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Protein

tRNA-dihydrouridine(16) synthase

Gene

dusC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. DusC specifically modifies U16 in tRNAs.UniRule annotation2 Publications

Catalytic activityi

5,6-dihydrouracil(16) in tRNA + NAD(P)+ = uracil(16) in tRNA + NAD(P)H.UniRule annotation1 Publication

Cofactori

FMNUniRule annotation2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei35 – 351Interacts with tRNA; defines subfamily-specific binding signature1 Publication
Binding sitei68 – 681FMNCombined sources2 Publications
Sitei95 – 951Interacts with tRNA1 Publication
Active sitei98 – 981Proton donorBy similarity1 Publication
Binding sitei139 – 1391FMNCombined sources2 Publications
Sitei176 – 1761Interacts with tRNA1 Publication
Sitei272 – 2721Interacts with tRNA; defines subfamily-specific binding signature1 Publication
Sitei274 – 2741Interacts with tRNA; defines subfamily-specific binding signature1 Publication
Sitei279 – 2791Interacts with tRNA1 Publication
Sitei295 – 2951Interacts with tRNA; defines subfamily-specific binding signature1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi7 – 93FMNCombined sources2 Publications
Nucleotide bindingi200 – 2023FMNCombined sources2 Publications
Nucleotide bindingi224 – 2252FMNCombined sources2 Publications

GO - Molecular functioni

  • flavin adenine dinucleotide binding Source: InterPro
  • FMN binding Source: UniProtKB
  • tRNA binding Source: UniProtKB
  • tRNA dihydrouridine synthase activity Source: UniProtKB

GO - Biological processi

  • tRNA dihydrouridine synthesis Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

Flavoprotein, FMN, NADP, RNA-binding, tRNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12022-MONOMER.
ECOL316407:JW2128-MONOMER.
MetaCyc:EG12022-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-dihydrouridine(16) synthaseUniRule annotation1 Publication (EC:1.3.1.-UniRule annotation1 Publication)
Alternative name(s):
U16-specific dihydrouridine synthase1 PublicationUniRule annotation
Short name:
U16-specific Dus1 PublicationUniRule annotation
tRNA-dihydrouridine synthase C1 PublicationUniRule annotation
Gene namesi
Name:dusC1 PublicationUniRule annotation
Synonyms:yohI
Ordered Locus Names:b2140, JW2128
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12022. dusC.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

A dusA dusB dusC triple mutant exhibits a complete lack of 5,6-dihydrouridine modification in cellular tRNA, whereas each single mutant exhibits a partial reduction, compared to wild type.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi98 – 981C → A: Loss of enzymatic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 315315tRNA-dihydrouridine(16) synthasePRO_0000162109Add
BLAST

Proteomic databases

PaxDbiP33371.
PRIDEiP33371.

Interactioni

Protein-protein interaction databases

BioGridi4260457. 10 interactions.
DIPiDIP-12808N.
IntActiP33371. 24 interactions.
STRINGi511145.b2140.

Structurei

Secondary structure

1
315
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Turni9 – 113Combined sources
Helixi14 – 229Combined sources
Beta strandi27 – 359Combined sources
Beta strandi37 – 393Combined sources
Helixi43 – 497Combined sources
Helixi51 – 555Combined sources
Beta strandi64 – 707Combined sources
Helixi74 – 8613Combined sources
Beta strandi90 – 989Combined sources
Helixi109 – 1146Combined sources
Helixi116 – 12914Combined sources
Beta strandi136 – 1427Combined sources
Beta strandi144 – 1474Combined sources
Helixi150 – 15910Combined sources
Beta strandi163 – 1708Combined sources
Turni173 – 1764Combined sources
Helixi178 – 1803Combined sources
Helixi183 – 19210Combined sources
Beta strandi197 – 2015Combined sources
Helixi206 – 21611Combined sources
Beta strandi219 – 2246Combined sources
Helixi225 – 2295Combined sources
Helixi233 – 2397Combined sources
Helixi246 – 25813Combined sources
Helixi268 – 28013Combined sources
Turni281 – 2833Combined sources
Helixi285 – 29410Combined sources
Helixi300 – 30910Combined sources
Turni312 – 3143Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3W9ZX-ray2.10A1-315[»]
4BF9X-ray2.60A1-315[»]
4BFAX-ray1.65A/B1-315[»]
4YCOX-ray2.10A/B/C1-315[»]
4YCPX-ray2.55A1-315[»]
ProteinModelPortaliP33371.
SMRiP33371. Positions 1-315.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Is composed of two domains: an N-terminal catalytic domain (residues 1-242) and a C-terminal tRNA recognition domain (residues 245-309).2 Publications

