Cold-shock DEAD box protein A - Escherichia coli (strain K12)

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P0A9P6 (DEAD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 77. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Cold-shock DEAD box protein A
EC=3.6.4.13

Alternative name(s):
ATP-dependent RNA helicase DeaD
Translation factor W2

Gene names

Name:	deaD
Synonyms:	csdA, mssB, rhlD
Ordered Locus Names:	b3162, JW5531

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	629 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as an ATP-dependent RNA helicase, able to unwind ds-RNA. May play a role in the RNA degradosome at low temperatures. Ref.1 Ref.4 Ref.5 Ref.7 Ref.8 Ref.10 Acts in 50S ribosomal subunit biogenesis at low temperatures, acting after SrmB. Has a helix-destabilizing activity; however it is unclear whether it requires ATP: according to Ref.4, it does not require ATP, while according to Ref.8 and Ref.9, it requires ATP. Requires a helicase substrate with a single-stranded overhang. Plays a key role in optimal cell growth at low temperature and is required for normal cell division. When overexpressed suppresses cold-sensitive mutants of the rpsB gene (ribosomal protein S2) and of the smbA2 cold-sensitive mutant (pyrH, uridylate kinase). Can replace RhlB, another ATP-dependent RNA helicase, in the RNA degradosome in vitro. Stimulates translation, probably at the level of initiation, of some mRNAs. Ref.1 Ref.4 Ref.5 Ref.7 Ref.8 Ref.10
Catalytic activity	ATP + H₂O = ADP + phosphate.
Subunit structure	Associates with the 70S ribosome upon shifting to 15 degrees Celsius. Also found associated with the RNA degradosome at 15 degrees Celsius; binds rne (RNase E). Ref.4
Subcellular location	Cytoplasm Ref.4.
Induction	In response to low temperature. Ref.4
Disruption phenotype	Cells lacking this gene grows very poorly at 15-20 degrees Celsius and accumulate an abnormal large ribosomal subunit. Ref.4 Ref.10
Sequence similarities	Belongs to the DEAD box helicase family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.
Sequence caution	The sequence AAA23674.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence AAA23674.1 differs from that shown. Reason: Frameshift at positions 536 and 565. The sequence AAA57965.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Stress response
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Activator Helicase Hydrolase
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	RNA catabolic process Inferred from genetic interaction Ref.9. Source: EcoCyc cellular response to cold Inferred from mutant phenotype Ref.4. Source: EcoCyc ribosomal large subunit assembly Inferred from mutant phenotype Ref.10. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell preribosome Inferred from direct assay Ref.10. Source: EcoCyc
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Inferred from direct assay Ref.8 Ref.11. Source: EcoCyc RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4 Ref.5

Chain

2 – 629

628

Cold-shock DEAD box protein A

PRO_0000055101

Regions

Domain

37 – 208

172

Helicase ATP-binding

Domain

232 – 379

148

Helicase C-terminal

Nucleotide binding

50 – 57

ATP By similarity

Motif

6 – 34

Q motif

Motif

156 – 159

DEAD box

Compositional bias

568 – 629

Arg/Glu/Gly-rich

Experimental info

Mutagenesis

157

E → Q: Abolishes ATPase activity, drastically reduces helicase activity. In vivo acts as a dominant negative mutation in the presence of the wild-type protein at low temperature. Ref.11

Sequence conflict

444

A → G in AAA23674. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

P0A9P6 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 9DB692D41C38D17C
Show »

FASTA

629

70,546

        10         20         30         40         50         60 
MAEFETTFAD LGLKAPILEA LNDLGYEKPS PIQAECIPHL LNGRDVLGMA QTGSGKTAAF 

        70         80         90        100        110        120 
SLPLLQNLDP ELKAPQILVL APTRELAVQV AEAMTDFSKH MRGVNVVALY GGQRYDVQLR 

       130        140        150        160        170        180 
ALRQGPQIVV GTPGRLLDHL KRGTLDLSKL SGLVLDEADE MLRMGFIEDV ETIMAQIPEG 

       190        200        210        220        230        240 
HQTALFSATM PEAIRRITRR FMKEPQEVRI QSSVTTRPDI SQSYWTVWGM RKNEALVRFL 

       250        260        270        280        290        300 
EAEDFDAAII FVRTKNATLE VAEALERNGY NSAALNGDMN QALREQTLER LKDGRLDILI 

       310        320        330        340        350        360 
ATDVAARGLD VERISLVVNY DIPMDSESYV HRIGRTGRAG RAGRALLFVE NRERRLLRNI 

       370        380        390        400        410        420 
ERTMKLTIPE VELPNAELLG KRRLEKFAAK VQQQLESSDL DQYRALLSKI QPTAEGEELD 

