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Protein

DEAD-box ATP-dependent RNA helicase CshA

Gene

cshA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The most abundant DEAD-box RNA helicase. An ATP-dependent RNA helicase with RNA-dependent ATPase activity. May work in conjunction with the cold shock proteins to ensure proper initiation of transcription at low and optimal temperatures. In vitro, unwinds dsRNA in both 5'- and 3'- directions. Plays a role in ribosomal 50S subunit assembly. Its deletion leads to changes in mRNA levels for over 200 transcripts.3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.UniRule annotation

Cofactori

Mg2+1 Publication

Enzyme regulationi

RNA helicase activity is inhibited by EDTA.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi47 – 54ATPUniRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB
  • ATP-dependent RNA helicase activity Source: UniProtKB
  • RNA binding Source: UniProtKB

GO - Biological processi

  • response to cold Source: UniProtKB
  • ribosome biogenesis Source: UniProtKB-KW
  • RNA secondary structure unwinding Source: UniProtKB

Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processRibosome biogenesis, Stress response
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU04580-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DEAD-box ATP-dependent RNA helicase CshAUniRule annotation (EC:3.6.4.13UniRule annotation)
Gene namesi
Name:cshAUniRule annotation
Synonyms:ydbR
Ordered Locus Names:BSU04580
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

  • bacterial nucleoid Source: UniProtKB
  • cytoplasm Source: UniProtKB-KW
  • plasma membrane Source: UniProtKB-SubCell

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Membrane

Pathology & Biotechi

Disruption phenotypei

Slow vegetative growth at 37 degrees Celsius, impaired growth at 22 degrees Celsius (PubMed:16861794) and 16 degrees Celsius (PubMed:23175651). Another report shows no growth difference at 15 degrees Celsius (PubMed:16352840). The presence of CshA or CshB is essential for viability; in a cshA disruption mutant further depletion of cshB stops growth after 1 cell duplication (PubMed:16352840). Others show a quadruple disruption of all RNA helicases (cshA, cshB, deaD, yfmL) was not lethal at 37 degrees Celsius, although both 50S and 70S ribosomes are decreased, growth stops at 16 degrees (PubMed:23175651). At 20 degrees Celsius cells are elongated and wrinkled, with smaller cell diameter and thickened walls, and decreased amounts of 70S and 50S ribosomes; levels of over 200 transcripts are altered (PubMed:23175651).3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002800541 – 494DEAD-box ATP-dependent RNA helicase CshAAdd BLAST494

Proteomic databases

PaxDbiP96614.
PRIDEiP96614.

Expressioni

Inductioni

Induced by cold shock (PubMed:12399512). Constitutively expressed at 37 and 16 degrees Celsius in rich and minimal medium and in exponential, transition and stationary phase (at protein level) (PubMed:20572937, PubMed:23175651). Protein level not increased at 16 degrees Celsius (at protein level) (PubMed:20572937).4 Publications

Interactioni

Subunit structurei

Homodimer or oligomer. May interact with RNA helicases CshB and DbpA (DeaD). Probably a component of the RNA degradosome complex composed of rny, rnjA, rnjB, pnp, pfkA and eno, and possibly also rnpA (although rnjA and rnjB's presence is unclear). Interacts with ribosomal proteins L1 and L3 (rplA and rplC) and the protein component of RNase RnpA.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
rnyO317742EBI-6415210,EBI-6415578

Protein-protein interaction databases

IntActiP96614. 3 interactors.
MINTiMINT-8365063.
STRINGi224308.Bsubs1_010100002593.

Structurei

3D structure databases

ProteinModelPortaliP96614.
SMRiP96614.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini34 – 204Helicase ATP-bindingUniRule annotationAdd BLAST171
Domaini215 – 375Helicase C-terminalUniRule annotationAdd BLAST161

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni413 – 494Required for dimerization or oligomerizationAdd BLAST82

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi3 – 31Q motifAdd BLAST29
Motifi152 – 155DEAD box4

Domaini

The C-terminal half of the protein (residues 225-494) is required for interaction with most RNA degradosome partners, whereas dimerization or oligomerization only requires the extreme C-terminus (residues 413-494). Addition of the latter domain to CshB confers on it the ability to interact with Rny.1 Publication

Sequence similaritiesi

Belongs to the DEAD box helicase family. CshA subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268810.
InParanoidiP96614.
KOiK05592.
OMAiFKKGQHK.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01493. DEAD_helicase_CshA. 1 hit.
InterProiView protein in InterPro
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR030880. DEAD_helicase_CshA.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
PfamiView protein in Pfam
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
SMARTiView protein in SMART
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiView protein in PROSITE
PS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.

