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Protein

Putative pre-16S rRNA nuclease

Gene

yqgF

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

Functioni

Involved in the processing of the 5'-end of pre-16S rRNA during 70S ribosome maturation (processing does not occur on total cellular RNA off the ribosome); may be a nuclease (PubMed:25545592). A temperature-sensitive yqgF mutant no longer grows when Rho or NusA are overproduced, and has reduced transcription of genes encoded downstream of Rho terminators; transcription increases again in the presence of the Rho inhibitor bicylomycin (PubMed:22353788).2 Publications

GO - Molecular functioni

GO - Biological processi

  • ribosome biogenesis Source: UniProtKB
  • rRNA 5'-end processing Source: UniProtKB
  • transcription antitermination Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nuclease

Keywords - Biological processi

Ribosome biogenesis

Enzyme and pathway databases

BioCyciEcoCyc:G7525-MONOMER.
ECOL316407:JW2916-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative pre-16S rRNA nucleaseUniRule annotationCurated (EC:3.1.-.-UniRule annotation)
Gene namesi
Name:yqgFUniRule annotation
Synonyms:ruvXCurated
Ordered Locus Names:b2949, JW2916
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13290. yqgF.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Essential, it cannot be disrupted.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi9 – 91D → A: Does not process pre-16S rRNA in 70S ribosomes, binds to pre-16S rRNA-containing ribosomes. 1 Publication
Mutagenesisi96 – 961E → A: Does not process pre-16S rRNA in 70S ribosomes. 1 Publication
Mutagenesisi100 – 1001T → I: Does not process pre-16S rRNA in 70S ribosomes. 1 Publication
Mutagenesisi103 – 1031A → I: Allows cell growth, i.e. not toxic. 1 Publication
Mutagenesisi105 – 1051S → I: Allows cell growth, i.e. not toxic. 1 Publication
Mutagenesisi108 – 1158Missing : Does not process pre-16S rRNA in 70S ribosomes. 1 Publication
Mutagenesisi122 – 1221D → A: Does not process pre-16S rRNA in 70S ribosomes, binds quite strongly to pre-16S rRNA-containing ribosomes. 1 Publication
Mutagenesisi125 – 1251S → A: Allows cell growth, i.e. not toxic. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 138138Putative pre-16S rRNA nucleasePRO_0000172058Add
BLAST

Proteomic databases

PaxDbiP0A8I1.
PRIDEiP0A8I1.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4259241. 196 interactions.
IntActiP0A8I1. 9 interactions.
MINTiMINT-1317755.
STRINGi511145.b2949.

Structurei

Secondary structure

1
138
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Beta strandi12 – 2110Combined sources
Turni22 – 254Combined sources
Beta strandi26 – 3611Combined sources
Helixi42 – 5211Combined sources
Beta strandi55 – 639Combined sources
Beta strandi65 – 684Combined sources
Helixi71 – 8717Combined sources
Beta strandi91 – 977Combined sources
Helixi118 – 1214Combined sources
Helixi124 – 13512Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NMNX-ray2.30A/B1-138[»]
1NU0X-ray1.60A/B1-138[»]
1OVQNMR-A1-138[»]
ProteinModelPortaliP0A8I1.
SMRiP0A8I1. Positions 1-138.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8I1.

Family & Domainsi

Sequence similaritiesi

Belongs to the YqgF nuclease family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107Y66. Bacteria.
COG0816. LUCA.
HOGENOMiHOG000016954.
InParanoidiP0A8I1.
KOiK07447.
OMAiPMGWTAQ.
OrthoDBiEOG6N94FV.
PhylomeDBiP0A8I1.

Family and domain databases

Gene3Di3.30.420.140. 1 hit.
HAMAPiMF_00651. Nuclease_YqgF.
InterProiIPR012337. RNaseH-like_dom.
IPR005227. YqgF.
IPR006641. YqgF/RNaseH-like_dom.
[Graphical view]
PfamiPF03652. RuvX. 1 hit.
[Graphical view]
SMARTiSM00732. YqgFc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
TIGRFAMsiTIGR00250. RNAse_H_YqgF. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8I1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGTLLAFDF GTKSIGVAVG QRITGTARPL PAIKAQDGTP DWNIIERLLK
60 70 80 90 100
EWQPDEIIVG LPLNMDGTEQ PLTARARKFA NRIHGRFGVE VKLHDERLST
110 120 130
VEARSGLFEQ GGYRALNKGK VDSASAVIIL ESYFEQGY
Length:138
Mass (Da):15,186
Last modified:June 7, 2005 - v1
Checksum:i89650665AA5C1E50
GO

