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23  structures 8542  species 0  interactions 20619  sequences 184  architectures

Family: Dus (PF01207)

Summary: Dihydrouridine synthase (Dus)

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This is the Wikipedia entry entitled "TRNA-dihydrouridine synthase". More...

TRNA-dihydrouridine synthase Edit Wikipedia article

Dihydrouridine synthase (Dus)
PDB 1vhn EBI.jpg
crystal structure of a putative flavin oxidoreductase with flavin
Identifiers
SymbolDus
PfamPF01207
Pfam clanCL0036
InterProIPR001269
PROSITEPDOC00874
SCOP21vhn / SCOPe / SUPFAM

In molecular biology, tRNA-dihydrouridine synthase is a family of enzymes which catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae (Baker's yeast) acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD.[1][2] Some family members may be targeted to the mitochondria and even have a role in mitochondria.[2]

References

  1. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 14970222, please use {{cite journal}} with |pmid=14970222 instead.
  2. ^ a b Xing F, Martzen MR, Phizicky EM (2002). "A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA". RNA. 8 (3): 370–81. PMC 1370258. PMID 12003496. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR001269

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.

Dihydrouridine synthase (Dus) Provide feedback

Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 (Q9HGN6) from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 (P53720) acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD [1]. Some family members may be targeted to the mitochondria and even have a role in mitochondria [1].

Literature references

  1. Xing F, Martzen MR, Phizicky EM; , RNA 2002;8:370-381.: A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. PUBMED:12003496 EPMC:12003496


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR035587

This entry represents a dihydrouridine synthase-like (DUS-like) FMN-binding domain [ PUBMED:15103641 ]. Proteins containing this domain catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap [ PUBMED:12003496 , PUBMED:11983710 ]. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present [ PUBMED:15103641 ].

Dihydrouridine synthases (Dus) is a large family of flavoenzymes comprising eight subfamilies. They catalyse the NADPH-dependent synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. Mainly, they contain two functional conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition. However, DUS2 is distinguished from its paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module [ PUBMED:30149704 , PUBMED:30605527 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 (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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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
(15)
Full
(20619)
Representative proteomes UniProt
(82154)
RP15
(3487)
RP35
(10015)
RP55
(19202)
RP75
(31559)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(15)
Full
(20619)
Representative proteomes UniProt
(82154)
RP15
(3487)
RP35
(10015)
RP55
(19202)
RP75
(31559)
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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
(15)
Full
(20619)
Representative proteomes UniProt
(82154)
RP15
(3487)
RP35
(10015)
RP55
(19202)
RP75
(31559)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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 View help on the curation process

Seed source: Prosite
Previous IDs: UPF0034;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Kerrison ND
Number in seed: 15
Number in full: 20619
Average length of the domain: 282.3 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 75.22 %

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 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 310
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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 Dus domain has been found. There are 23 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044RBY8 View 3D Structure Click here
A0A044RW39 View 3D Structure Click here
A0A044UVX5 View 3D Structure Click here
A0A077YYZ1 View 3D Structure Click here
A0A077Z2Z2 View 3D Structure Click here
A0A077Z6E3 View 3D Structure Click here
A0A077ZK02 View 3D Structure Click here
A0A077ZLZ7 View 3D Structure Click here
A0A0D2GXW8 View 3D Structure Click here
A0A0D2HAA0 View 3D Structure Click here
A0A0D2HKT4 View 3D Structure Click here
A0A0G2K3I5 View 3D Structure Click here
A0A0H3GKY9 View 3D Structure Click here
A0A0H3GVF9 View 3D Structure Click here
A0A0H3H3Q9 View 3D Structure Click here
A0A0K0DVX7 View 3D Structure Click here
A0A0K0E0S2 View 3D Structure Click here
A0A0K0ELJ9 View 3D Structure Click here
A0A0N4U212 View 3D Structure Click here
A0A0N4U9Z6 View 3D Structure Click here
A0A0N4UF90 View 3D Structure Click here
A0A0R0IJ97 View 3D Structure Click here
A0A0R0K1U3 View 3D Structure Click here
A0A0R4IIP1 View 3D Structure Click here
A0A175VZM5 View 3D Structure Click here
A0A175VZP8 View 3D Structure Click here
A0A175WBX6 View 3D Structure Click here
A0A1C1CJX8 View 3D Structure Click here
A0A1C1CN92 View 3D Structure Click here
A0A1C1CNV4 View 3D Structure Click here
A0A1D6EEF2 View 3D Structure Click here
A0A1D8PIH5 View 3D Structure Click here
A0A1D8PIL3 View 3D Structure Click here
A0A3P7DJG5 View 3D Structure Click here
A0A3P7E1U8 View 3D Structure Click here
A0A3P7E811 View 3D Structure Click here
A0A3P7FMX8 View 3D Structure Click here
A0A3Q0KDJ4 View 3D Structure Click here
A1CNY3 View 3D Structure Click here
A1D1U0 View 3D Structure Click here