SRMB_ECOLI
ID SRMB_ECOLI Reviewed; 444 AA.
AC P21507; Q2MAF4;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1991, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=ATP-dependent RNA helicase SrmB {ECO:0000255|HAMAP-Rule:MF_00967};
DE EC=3.6.4.13 {ECO:0000255|HAMAP-Rule:MF_00967};
GN Name=srmB {ECO:0000255|HAMAP-Rule:MF_00967}; Synonyms=rbaB, rhlA;
GN OrderedLocusNames=b2576, JW2560;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2461520; DOI=10.1038/336496a0;
RA Nishi K., Morel-Deville F., Hershey J.W.B., Leighton T., Schnier J.;
RT "An eIF-4A-like protein is a suppressor of an Escherichia coli mutant
RT defective in 50S ribosomal subunit assembly.";
RL Nature 336:496-498(1988).
RN [2]
RP ERRATUM OF PUBMED:2461520, AND SEQUENCE REVISION.
RA Nishi K., Morel-Deville F., Hershey J.W.B., Leighton T., Schnier J.;
RL Nature 340:246-246(1989).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Nashimoto H.;
RT "Non-ribosomal proteins affecting the assembly of ribosomes in Escherichia
RT coli.";
RL (In) Nierhaus K.H. (eds.);
RL The translational apparatus, pp.185-195, Plenum Press, New York (1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Nashimoto H., Saito N.;
RL Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
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 [7]
RP FUNCTION IN 50S RIBOSOME BIOGENESIS, AND DISRUPTION PHENOTYPE.
RC STRAIN=B / BL21-DE3, and K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=12787353; DOI=10.1046/j.1365-2958.2003.03513.x;
RA Charollais J., Pflieger D., Vinh J., Dreyfus M., Iost I.;
RT "The DEAD-box RNA helicase SrmB is involved in the assembly of 50S
RT ribosomal subunits in Escherichia coli.";
RL Mol. Microbiol. 48:1253-1265(2003).
RN [8]
RP FUNCTION AS RNA-HELICASE, FUNCTION AS ATPASE, AND CATALYTIC ACTIVITY.
RX PubMed=15196029; DOI=10.1021/bi049852s;
RA Bizebard T., Ferlenghi I., Iost I., Dreyfus M.;
RT "Studies on three E. coli DEAD-box helicases point to an unwinding
RT mechanism different from that of model DNA helicases.";
RL Biochemistry 43:7857-7866(2004).
RN [9]
RP FUNCTION IN 50S RIBOSOME BIOGENESIS, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=15148362; DOI=10.1093/nar/gkh603;
RA Charollais J., Dreyfus M., Iost I.;
RT "CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the
RT biogenesis of 50S ribosomal subunit.";
RL Nucleic Acids Res. 32:2751-2759(2004).
RN [10]
RP INTERACTION WITH L4, L24 AND 23S RRNA, AND DOMAIN.
RC STRAIN=B / BL21-DE3;
RX PubMed=19734346; DOI=10.1093/nar/gkp685;
RA Trubetskoy D., Proux F., Allemand F., Dreyfus M., Iost I.;
RT "SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly,
RT is specifically targeted to 23S rRNA in vivo.";
RL Nucleic Acids Res. 37:6540-6549(2009).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 219-388.
RA Pietras Z., Hardwick S.W., Luisi B.F.;
RT "Interactions of Escherichia Coli DEAD-box helicases with the RraA
RT protein.";
RL Submitted (MAY-2011) to the PDB data bank.
CC -!- FUNCTION: DEAD-box RNA helicase involved in the assembly of the 50S
CC ribosomal subunit at low temperature. Exhibits RNA-stimulated ATP
CC hydrolysis and RNA unwinding activity. Acts before DeaD.
CC {ECO:0000255|HAMAP-Rule:MF_00967, ECO:0000269|PubMed:12787353,
CC ECO:0000269|PubMed:15148362, ECO:0000269|PubMed:15196029}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00967,
CC ECO:0000269|PubMed:15196029};
CC -!- SUBUNIT: Interacts with the 50S ribosomal subunit. Forms a complex with
CC the 50S ribosomal proteins L4 and L24, and a region near the 5'-end of
CC 23S rRNA. {ECO:0000255|HAMAP-Rule:MF_00967,
CC ECO:0000269|PubMed:19734346}.
CC -!- INTERACTION:
CC P21507; P05055: pnp; NbExp=3; IntAct=EBI-546628, EBI-548080;
CC P21507; P36979: rlmN; NbExp=4; IntAct=EBI-546628, EBI-559071;
CC P21507; P37765: rluB; NbExp=6; IntAct=EBI-546628, EBI-561550;
CC P21507; P21513: rne; NbExp=3; IntAct=EBI-546628, EBI-549958;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00967}.
CC -!- DOMAIN: The C-terminal extension is not essential for ribosome
CC assembly, but is important for the formation or the stability of the
CC complex. {ECO:0000269|PubMed:19734346}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene grow very poorly at 20
CC degrees Celsius, show a severe deficit of free 50S ribosomal subunits
CC and accumulate an abnormal large ribosomal subunit. Disruption also
CC impairs the processing of both 23S and 16S rRNAs.