Sequencei

Sequence statusi: Complete.

P96614-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTITFQDFNL SSDLMKAINR MGFEEATPIQ AQTIPLGLSN KDVIGQAQTG
60 70 80 90 100
TGKTAAFGIP LVEKINPESP NIQAIVIAPT RELAIQVSEE LYKIGQDKRA
110 120 130 140 150
KVLPIYGGQD IGRQIRALKK NPNIIVGTPG RLLDHINRRT IRLNNVNTVV
160 170 180 190 200
MDEADEMLNM GFIDDIESIL SNVPSEHQTL LFSATMPAPI KRIAERFMTE
210 220 230 240 250
PEHVKVKAKE MTVSNIQQFY LEVQERKKFD TLTRLLDIQS PELAIVFGRT
260 270 280 290 300
KRRVDELAEA LNLRGYAAEG IHGDLTQAKR MVALRKFKEG AIEVLVATDV
310 320 330 340 350
AARGLDISGV THVYNFDVPQ DPESYVHRIG RTGRAGKTGM AMTFITPREK
360 370 380 390 400
SMLRAIEQTT KRKMDRMKEP TLDEALEGQQ QVTVERLRTT ISENNLNFYM
410 420 430 440 450
TAAAELLEDH DAVTVVAAAI KMATKEPDDT PVRLTDEAPM VSKRYKNQRS
460 470 480 490
SKRRDGQGGG YRGGKGKSNN RSSYDKKRSN DRRSSGDRRQ KKSY
Length:494
Mass (Da):55,330
Last modified:March 6, 2007 - v2
Checksum:iA44C5EAE314E46ED
GO

Sequence cautioni

The sequence BAA19295 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19295.1. Different initiation.
AL009126 Genomic DNA. Translation: CAB12265.2.
PIRiD69772.
RefSeqiNP_388339.1. NC_000964.3.
WP_003246685.1. NZ_JNCM01000031.1.

Genome annotation databases

EnsemblBacteriaiCAB12265; CAB12265; BSU04580.
GeneIDi938170.
KEGGibsu:BSU04580.
PATRICi18972500. VBIBacSub10457_0478.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19295.1. Different initiation.
AL009126 Genomic DNA. Translation: CAB12265.2.
PIRiD69772.
RefSeqiNP_388339.1. NC_000964.3.
WP_003246685.1. NZ_JNCM01000031.1.

3D structure databases

ProteinModelPortaliP96614.
SMRiP96614.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP96614. 3 interactors.
MINTiMINT-8365063.
STRINGi224308.Bsubs1_010100002593.

Proteomic databases

PaxDbiP96614.
PRIDEiP96614.

Protocols and materials databases

DNASUi938170.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12265; CAB12265; BSU04580.
GeneIDi938170.
KEGGibsu:BSU04580.
PATRICi18972500. VBIBacSub10457_0478.

Phylogenomic databases

eggNOGiENOG4105C1J. Bacteria.
COG0513. LUCA.
HOGENOMiHOG000268810.
InParanoidiP96614.
KOiK05592.
OMAiFKKGQHK.

Enzyme and pathway databases

BioCyciBSUB:BSU04580-MONOMER.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01493. DEAD_helicase_CshA. 1 hit.
InterProiView protein in InterPro
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR030880. DEAD_helicase_CshA.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
PfamiView protein in Pfam
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
SMARTiView protein in SMART
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiView protein in PROSITE
PS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCSHA_BACSU
AccessioniPrimary (citable) accession number: P96614
Secondary accession number(s): Q797L0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 6, 2007
Last modified: March 15, 2017
This is version 116 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. 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.