Summary: Nucleoside 2-deoxyribosyltransferase
This is the Wikipedia entry entitled "Nucleoside deoxyribosyltransferase". More...
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Nucleoside deoxyribosyltransferase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
- 2-deoxy-D-ribosyl-base1 + base2 2-deoxy-D-ribosyl-base2 + base1
This enzyme belongs to the family of glycosyltransferases, specifically the pentosyltransferases. The systematic name of this enzyme class is nucleoside:purine(pyrimidine) deoxy-D-ribosyltransferase. Other names in common use include purine(pyrimidine) nucleoside:purine(pyrimidine) deoxyribosyl, transferase, deoxyribose transferase, nucleoside trans-N-deoxyribosylase, trans-deoxyribosylase, trans-N-deoxyribosylase, trans-N-glycosidase, nucleoside deoxyribosyltransferase I (purine nucleoside:purine, deoxyribosyltransferase: strictly specific for transfer between, purine bases), nucleoside deoxyribosyltransferase II [purine(pyrimidine), and nucleoside:purine(pyrimidine) deoxyribosyltransferase]. This enzyme participates in pyrimidine metabolism.
- KALCKAR HM, MACNUTT WS, HOFF-JORGENSEN E (1952). "Trans-N-glycosidase studied with radioactive adenine". Biochem. J. 50 (3): 397–400. PMC 1197666. PMID 14915963.
- MACNUTT WS (1952). "The enzymically catalysed transfer of the deoxyribosyl group from one purine or pyrimidine to another". Biochem. J. 50 (3): 384–97. PMC 1197665. PMID 14915962.
- ROUSH AH, BETZ RF (1958). "Purification and properties of trans-N-deoxyribosylase". J. Biol. Chem. 233 (2): 261–6. PMID 13563482.
|This enzyme-related article is a stub. You can help Wikipedia by expanding it.|
Nucleoside 2-deoxyribosyltransferase Provide feedback
Nucleoside 2-deoxyribosyltransferase EC:220.127.116.11 catalyses the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides .
Porter DJ, Merrill BM, Short SA; , J Biol Chem 1995;270:15551-15556.: Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98. PUBMED:7797550 EPMC:7797550
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007710
Nucleoside 2-deoxyribosyltransferase (EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [PUBMED:14992575] and class II [PUBMED:8805514] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||deoxyribonucleoside 5'-monophosphate N-glycosidase activity (GO:0070694)|
|nucleoside deoxyribosyltransferase activity (GO:0050144)|
|Biological process||deoxyribonucleoside monophosphate catabolic process (GO:0009159)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This superfamily includes the N-deoxyribosyltransferase and ADP-ribosyl cyclase-like families as well as the family that includes the hypothetical protein PA1492 for which the structure is known. PA1942 has a very similar putative active site and is predicted by SCOP to have a deoxyribosyltransferase activity .
The clan contains the following 6 members:DUF1937 DUF4406 Nuc_deoxyri_tr2 Nuc_deoxyri_tr3 Nuc_deoxyrib_tr Rib_hydrolayse
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
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Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||56|
|Number in full:||3173|
|Average length of the domain:||129.30 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||75.81 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Nuc_deoxyrib_tr domain has been found. There are 82 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.
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