Summary: Pyrimidine nucleoside phosphorylase C-terminal domain
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Pyrimidine nucleoside phosphorylase C-terminal domain Provide feedback
This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, P77826) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, P07650) [1]. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer [1].
Literature references
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Pugmire MJ, Ealick SE; , Structure 1998;6:1467-1479.: The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation. PUBMED:9817849 EPMC:9817849
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Walter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE; , J Biol Chem 1990;265:14016-14022.: Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. PUBMED:2199449 EPMC:2199449
Internal database links
SCOOP: | DUF2254 |
External database links
SCOP: | 1brw |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013102
This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [PUBMED:9817849, PUBMED:2199449]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, SWISSPROT) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as Escherichia coli thymidine phosphorylase (TP, SWISSPROT) [PUBMED:9817849]. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer [PUBMED:9817849].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | transferase activity, transferring pentosyl groups (GO:0016763) |
Biological process | pyrimidine nucleoside metabolic process (GO:0006213) |
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 Hybrid (CL0105), which has the following description:
This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.
The clan contains the following 24 members:
Apocytochr_F_C Biotin_carb_C Biotin_lipoyl Biotin_lipoyl_2 Complex1_51K DUF2118 DUF2254 GARS_C GCV_H HlyD HlyD_2 HlyD_3 HlyD_D23 HlyD_D4 LAL_C2 NAPRTase_N NQRA OEP Peptidase_M23 PTS_EIIA_1 PurK_C PYNP_C QRPTase_N RnfC_NAlignments
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, the UniProtKB sequence database, 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 (45) |
Full (4184) |
Representative proteomes | UniProt (18932) |
NCBI (26940) |
Meta (414) |
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RP15 (525) |
RP35 (2013) |
RP55 (4237) |
RP75 (7073) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (45) |
Full (4184) |
Representative proteomes | UniProt (18932) |
NCBI (26940) |
Meta (414) |
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RP15 (525) |
RP35 (2013) |
RP55 (4237) |
RP75 (7073) |
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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: | Pfam-B_1661 (release 14.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Fenech M |
Number in seed: | 45 |
Number in full: | 4184 |
Average length of the domain: | 73.40 aa |
Average identity of full alignment: | 32 % |
Average coverage of the sequence by the domain: | 16.56 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 75 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 4 interactions for this family. More...
Glycos_trans_3N Glycos_transf_3 Glycos_transf_3 Glycos_trans_3NStructures
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 PYNP_C domain has been found. There are 50 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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