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35  structures 886  species 1  interaction 1106  sequences 7  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

nucleoside deoxyribosyltransferase
Identifiers
EC number 2.4.2.6
CAS number 9026-86-2
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

In enzymology, a nucleoside deoxyribosyltransferase (EC 2.4.2.6) is an enzyme that catalyzes the chemical reaction

2-deoxy-D-ribosyl-base1 + base2 \rightleftharpoons 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.

[edit] 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.

[edit] References

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:2.4.2.6 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


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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 contains the following 4 members:

DUF1937 DUF4406 Nuc_deoxyrib_tr Rib_hydrolayse

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(107)
Full
(1106)
Representative proteomes NCBI
(866)
Meta
(351)
RP15
(83)
RP35
(165)
RP55
(228)
RP75
(291)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(107)
Full
(1106)
Representative proteomes NCBI
(866)
Meta
(351)
RP15
(83)
RP35
(165)
RP55
(228)
RP75
(291)
Alignment:
Format:
Order:
Sequence:
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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
(107)
Full
(1106)
Representative proteomes NCBI
(866)
Meta
(351)
RP15
(83)
RP35
(165)
RP55
(228)
RP75
(291)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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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 View help on the curation process

Seed source: COG3613
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 107
Number in full: 1106
Average length of the domain: 125.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 73.25 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.8 27.8
Trusted cut-off 27.8 27.8
Noise cut-off 27.7 27.6
Model length: 113
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Nuc_deoxyrib_tr

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 Nuc_deoxyrib_tr domain has been found. There are 35 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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