Summary: Nucleoside 2-deoxyribosyltransferase
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Nucleoside deoxyribosyltransferase Edit Wikipedia article
nucleoside deoxyribosyltransferase | |||||||||
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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 / QuickGO | ||||||||
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In enzymology, a nucleoside deoxyribosyltransferase (EC 2.4.2.6) 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.
References
- 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.
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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
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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
SCOOP: | DUF4406 Nuc_deoxyri_tr2 Nuc_deoxyri_tr3 TIR_2 |
Similarity to PfamA using HHSearch: | Nuc_deoxyri_tr3 DUF4406 Nuc_deoxyri_tr2 |
External database links
SCOP: | 1f8x |
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 6 members:
DUF1937 DUF4406 Nuc_deoxyri_tr2 Nuc_deoxyri_tr3 Nuc_deoxyrib_tr Rib_hydrolayseAlignments
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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Seed (47) |
Full (1323) |
Representative proteomes | UniProt (6944) |
NCBI (9209) |
Meta (339) |
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RP15 (180) |
RP35 (595) |
RP55 (1221) |
RP75 (2377) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (47) |
Full (1323) |
Representative proteomes | UniProt (6944) |
NCBI (9209) |
Meta (339) |
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RP15 (180) |
RP35 (595) |
RP55 (1221) |
RP75 (2377) |
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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.
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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
Seed source: | COG3613 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 47 |
Number in full: | 1323 |
Average length of the domain: | 132.00 aa |
Average identity of full alignment: | 20 % |
Average coverage of the sequence by the domain: | 73.11 % |
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: | 130 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
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Interactions
There is 1 interaction for this family. More...
Nuc_deoxyrib_trStructures
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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