Sequence similaritiesi

Belongs to the Dus family. DusC subfamily.UniRule annotationCurated

Phylogenomic databases

eggNOGiENOG4105FBT. Bacteria.
COG0042. LUCA.
HOGENOMiHOG000217854.
InParanoidiP33371.
KOiK05541.
OMAiGYKPPAH.
OrthoDBiEOG6VHZFQ.
PhylomeDBiP33371.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_02043. DusC_subfam.
InterProiIPR013785. Aldolase_TIM.
IPR032886. DusC.
IPR001269. tRNA_hU_synthase.
IPR018517. tRNA_hU_synthase_CS.
[Graphical view]
PANTHERiPTHR11082. PTHR11082. 1 hit.
PfamiPF01207. Dus. 1 hit.
[Graphical view]
PIRSFiPIRSF006621. Dus. 1 hit.
PROSITEiPS01136. UPF0034. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P33371-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVLLAPMEG VLDSLVRELL TEVNDYDLCI TEFVRVVDQL LPVKVFHRIC
60 70 80 90 100
PELQNASRTP SGTLVRVQLL GQFPQWLAEN AARAVELGSW GVDLNCGCPS
110 120 130 140 150
KTVNGSGGGA TLLKDPELIY QGAKAMREAV PAHLPVSVKV RLGWDSGEKK
160 170 180 190 200
FEIADAVQQA GATELVVHGR TKEQGYRAEH IDWQAIGDIR QRLNIPVIAN
210 220 230 240 250
GEIWDWQSAQ QCMAISGCDA VMIGRGALNI PNLSRVVKYN EPRMPWPEVV
260 270 280 290 300
ALLQKYTRLE KQGDTGLYHV ARIKQWLSYL RKEYDEATEL FQHVRVLNNS
310
PDIARAIQAI DIEKL
Length:315
Mass (Da):35,199
Last modified:February 1, 1994 - v1
Checksum:i83B33E5034E53565
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00007 Genomic DNA. Translation: AAA60503.1.
U00096 Genomic DNA. Translation: AAC75201.1.
AP009048 Genomic DNA. Translation: BAE76617.1.
PIRiC64982.
RefSeqiNP_416645.1. NC_000913.3.
WP_001264861.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75201; AAC75201; b2140.
BAE76617; BAE76617; BAE76617.
GeneIDi945458.
KEGGiecj:JW2128.
eco:b2140.
PATRICi32119623. VBIEscCol129921_2222.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00007 Genomic DNA. Translation: AAA60503.1.
U00096 Genomic DNA. Translation: AAC75201.1.
AP009048 Genomic DNA. Translation: BAE76617.1.
PIRiC64982.
RefSeqiNP_416645.1. NC_000913.3.
WP_001264861.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3W9ZX-ray2.10A1-315[»]
4BF9X-ray2.60A1-315[»]
4BFAX-ray1.65A/B1-315[»]
4YCOX-ray2.10A/B/C1-315[»]
4YCPX-ray2.55A1-315[»]
ProteinModelPortaliP33371.
SMRiP33371. Positions 1-315.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260457. 10 interactions.
DIPiDIP-12808N.
IntActiP33371. 24 interactions.
STRINGi511145.b2140.

Proteomic databases

PaxDbiP33371.
PRIDEiP33371.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75201; AAC75201; b2140.
BAE76617; BAE76617; BAE76617.
GeneIDi945458.
KEGGiecj:JW2128.
eco:b2140.
PATRICi32119623. VBIEscCol129921_2222.

Organism-specific databases

EchoBASEiEB1957.
EcoGeneiEG12022. dusC.

Phylogenomic databases

eggNOGiENOG4105FBT. Bacteria.
COG0042. LUCA.
HOGENOMiHOG000217854.
InParanoidiP33371.
KOiK05541.
OMAiGYKPPAH.
OrthoDBiEOG6VHZFQ.
PhylomeDBiP33371.

Enzyme and pathway databases

BioCyciEcoCyc:EG12022-MONOMER.
ECOL316407:JW2128-MONOMER.
MetaCyc:EG12022-MONOMER.

Miscellaneous databases

PROiP33371.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_02043. DusC_subfam.
InterProiIPR013785. Aldolase_TIM.
IPR032886. DusC.
IPR001269. tRNA_hU_synthase.
IPR018517. tRNA_hU_synthase_CS.
[Graphical view]
PANTHERiPTHR11082. PTHR11082. 1 hit.
PfamiPF01207. Dus. 1 hit.
[Graphical view]
PIRSFiPIRSF006621. Dus. 1 hit.
PROSITEiPS01136. UPF0034. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Automated multiplex sequencing of the E.coli genome."
    Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
    Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / BHB2600.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: K12.
  5. "Structure of dihydrouridine synthase C (DusC) from Escherichia coli."
    Chen M., Yu J., Tanaka Y., Tanaka M., Tanaka I., Yao M.
    Acta Crystallogr. F 69:834-838(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH FMN, DOMAIN.
  6. Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-98 IN COMPLEXES WITH FMN AND TWO SUBSTRATE TRNAS, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN, ACTIVE SITE, MUTAGENESIS OF CYS-98.

Entry informationi

Entry nameiDUSC_ECOLI
AccessioniPrimary (citable) accession number: P33371
Secondary accession number(s): Q2MAT9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: January 20, 2016
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

DusB and DusC together account for about half of the 5,6-dihydrouridine modification observed in wild-type cellular tRNA, and DusA accounts for the other half. These three enzymes seem to act site-specifically on the tRNA D-loop and contain nonredundant catalytic functions in vivo.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.