Sequence cautioni

The sequence AAA69116.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28377 Genomic DNA. Translation: AAA69116.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75986.1.
AP009048 Genomic DNA. Translation: BAE77012.1.
PIRiD65080.
RefSeqiNP_417424.1. NC_000913.3.
WP_000017106.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75986; AAC75986; b2949.
BAE77012; BAE77012; BAE77012.
GeneIDi947439.
KEGGiecj:JW2916.
eco:b2949.
PATRICi32121308. VBIEscCol129921_3042.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28377 Genomic DNA. Translation: AAA69116.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75986.1.
AP009048 Genomic DNA. Translation: BAE77012.1.
PIRiD65080.
RefSeqiNP_417424.1. NC_000913.3.
WP_000017106.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NMNX-ray2.30A/B1-138[»]
1NU0X-ray1.60A/B1-138[»]
1OVQNMR-A1-138[»]
ProteinModelPortaliP0A8I1.
SMRiP0A8I1. Positions 1-138.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259241. 196 interactions.
IntActiP0A8I1. 9 interactions.
MINTiMINT-1317755.
STRINGi511145.b2949.

Proteomic databases

PaxDbiP0A8I1.
PRIDEiP0A8I1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75986; AAC75986; b2949.
BAE77012; BAE77012; BAE77012.
GeneIDi947439.
KEGGiecj:JW2916.
eco:b2949.
PATRICi32121308. VBIEscCol129921_3042.

Organism-specific databases

EchoBASEiEB3075.
EcoGeneiEG13290. yqgF.

Phylogenomic databases

eggNOGiENOG4107Y66. Bacteria.
COG0816. LUCA.
HOGENOMiHOG000016954.
InParanoidiP0A8I1.
KOiK07447.
OMAiPMGWTAQ.
OrthoDBiEOG6N94FV.
PhylomeDBiP0A8I1.

Enzyme and pathway databases

BioCyciEcoCyc:G7525-MONOMER.
ECOL316407:JW2916-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A8I1.
PROiP0A8I1.

Family and domain databases

Gene3Di3.30.420.140. 1 hit.
HAMAPiMF_00651. Nuclease_YqgF.
InterProiIPR012337. RNaseH-like_dom.
IPR005227. YqgF.
IPR006641. YqgF/RNaseH-like_dom.
[Graphical view]
PfamiPF03652. RuvX. 1 hit.
[Graphical view]
SMARTiSM00732. YqgFc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
TIGRFAMsiTIGR00250. RNAse_H_YqgF. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "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.
  3. "Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories."
    Aravind L., Makarova K.S., Koonin E.V.
    Nucleic Acids Res. 28:3417-3432(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISCUSSION OF POSSIBLE FUNCTION.
  4. "Mutations in the essential Escherichia coli gene, yqgF, and their effects on transcription."
    Iwamoto A., Osawa A., Kawai M., Honda H., Yoshida S., Furuya N., Kato J.
    J. Mol. Microbiol. Biotechnol. 22:17-23(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ALA-103; SER-105 AND SER-125.
  5. "Novel essential gene Involved in 16S rRNA processing in Escherichia coli."
    Kurata T., Nakanishi S., Hashimoto M., Taoka M., Yamazaki Y., Isobe T., Kato J.
    J. Mol. Biol. 427:955-965(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF ASP-9; GLU-96; THR-100; 108-PHE--ALA-115 AND ASP-122.
    Strain: K12 / MG1655 / ATCC 47076.
  6. "Backbone 1H, 15N and 13C resonance assignments of YqgF, an Escherichia coli protein of unknown structure and function."
    Liu D., Repaka P., Taremi S.S., Wyss D.F.
    J. Biomol. NMR 23:159-160(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  7. "Solution structure of the hypothetical protein YqgF from Escherichia coli reveals an RNAse H fold."
    Liu D., Wang Y.-S., Wyss D.F.
    J. Biomol. NMR 27:389-392(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, SUBUNIT.

Entry informationi

Entry nameiYQGF_ECOLI
AccessioniPrimary (citable) accession number: P0A8I1
Secondary accession number(s): P52050, Q2M9P4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: April 13, 2016
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally suggested to be a nuclease that resolves Holliday junction intermediates during genetic recombination.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.