P21507 (SRMB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent RNA helicase SrmB
EC=3.6.4.13

Gene names

Name:	srmB
Synonyms:	rbaB
Ordered Locus Names:	b2576, JW2560

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	444 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as an ATP-dependent RNA helicase, able to unwind ds-RNA. Ref.7 Ref.8 Ref.9 RNA-dependent ATPase activity. Acts in 50S ribosomal subunit biogenesis at low temperatures, acting before DeaD/CsdA. Suppressor of a mutant defective in 50S ribosomal subunit assembly. Ref.7 Ref.8 Ref.9
Catalytic activity	ATP + H2O = ADP + phosphate.
Subunit structure	Forms a complex with the 50S ribosomal proteins L4 and L24, and a region near the 5'-end of 23S rRNA.
Domain	The C-terminal extension is not essential for ribosome assembly, but is important for the formation or the stability of the complex. Ref.10
Disruption phenotype	Cells lacking this gene grow very poorly at 20 degrees Celsius, show a severe deficit of free 50S ribosomal subunits and accumulate an abnormal large ribosomal subunit. Disruption also impairs the processing of both 23S and 16S rRNAs. Ref.7 Ref.9
Sequence similarities	Belongs to the DEAD box helicase family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ribosomal large subunit assembly Inferred from genetic interaction Ref.1. Source: EcoCyc
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Inferred from direct assay Ref.8. Source: EcoCyc RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 444	444	ATP-dependent RNA helicase SrmB		PRO_0000055109
Regions
	Domain	35 – 209	175	Helicase ATP-binding
	Domain	238 – 387	150	Helicase C-terminal
	Nucleotide binding	48 – 55	8	ATP By similarity
	Motif	4 – 32	29	Q motif
	Motif	157 – 160	4	DEAD box

Sequences

	Sequence		Length	Mass (Da)
	P21507 [UniParc]. Last modified May 1, 1991. Version 1. Checksum: 1A459538A25807A7	FASTA	444	49,914
	10 20 30 40 50 60 MTVTTFSELE LDESLLEALQ DKGFTRPTAI QAAAIPPALD GRDVLGSAPT GTGKTAAYLL 70 80 90 100 110 120 PALQHLLDFP RKKSGPPRIL ILTPTRELAM QVSDHARELA KHTHLDIATI TGGVAYMNHA 130 140 150 160 170 180 EVFSENQDIV VATTGRLLQY IKEENFDCRA VETLILDEAD RMLDMGFAQD IEHIAGETRW 190 200 210 220 230 240 RKQTLLFSAT LEGDAIQDFA ERLLEDPVEV SANPSTRERK KIHQWYYRAD DLEHKTALLV 250 260 270 280 290 300 HLLKQPEATR SIVFVRKRER VHELANWLRE AGINNCYLEG EMVQGKRNEA IKRLTEGRVN 310 320 330 340 350 360 VLVATDVAAR GIDIPDVSHV FNFDMPRSGD TYLHRIGRTA RAGRKGTAIS LVEAHDHLLL 370 380 390 400 410 420 GKVGRYIEEP IKARVIDELR PKTRAPSEKQ TGKPSKKVLA KRAEKKKAKE KEKPRVKKRH 430 440 RDTKNIGKRR KPSGTGVPPQ TTEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosomal subunit assembly." Nishi K., Morel-Deville F., Hershey J.W.B., Leighton T., Schnier J. Nature 336:496-498(1988) [PubMed: 2461520] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Erratum Nishi K., Morel-Deville F., Hershey J.W.B., Leighton T., Schnier J. Nature 340:246-246(1989) Cited for: SEQUENCE REVISION.
[3]	"Non-ribosomal proteins affecting the assembly of ribosomes in Escherichia coli." Nashimoto H. (In) Nierhaus K.H. (eds.); The translational apparatus, pp.185-195, Plenum Press, New York (1993) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[4]	Nashimoto H., Saito N. Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli." Charollais J., Pflieger D., Vinh J., Dreyfus M., Iost I. Mol. Microbiol. 48:1253-1265(2003) [PubMed: 12787353] [Abstract] Cited for: FUNCTION IN 50S RIBOSOME BIOGENESIS, DISRUPTION PHENOTYPE. Strain: B / BL21-DE3 and K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases." Bizebard T., Ferlenghi I., Iost I., Dreyfus M. Biochemistry 43:7857-7866(2004) [PubMed: 15196029] [Abstract] Cited for: FUNCTION AS RNA-HELICASE, FUNCTION AS ATPASE.
[9]	"CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit." Charollais J., Dreyfus M., Iost I. Nucleic Acids Res. 32:2751-2759(2004) [PubMed: 15148362] [Abstract] Cited for: FUNCTION IN 50S RIBOSOME BIOGENESIS, DISRUPTION PHENOTYPE. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[10]	"SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo." Trubetskoy D., Proux F., Allemand F., Dreyfus M., Iost I. Nucleic Acids Res. 37:6540-6549(2009) [PubMed: 19734346] [Abstract] Cited for: INTERACTION WITH L4, L24 AND 23S RRNA, DOMAIN. Strain: B / BL21-DE3.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X14152 Genomic DNA. Translation: CAA32364.1. D13169 Genomic DNA. Translation: BAA02447.1. D64044 Genomic DNA. Translation: BAA10922.1. U00096 Genomic DNA. Translation: AAC75629.1. AP009048 Genomic DNA. Translation: BAE76752.1.
PIR	G65035.
RefSeq	NP_417071.1. NC_000913.2.
3D structure databases
ProteinModelPortal	P21507.
SMR	P21507. Positions 5-356.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-10920N.
IntAct	P21507. 32 interactions.
MINT	MINT-1225512.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBESCT00000003180; EBESCP00000003180; EBESCG00000002610. EBESCT00000015098; EBESCP00000014389; EBESCG00000014158.
GeneID	947055.
GenomeReviews	Gene locus JW2560 in contig AP009048_GR. Gene locus b2576 in contig U00096_GR.
KEGG	ecj:JW2560. eco:b2576.
PATRIC	32120551. VBIEscCol129921_2678.
Organism-specific databases
EchoBASE	EB0968.
EcoGene	EG10975. srmB.
Phylogenomic databases
eggNOG	COG0513.
GeneTree	EBGT00050000008320.
HOGENOM	HBG737336.
OMA	FPRRKPG.
PhylomeDB	P21507.
ProtClustDB	PRK11192.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10975-MONOMER.
Gene expression databases
Genevestigator	P21507.
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001650. Helicase_C. IPR000629. RNA-helicase_DEAD-box_CS. IPR014014. RNA_helicase_DEAD_Q_motif. [Graphical view]
KO	K05590.
Pfam	PF00270. DEAD. 1 hit. PF00271. Helicase_C. 1 hit. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
PROSITE	PS00039. DEAD_ATP_HELICASE. 1 hit. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51195. Q_MOTIF. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

SRMB_ECOLI

Accession

Primary (citable) accession number: P21507
Secondary accession number(s): Q2MAF4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	May 1, 1991
Last modified:	January 25, 2012
This is version 104 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program