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83  structures 1228  species 0  interactions 1594  sequences 14  architectures

Family: Nuc_deoxyrib_tr (PF05014)

Summary: Nucleoside 2-deoxyribosyltransferase

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This is the Wikipedia entry entitled "Nucleoside deoxyribosyltransferase". More...

Nucleoside deoxyribosyltransferase Edit Wikipedia article

In enzymology, a nucleoside deoxyribosyltransferase (EC is an enzyme that catalyzes the chemical reaction

2-deoxy-D-ribosyl-base1 + base2 2-deoxy-D-ribosyl-base2 + base1

Thus, the two substrates of this enzyme are 2-deoxy-D-ribosyl-base1 and base2, whereas its two products are 2-deoxy-D-ribosyl-base2 and 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.

Structural studies

As of late 2007, 12 structures have been solved for this class of enzymes, with PDB accession codes 1F8X, 1F8Y, 1S2D, 1S2G, 1S2I, 1S2L, 1S3F, 2A0K, 2F2T, 2F62, 2F64, and 2F67.


Template:Enzyme references

  • KALCKAR HM, MACNUTT WS, HOFF-JORGENSEN E (1952). "Trans-N-glycosidase studied with radioactive adenine". Biochem. J. 50: 397–400. PMID 14915963.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  • MACNUTT WS (1952). "The enzymically catalysed transfer of the deoxyribosyl group from one purine or pyrimidine to another". Biochem. J. 50: 384–97. PMID 14915962.
  • ROUSH AH, BETZ RF (1958). "Purification and properties of trans-N-deoxyribosylase". J. Biol. Chem. 233: 261–6. PMID 13563482.

External links

The CAS registry number for this enzyme class is Template:CAS registry.

Template:Enzyme links

Gene Ontology (GO) codes

Template:GO code links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Nucleoside 2-deoxyribosyltransferase Provide feedback

Nucleoside 2-deoxyribosyltransferase EC: catalyses the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides [1].

Literature references

  1. 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

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007710

Nucleoside 2-deoxyribosyltransferase (NDT) ( 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.

This entry also includes the related enzyme deoxynucleoside 5-monophosphate N-glycosidase (DNPH1), a nucleotide hydrolase ( EC ). DNPH1 is related to NDT in structure and enzymatic activity, but in contrast to NDT catalyzes the hydrolysis of 2'-deoxyribonucleoside 5'-monophosphate to yield a free nucleobase and 2-deoxyribose 5-phosphate [ PUBMED:17234634 , PUBMED:29273295 ]. DNPH1 is a potential proto-oncogene [ PUBMED:11526483 ].

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 Nribosyltransf (CL0498), which has the following description:

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 [1].

The clan contains the following 7 members:

DRHyd-ASK DUF1937 DUF4406 Nuc_deoxyri_tr2 Nuc_deoxyri_tr3 Nuc_deoxyrib_tr Rib_hydrolayse


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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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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Curation and family details

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Seed source: COG3613
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 42
Number in full: 1594
Average length of the domain: 129.1 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 70.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.8 28.8
Trusted cut-off 28.8 28.9
Noise cut-off 28.7 28.7
Model length: 118
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Nuc_deoxyrib_tr domain has been found. There are 83 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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