       430        440        450        460        470        480 
LETLAAALLK MAQGERTLIV PPDAPMRPKR EFRDRDDRGP RDRNDRGPRG DREDRPRRER 

       490        500        510        520        530        540 
RDVGDMQLYR IEVGRDDGVE VRHIVGAIAN EGDISSRYIG NIKLFASHST IELPKGMPGE 

       550        560        570        580        590        600 
VLQHFTRTRI LNKPMNMQLL GDAQPHTGGE RRGGGRGFGG ERREGGRNFS GERREGGRGD 

       610        620 
GRRFSGERRE GRAPRRDDST GRRRFGGDA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB, the gene encoding ribosomal protein S2." Toone W.M., Rudd K.E., Friesen J.D. J. Bacteriol. 173:3291-3302(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"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] [Europe PMC] [Abstract] 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]	"Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli." Jones P.G., Mitta M., Kim Y., Jiang W., Inouye M. Proc. Natl. Acad. Sci. U.S.A. 93:76-80(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-21, FUNCTION IN HELIX-DESTABILIZING, SUBUNIT, SUBCELLULAR LOCATION, INDUCTION, DISRUPTION PHENOTYPE.
[5]	"Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF4A." Lu J., Aoki H., Ganoza M.C. Int. J. Biochem. Cell Biol. 31:215-229(1999) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-16, FUNCTION AS A TRANSLATION FACTOR.
[6]	"Nucleotide sequence and expression in Escherichia coli of the Klebsiella pneumoniae deaD gene." Peng H.L., Hsieh M.J., Zao C.L., Chang H.-Y. J. Biochem. 115:409-414(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 519-629. Strain: K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926.
[7]	"Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli." Yamanaka K., Ogura T., Koonin E.V., Niki H., Hiraga S. Mol. Gen. Genet. 243:9-16(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN PYRH MUTANT SUPPRESSION.
[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] [Europe PMC] [Abstract] Cited for: FUNCTION AS AN RNA-HELICASE, FUNCTION AS AN ATPASE.
[9]	"Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'." Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A., Simons R.W. Mol. Microbiol. 54:1409-1421(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RNE, ASSOCIATION WITH RNA DEGRADOSOME. Strain: CF881.
[10]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION IN 50S RIBOSOME BIOGENESIS, DISRUPTION PHENOTYPE. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[11]	"Mutational analysis of the Escherichia coli DEAD box protein CsdA." Turner A.-M.W., Love C.F., Alexander R.W., Jones P.G. J. Bacteriol. 189:2769-2776(2007) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLU-157, HELICASE ACTIVITY, ATPASE ACTIVITY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M63288 Genomic DNA. Translation: AAA23674.1. Sequence problems. U18997 Genomic DNA. Translation: AAA57965.1. Different initiation. U00096 Genomic DNA. Translation: AAC76196.2. AP009048 Genomic DNA. Translation: BAE77208.1. U03750 Genomic DNA. Translation: AAA03626.1.
PIR	F65106.
RefSeq	NP_417631.2. NC_000913.2. YP_491349.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A9P6.
SMR	P0A9P6. Positions 8-372.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-35752N.
IntAct	P0A9P6. 84 interactions.
MINT	MINT-1219396.
STRING	511145.b3162.
2D gel databases
SWISS-2DPAGE	P0A9P6.
Proteomic databases
PaxDb	P0A9P6.
PRIDE	P0A9P6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76196; AAC76196; b3162. BAE77208; BAE77208; BAE77208.
GeneID	12933435. 947674.
KEGG	ecj:Y75_p3084. eco:b3162.
PATRIC	32121742. VBIEscCol129921_3257.
Organism-specific databases
EchoBASE	EB0211.
EcoGene	EG10215. deaD.
Phylogenomic databases
eggNOG	COG0513.
HOGENOM	HOG000268810.
KO	K05592.
OMA	ILFMTPR.
ProtClustDB	PRK11634.
Enzyme and pathway databases
BioCyc	EcoCyc:EG10215-MONOMER. ECOL316407:JW5531-MONOMER.
Gene expression databases
Genevestigator	P0A9P6.
Family and domain databases
InterPro	IPR021046. Cold-shock_DEAD_Abox_C. IPR005580. DbpA_RNA-bd. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR000629. RNA-helicase_DEAD-box_CS. IPR014014. RNA_helicase_DEAD_Q_motif. [Graphical view]
Pfam	PF03880. DbpA. 1 hit. PF00270. DEAD. 1 hit. PF12343. DEADboxA. 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

DEAD_ECOLI

Accession

Primary (citable) accession number: P0A9P6
Secondary accession number(s): P23304, Q2M948, Q8FD90

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 77 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents