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) | |||||||||
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![]() crystal structure of a putative flavin oxidoreductase with flavin | |||||||||
Identifiers | |||||||||
Symbol | Dus | ||||||||
Pfam | PF01207 | ||||||||
Pfam clan | CL0036 | ||||||||
InterPro | IPR001269 | ||||||||
PROSITE | PDOC00874 | ||||||||
SCOP2 | 1vhn / SCOPe / SUPFAM | ||||||||
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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
- ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 14970222, please use {{cite journal}} with
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instead. - ^ 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.
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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.
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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
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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
SCOOP: | DeoC DHO_dh DUF561 FMN_dh G3P_antiterm Glu_synthase His_biosynth IGPS IMPDH MR_MLE_C NanE NMO Oxidored_FMN PcrB PEP_mutase SOR_SNZ ThiG TMP-TENI Trp_syntA |
Similarity to PfamA using HHSearch: | His_biosynth His_biosynth FMN_dh DHO_dh |
External database links
PROSITE: | PDOC00874 |
SCOP: | 1vhn |
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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Pfam Clan
This family is a member of clan TIM_barrel (CL0036), which has the following description:
This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 61 members:
4HFCP_synth Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD ComA CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF2090 DUF4862 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm GatZ_KbaZ-like Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH KDGP_aldolase Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI PRMT5_TIM Pterin_bind QRPTase_C Radical_SAM Radical_SAM_2 RhaA Ribul_P_3_epim SOR_SNZ TAL_FSA ThiC_Rad_SAM ThiG TIM TMP-TENI Trp_syntA UvdE UxuAAlignments
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) |
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RP15 (3487) |
RP35 (10015) |
RP55 (19202) |
RP75 (31559) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (15) |
Full (20619) |
Representative proteomes | UniProt (82154) |
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RP15 (3487) |
RP35 (10015) |
RP55 (19202) |
RP75 (31559) |
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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.
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
Seed source: | Prosite |
Previous IDs: | UPF0034; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
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
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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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.