CC {ECO:0000269|PubMed:12787353, ECO:0000269|PubMed:15148362}.
CC -!- MISCELLANEOUS: Overexpression suppresses a mutant defective in 50S
CC ribosomal subunit assembly. {ECO:0000305|PubMed:2461520}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. SrmB subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00967}.
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DR EMBL; X14152; CAA32364.1; -; Genomic_DNA.
DR EMBL; D13169; BAA02447.1; -; Genomic_DNA.
DR EMBL; D64044; BAA10922.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75629.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76752.1; -; Genomic_DNA.
DR PIR; G65035; G65035.
DR RefSeq; NP_417071.1; NC_000913.3.
DR RefSeq; WP_000219203.1; NZ_LN832404.1.
DR PDB; 2YJT; X-ray; 2.90 A; D=219-388.
DR PDBsum; 2YJT; -.
DR AlphaFoldDB; P21507; -.
DR SMR; P21507; -.
DR BioGRID; 4263366; 231.
DR BioGRID; 851393; 5.
DR DIP; DIP-10920N; -.
DR IntAct; P21507; 34.
DR STRING; 511145.b2576; -.
DR jPOST; P21507; -.
DR PaxDb; P21507; -.
DR PRIDE; P21507; -.
DR EnsemblBacteria; AAC75629; AAC75629; b2576.
DR EnsemblBacteria; BAE76752; BAE76752; BAE76752.
DR GeneID; 947055; -.
DR KEGG; ecj:JW2560; -.
DR KEGG; eco:b2576; -.
DR PATRIC; fig|1411691.4.peg.4158; -.
DR EchoBASE; EB0968; -.
DR eggNOG; COG0513; Bacteria.
DR HOGENOM; CLU_003041_1_3_6; -.
DR InParanoid; P21507; -.
DR OMA; YDIELYQ; -.
DR PhylomeDB; P21507; -.
DR BioCyc; EcoCyc:EG10975-MON; -.
DR BioCyc; MetaCyc:EG10975-MON; -.
DR PRO; PR:P21507; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0008186; F:ATP-dependent activity, acting on RNA; IDA:UniProtKB.
DR GO; GO:0008143; F:poly(A) binding; IDA:UniProtKB.
DR GO; GO:0003724; F:RNA helicase activity; IDA:UniProtKB.
DR GO; GO:0033592; F:RNA strand annealing activity; IDA:EcoCyc.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IDA:EcoCyc.
DR GO; GO:0031555; P:transcriptional attenuation; IDA:EcoCyc.
DR Gene3D; 3.40.50.300; -; 2.
DR HAMAP; MF_00967; DEAD_helicase_SrmB; 1.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR028621; DEAD_helicase_SrmB.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Helicase; Hydrolase;
KW Nucleotide-binding; Reference proteome; Ribosome biogenesis; RNA-binding.
FT CHAIN 1..444
FT /note="ATP-dependent RNA helicase SrmB"
FT /id="PRO_0000055109"
FT DOMAIN 35..209
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00967"
FT DOMAIN 238..387
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00967"
FT REGION 382..444
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 4..32
FT /note="Q motif"
FT MOTIF 157..160
FT /note="DEAD box"
FT COMPBIAS 382..398
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 411..427
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 48..55
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00967"
FT STRAND 223..231
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 232..243
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 250..254
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 259..272
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 276..278
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 284..294
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 301..304
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 307..309
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 319..324
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 329..335
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 347..353
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 354..356
FT /evidence="ECO:0007829|PDB:2YJT"
FT HELIX 357..366
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 367..369
FT /evidence="ECO:0007829|PDB:2YJT"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:2YJT"
SQ SEQUENCE 444 AA; 49914 MW; 1A459538A25807A7 CRC64;
MTVTTFSELE LDESLLEALQ DKGFTRPTAI QAAAIPPALD GRDVLGSAPT GTGKTAAYLL
PALQHLLDFP RKKSGPPRIL ILTPTRELAM QVSDHARELA KHTHLDIATI TGGVAYMNHA
EVFSENQDIV VATTGRLLQY IKEENFDCRA VETLILDEAD RMLDMGFAQD IEHIAGETRW
RKQTLLFSAT LEGDAIQDFA ERLLEDPVEV SANPSTRERK KIHQWYYRAD DLEHKTALLV
HLLKQPEATR SIVFVRKRER VHELANWLRE AGINNCYLEG EMVQGKRNEA IKRLTEGRVN
VLVATDVAAR GIDIPDVSHV FNFDMPRSGD TYLHRIGRTA RAGRKGTAIS LVEAHDHLLL
GKVGRYIEEP IKARVIDELR PKTRAPSEKQ TGKPSKKVLA KRAEKKKAKE KEKPRVKKRH
RDTKNIGKRR KPSGTGVPPQ TTEE
