YQGF_ECOLI
ID YQGF_ECOLI Reviewed; 138 AA.
AC P0A8I1; P52050; Q2M9P4;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Putative pre-16S rRNA nuclease {ECO:0000255|HAMAP-Rule:MF_00651, ECO:0000305};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00651};
GN Name=yqgF {ECO:0000255|HAMAP-Rule:MF_00651}; Synonyms=ruvX {ECO:0000305};
GN OrderedLocusNames=b2949, JW2916;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP DISCUSSION OF POSSIBLE FUNCTION.
RX PubMed=10982859; DOI=10.1093/nar/28.18.3417;
RA Aravind L., Makarova K.S., Koonin E.V.;
RT "Holliday junction resolvases and related nucleases: identification of new
RT families, phyletic distribution and evolutionary trajectories.";
RL Nucleic Acids Res. 28:3417-3432(2000).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ALA-103; SER-105 AND
RP SER-125.
RX PubMed=22353788; DOI=10.1159/000336517;
RA Iwamoto A., Osawa A., Kawai M., Honda H., Yoshida S., Furuya N., Kato J.;
RT "Mutations in the essential Escherichia coli gene, yqgF, and their effects
RT on transcription.";
RL J. Mol. Microbiol. Biotechnol. 22:17-23(2012).
RN [5]
RP FUNCTION, AND MUTAGENESIS OF ASP-9; GLU-96; THR-100; 108-PHE--ALA-115 AND
RP ASP-122.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=25545592; DOI=10.1016/j.jmb.2014.12.013;
RA Kurata T., Nakanishi S., Hashimoto M., Taoka M., Yamazaki Y., Isobe T.,
RA Kato J.;
RT "Novel essential gene Involved in 16S rRNA processing in Escherichia
RT coli.";
RL J. Mol. Biol. 427:955-965(2015).
RN [6]
RP STRUCTURE BY NMR.
RX PubMed=12153044; DOI=10.1023/a:1016368102539;
RA Liu D., Repaka P., Taremi S.S., Wyss D.F.;
RT "Backbone 1H, 15N and 13C resonance assignments of YqgF, an Escherichia
RT coli protein of unknown structure and function.";
RL J. Biomol. NMR 23:159-160(2002).
RN [7]
RP STRUCTURE BY NMR, AND SUBUNIT.
RX PubMed=14512736; DOI=10.1023/a:1025840121177;
RA Liu D., Wang Y.-S., Wyss D.F.;
RT "Solution structure of the hypothetical protein YqgF from Escherichia coli
RT reveals an RNAse H fold.";
RL J. Biomol. NMR 27:389-392(2003).
CC -!- FUNCTION: Involved in the processing of the 5'-end of pre-16S rRNA
CC during 70S ribosome maturation (processing does not occur on total
CC cellular RNA off the ribosome); may be a nuclease (PubMed:25545592). A
CC temperature-sensitive yqgF mutant no longer grows when Rho or NusA are
CC overproduced, and has reduced transcription of genes encoded downstream
CC of Rho terminators; transcription increases again in the presence of
CC the Rho inhibitor bicylomycin (PubMed:22353788).
CC {ECO:0000269|PubMed:22353788, ECO:0000269|PubMed:25545592}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:14512736}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00651}.
CC -!- DISRUPTION PHENOTYPE: Essential, it cannot be disrupted.
CC {ECO:0000269|PubMed:22353788}.
CC -!- SIMILARITY: Belongs to the YqgF nuclease family. {ECO:0000255|HAMAP-
CC Rule:MF_00651}.
CC -!- CAUTION: Was originally suggested to be a nuclease that resolves
CC Holliday junction intermediates during genetic recombination.
CC {ECO:0000303|PubMed:10982859}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA69116.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U28377; AAA69116.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC75986.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77012.1; -; Genomic_DNA.
DR PIR; D65080; D65080.
DR RefSeq; NP_417424.1; NC_000913.3.
DR RefSeq; WP_000017106.1; NZ_STEB01000001.1.
DR PDB; 1NMN; X-ray; 2.30 A; A/B=1-138.
DR PDB; 1NU0; X-ray; 1.60 A; A/B=1-138.
DR PDB; 1OVQ; NMR; -; A=1-138.
DR PDBsum; 1NMN; -.
DR PDBsum; 1NU0; -.
DR PDBsum; 1OVQ; -.
DR AlphaFoldDB; P0A8I1; -.
DR SMR; P0A8I1; -.
DR BioGRID; 4259241; 196.
DR IntAct; P0A8I1; 9.
DR STRING; 511145.b2949; -.
DR jPOST; P0A8I1; -.
DR PaxDb; P0A8I1; -.
DR PRIDE; P0A8I1; -.
