Summary: Xylose isomerase-like TIM barrel
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Xylose isomerase-like TIM barrel Provide feedback
This TIM alpha/beta barrel structure is found in xylose isomerase (P19148) and in endonuclease IV (P12638 EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae [1].
Literature references
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Fry J, Wood M, Poole PS; , Mol Plant Microbe Interact 2001;14:1016-1025.: Investigation of myo-inositol catabolism in Rhizobium leguminosarum bv. viciae and its effect on nodulation competitiveness. PUBMED:11497462 EPMC:11497462
Internal database links
SCOOP: | DeoC DUF4862 DUF692 Glyco_hydro_97 HisKA Orn_Arg_deC_N Orn_DAP_Arg_deC PdxJ Pro_dh RhaA UvdE UxuA |
Similarity to PfamA using HHSearch: | UxuA UvdE DUF692 |
External database links
PROSITE: | PDOC00599 |
SCOP: | 1qtw |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013022
This entry represents a structural motif with a beta/alpha TIM barrel found in several proteins families:
- Endonuclease IV ( EC ), an AP (apurinic/apyrimidinic) endonuclease that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites [ PUBMED:10458614 ].
- L-rhamnose isomerase ( EC ), a tetramer of four TIM barrels that catalyses the isomerisation between aldoses and ketoses, such as between L-rhamnose and L-rhamnulose [ PUBMED:17141803 ].
- Xylose isomerase ( EC ), which catalyses the first reaction in the catabolism of D-xylose by converting D-xylose to D-xylulose [ PUBMED:16673077 ].
- Mannonate dehydratase UxuA, which along with mannonate oxidoreductase converts D-fructuronate to 2-keto-3-deoxy-D-gluconate [ PUBMED:7007313 ].
These proteins share similar, but not identical, metal-binding sites. In addition, xylose isomerase and L-rhamnose isomerase each have additional alpha-helical domains involved in tetramer formation.
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 has the following description:
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 UxuAAlignments
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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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 (163) |
Full (43752) |
Representative proteomes | UniProt (196516) |
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RP15 (4805) |
RP35 (19981) |
RP55 (43911) |
RP75 (75915) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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Seed (163) |
Full (43752) |
Representative proteomes | UniProt (196516) |
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RP15 (4805) |
RP35 (19981) |
RP55 (43911) |
RP75 (75915) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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: | Prosite & Pfam-B_3980 (Release 7.5) |
Previous IDs: | AP_endonulease2; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 163 |
Number in full: | 43752 |
Average length of the domain: | 251.00 aa |
Average identity of full alignment: | 14 % |
Average coverage of the sequence by the domain: | 79.50 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 250 | ||||||||||||
Family (HMM) version: | 26 | ||||||||||||
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 AP_endonuc_2 domain has been found. There are 612 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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