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7  structures 4628  species 0  interactions 9141  sequences 33  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[edit]

  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.  edit
  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 1370258. PMID 12003496. 

This article incorporates text from the public domain Pfam and InterPro IPR001269

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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.

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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001269

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 (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

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Domain organisation

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Alignments

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  Seed
(17)
Full
(9141)
Representative proteomes NCBI
(10106)
Meta
(4606)
RP15
(870)
RP35
(1575)
RP55
(2170)
RP75
(2600)
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  Seed
(17)
Full
(9141)
Representative proteomes NCBI
(10106)
Meta
(4606)
RP15
(870)
RP35
(1575)
RP55
(2170)
RP75
(2600)
Alignment:
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  Seed
(17)
Full
(9141)
Representative proteomes NCBI
(10106)
Meta
(4606)
RP15
(870)
RP35
(1575)
RP55
(2170)
RP75
(2600)
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:

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Curation and family details

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Curation View help on the curation process

Seed source: Prosite
Previous IDs: UPF0034;
Type: Family
Author: Finn RD, Bateman A, Kerrison ND
Number in seed: 17
Number in full: 9141
Average length of the domain: 294.60 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 86.25 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 310
Family (HMM) version: 12
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 7 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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