DR EnsemblBacteria; AAC75986; AAC75986; b2949.
DR EnsemblBacteria; BAE77012; BAE77012; BAE77012.
DR GeneID; 60669791; -.
DR GeneID; 66673170; -.
DR GeneID; 947439; -.
DR KEGG; ecj:JW2916; -.
DR KEGG; eco:b2949; -.
DR PATRIC; fig|1411691.4.peg.3784; -.
DR EchoBASE; EB3075; -.
DR eggNOG; COG0816; Bacteria.
DR HOGENOM; CLU_098240_3_0_6; -.
DR InParanoid; P0A8I1; -.
DR OMA; PMGWTAQ; -.
DR PhylomeDB; P0A8I1; -.
DR BioCyc; EcoCyc:G7525-MON; -.
DR BioCyc; MetaCyc:G7525-MON; -.
DR EvolutionaryTrace; P0A8I1; -.
DR PRO; PR:P0A8I1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IDA:EcoCyc.
DR GO; GO:0042254; P:ribosome biogenesis; IDA:UniProtKB.
DR GO; GO:0000967; P:rRNA 5'-end processing; IDA:UniProtKB.
DR CDD; cd16964; YqgF; 1.
DR Gene3D; 3.30.420.140; -; 1.
DR HAMAP; MF_00651; Nuclease_YqgF; 1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR005227; YqgF.
DR InterPro; IPR006641; YqgF/RNaseH-like_dom.
DR InterPro; IPR037027; YqgF/RNaseH-like_dom_sf.
DR PANTHER; PTHR33317; PTHR33317; 1.
DR Pfam; PF03652; RuvX; 1.
DR SMART; SM00732; YqgFc; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR TIGRFAMs; TIGR00250; RNAse_H_YqgF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Nuclease; Reference proteome;
KW Ribosome biogenesis.
FT CHAIN 1..138
FT /note="Putative pre-16S rRNA nuclease"
FT /id="PRO_0000172058"
FT MUTAGEN 9
FT /note="D->A: Does not process pre-16S rRNA in 70S
FT ribosomes, binds to pre-16S rRNA-containing ribosomes."
FT /evidence="ECO:0000269|PubMed:25545592"
FT MUTAGEN 96
FT /note="E->A: Does not process pre-16S rRNA in 70S
FT ribosomes."
FT /evidence="ECO:0000269|PubMed:25545592"
FT MUTAGEN 100
FT /note="T->I: Does not process pre-16S rRNA in 70S
FT ribosomes."
FT /evidence="ECO:0000269|PubMed:25545592"
FT MUTAGEN 103
FT /note="A->I: Allows cell growth, i.e. not toxic."
FT /evidence="ECO:0000269|PubMed:22353788"
FT MUTAGEN 105
FT /note="S->I: Allows cell growth, i.e. not toxic."
FT /evidence="ECO:0000269|PubMed:22353788"
FT MUTAGEN 108..115
FT /note="Missing: Does not process pre-16S rRNA in 70S
FT ribosomes."
FT /evidence="ECO:0000269|PubMed:25545592"
FT MUTAGEN 122
FT /note="D->A: Does not process pre-16S rRNA in 70S
FT ribosomes, binds quite strongly to pre-16S rRNA-containing
FT ribosomes."
FT /evidence="ECO:0000269|PubMed:25545592"
FT MUTAGEN 125
FT /note="S->A: Allows cell growth, i.e. not toxic."
FT /evidence="ECO:0000269|PubMed:22353788"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:1NU0"
FT STRAND 12..21
FT /evidence="ECO:0007829|PDB:1NU0"
FT TURN 22..25
FT /evidence="ECO:0007829|PDB:1NU0"
FT STRAND 26..36
FT /evidence="ECO:0007829|PDB:1NU0"
FT HELIX 42..52
FT /evidence="ECO:0007829|PDB:1NU0"
FT STRAND 55..63
FT /evidence="ECO:0007829|PDB:1NU0"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:1OVQ"
FT HELIX 71..87
FT /evidence="ECO:0007829|PDB:1NU0"
FT STRAND 91..97
FT /evidence="ECO:0007829|PDB:1NU0"
FT HELIX 118..121
FT /evidence="ECO:0007829|PDB:1NU0"
FT HELIX 124..135
FT /evidence="ECO:0007829|PDB:1NU0"
SQ SEQUENCE 138 AA; 15186 MW; 89650665AA5C1E50 CRC64;
MSGTLLAFDF GTKSIGVAVG QRITGTARPL PAIKAQDGTP DWNIIERLLK EWQPDEIIVG
LPLNMDGTEQ PLTARARKFA NRIHGRFGVE VKLHDERLST VEARSGLFEQ GGYRALNKGK
VDSASAVIIL ESYFEQGY
