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23  structures 8337  species 0  interactions 19449  sequences 178  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
Symbol Dus
Pfam PF01207
Pfam clan CL0036
InterPro IPR001269
PROSITE PDOC00874
SCOP 1vhn
SUPERFAMILY 1vhn

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. ^ Xing, F.; Hiley, S. L.; Hughes, T. R.; Phizicky, E. M. (2004). "The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs". Journal of Biological Chemistry. 279 (17): 17850–17860. doi:10.1074/jbc.M401221200. PMID 14970222. 
  2. ^ a b Xing F, Martzen MR, Phizicky EM (March 2002). "A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA". RNA. 8 (3): 370–81. doi:10.1017/S1355838202029825. PMC 1370258Freely accessible. PMID 12003496. 

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 IPR001269

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 ].

Dus 1 ( SWISSPROT ) from Saccharomyces cerevisiae (Baker's yeast) acts on pre-tRNA-Phe, while Dus 2 ( SWISSPROT ) 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 [ PUBMED:12003496 ]. Some family members may be targeted to the mitochondria and even have a role in mitochondria [ PUBMED:12003496 ].

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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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
(19449)
Representative proteomes UniProt
(79011)
RP15
(3235)
RP35
(9507)
RP55
(18142)
RP75
(29735)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(15)
Full
(19449)
Representative proteomes UniProt
(79011)
RP15
(3235)
RP35
(9507)
RP55
(18142)
RP75
(29735)
Alignment:
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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
(19449)
Representative proteomes UniProt
(79011)
RP15
(3235)
RP35
(9507)
RP55
(18142)
RP75
(29735)
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: 19449
Average length of the domain: 282.30 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 75.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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: 19
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
A0A0G2K3I5 View 3D Structure Click here
A0A0R0IJ97 View 3D Structure Click here
A0A0R0K1U3 View 3D Structure Click here
A0A0R4IIP1 View 3D Structure Click here
A0A1D6EEF2 View 3D Structure Click here
A0A1D8PIH5 View 3D Structure Click here
A0A1D8PIL3 View 3D Structure Click here
A4HXA2 View 3D Structure Click here
A4I6W8 View 3D Structure Click here
A4I6W8 View 3D Structure Click here
A4I6W8 View 3D Structure Click here
A4I9S4 View 3D Structure Click here
A4ICU0 View 3D Structure Click here
B0BN89 View 3D Structure Click here
B0S7L0 View 3D Structure Click here
B4G0K9 View 3D Structure Click here
B7ZX41 View 3D Structure Click here
E7F220 View 3D Structure Click here
F4IY04 View 3D Structure Click here
I1J6W0 View 3D Structure Click here
I1K265 View 3D Structure Click here
I1MVU0 View 3D Structure Click here
K7K2I3 View 3D Structure Click here
K7KHG3 View 3D Structure Click here
K7L986 View 3D Structure Click here
K7LI80 View 3D Structure Click here
K7TQZ3 View 3D Structure Click here
O74553 View 3D Structure Click here
O74731 View 3D Structure Click here
O95620 View 3D Structure Click here
P0ABT5 View 3D Structure Click here
P32695 View 3D Structure Click here
P33371 View 3D Structure Click here
P53720 View 3D Structure Click here
P53759 View 3D Structure Click here
P9WNS7 View 3D Structure Click here
Q06053 View 3D Structure Click here
Q06063 View 3D Structure Click here
Q09504 View 3D Structure Click here
Q0D9J7 View 3D Structure Click here
Q0JEG3 View 3D Structure Click here
Q2G1R3 View 3D Structure Click here
Q2G2E8 View 3D Structure Click here
Q32M08 View 3D Structure Click here
Q3KRC5 View 3D Structure Click here
Q4CPS5 View 3D Structure Click here
Q4CS79 View 3D Structure Click here
Q4CX50 View 3D Structure Click here
Q4D174 View 3D Structure Click here
Q4D468 View 3D Structure Click here
Q4DCG2 View 3D Structure Click here
Q4DT07 View 3D Structure Click here
Q4E313 View 3D Structure Click here
Q54CU9 View 3D Structure Click here
Q54ES7 View 3D Structure Click here
Q54QJ2 View 3D Structure Click here
Q54XQ6 View 3D Structure Click here
Q57608 View 3D Structure Click here
Q5A4Y0 View 3D Structure Click here
Q5ALL3 View 3D Structure Click here
Q5RIX6 View 3D Structure Click here
Q6P1R4 View 3D Structure Click here
Q7XT07 View 3D Structure Click here
Q7XUN7 View 3D Structure Click here
Q86L21 View 3D Structure Click here
Q8C2P3 View 3D Structure Click here
Q8H128 View 3D Structure Click here
Q8I2W5 View 3D Structure Click here
Q8IM07 View 3D Structure Click here
Q8K582 View 3D Structure Click here
Q91XI1 View 3D Structure Click here
Q96G46 View 3D Structure Click here
Q9D7B1 View 3D Structure Click here
Q9FH91 View 3D Structure Click here
Q9FI41 View 3D Structure Click here
Q9HGN6 View 3D Structure Click here
Q9NX74 View 3D Structure Click here
Q9T0J6 View 3D Structure Click here
Q9TYN2 View 3D Structure Click here
Q9UTH9 View 3D Structure Click here
Q9VIS4 View 3D Structure Click here
Q9VJ06 View 3D Structure Click here
Q9VPM1 View 3D Structure Click here
Q9VY45 View 3D Structure Click here
Q9XVN8 View 3D Structure Click here
Q9XWJ9 View 3D Structure Click here