBMED:12509510 ].
The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure. The TIM barrel fold occurs ubiquitously and is found in numerous other enzymes that can be involved in energy metabolism, macromolecule metabolism, or small molecule metabolism [ PUBMED:12206759 ].
The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder [ PUBMED:12023819 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||triose-phosphate isomerase activity (GO:0004807)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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EGFdomains, and finally a single
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This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 61 members:4HFCP_synth Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD ComA CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF2090 DUF4862 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm GatZ_KbaZ-like Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH KDGP_aldolase Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI PRMT5_TIM Pterin_bind QRPTase_C Radical_SAM Radical_SAM_2 RhaA Ribul_P_3_epim SOR_SNZ TAL_FSA ThiC_Rad_SAM ThiG TIM TMP-TENI Trp_syntA UvdE UxuA
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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|Number in seed:||207|
|Number in full:||12345|
|Average length of the domain:||237.4 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||91.55 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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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 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:
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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".
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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The tree shows the occurrence of this domain across different species. More...
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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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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 TIM domain has been found. There are 578 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.