deaD:Gene Product(s)
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| Nomenclature | Function | Interactions | Localization | Sequence | Domains | Structure | Resources | Accessions | Links | References | Suggestions |
Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| Standard name |
DeaD |
|---|---|
| Synonyms |
ATP-dependent RNA helicase[1], B3162[2][1], RhlD[2][1], MssB[2][1], DeaD[2][1] , csdA, ECK3150, JW5531, mssB, rhlD, b3162 |
| Product description |
CsdA, DEAD-box RNA helicase[2][3] Translation factor W2, putative RNA helix-destabilizer; facilitates translation of mRNAs with 5' secondary structures; multicopy suppressor of rpsB(Ts) mutations[4] |
| EC number (for enzymes) |
|
| edit table |
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Notes
Function
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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.
| Qualifier | GO ID | GO term name | Reference | Evidence Code | with/from | Aspect | Notes | Status |
|---|---|---|---|---|---|---|---|---|
| GO:0000027 |
ribosomal large subunit assembly |
IMP: Inferred from Mutant Phenotype |
P |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0000166 |
nucleotide binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003724 |
RNA helicase activity |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0004004 |
ATP-dependent RNA helicase activity |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0004004 |
ATP-dependent RNA helicase activity |
IDA: Inferred from Direct Assay |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0005515 |
protein binding |
IPI: Inferred from Physical Interaction |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0005515 |
protein binding |
IPI: Inferred from Physical Interaction |
F |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005524 |
ATP binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005524 |
ATP binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005737 |
cytoplasm |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005737 |
cytoplasm |
IEA: Inferred from Electronic Annotation |
SP_SL:SL-0086 |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006401 |
RNA catabolic process |
IGI: Inferred from Genetic Interaction |
P |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0070417 |
cellular response to cold |
IEP: Inferred from Expression Pattern |
P |
Seeded from EcoCyc (v14.0) |
complete | |||
| GO:0070417 |
cellular response to cold |
IMP: Inferred from Mutant Phenotype |
P |
Seeded from EcoCyc (v14.0) |
complete | |||
| edit table |
Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.
| Partner Type | Partner | Notes | References | Evidence |
|---|---|---|---|---|
|
Protein |
accA |
Experiment(s):EBI-888958 | ||
|
Protein |
aceE |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
hrpA |
Experiment(s):EBI-888958 | ||
|
Protein |
rplA |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rplI |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rplM |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rplV |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsA |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsB |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsC |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsD |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsE |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsG |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsM |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rpsU |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
srmB |
Experiment(s):EBI-888958 | ||
|
Protein |
ycbY |
Experiment(s):EBI-888958 | ||
|
Protein |
rluB |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
yfiF |
Experiment(s):EBI-888958, EBI-879491, EBI-881486 | ||
|
Protein |
ygiF |
Experiment(s):EBI-888958 | ||
|
Protein |
rplB |
Experiment(s):EBI-888958, EBI-881486 | ||
|
Protein |
rnr |
Experiment(s):EBI-888958, EBI-883997, EBI-881486 | ||
|
Protein |
acpP |
Experiment(s):EBI-881486 | ||
|
Protein |
sixA |
Experiment(s):EBI-881486 | ||
|
Protein |
bglA |
Experiment(s):EBI-881486 | ||
|
Protein |
dacA |
Experiment(s):EBI-881486 | ||
|
Protein |
dppC |
Experiment(s):EBI-881486 | ||
|
Protein |
evgA |
Experiment(s):EBI-881486 | ||
|
Protein |
gsk |
Experiment(s):EBI-881486 | ||
|
Protein |
hupA |
Experiment(s):EBI-881486 | ||
|
Protein |
hupB |
Experiment(s):EBI-881486 | ||
|
Protein |
rplC |
Experiment(s):EBI-881486 | ||
|
Protein |
rplF |
Experiment(s):EBI-881486 | ||
|
Protein |
rplK |
Experiment(s):EBI-881486 | ||
|
Protein |
rplP |
Experiment(s):EBI-881486 | ||
|
Protein |
rplQ |
Experiment(s):EBI-881486 | ||
|
Protein |
rplR |
Experiment(s):EBI-881486 | ||
|
Protein |
rplS |
Experiment(s):EBI-881486 | ||
|
Protein |
rplU |
Experiment(s):EBI-881486 | ||
|
Protein |
rplW |
Experiment(s):EBI-881486 | ||
|
Protein |
rplX |
Experiment(s):EBI-881486 | ||
|
Protein |
rpmA |
Experiment(s):EBI-881486 | ||
|
Protein |
rpmB |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsF |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsH |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsI |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsJ |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsK |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsN |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsO |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsP |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsR |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsS |
Experiment(s):EBI-881486 | ||
|
Protein |
sucD |
Experiment(s):EBI-881486 | ||
|
Protein |
uraA |
Experiment(s):EBI-881486 | ||
|
Protein |
hcp |
Experiment(s):EBI-881486 | ||
|
Protein |
yhiR |
Experiment(s):EBI-881486 | ||
|
Protein |
yihQ |
Experiment(s):EBI-881486 | ||
|
Protein |
sufC |
Experiment(s):EBI-881486 | ||
|
Protein |
rpsT |
Experiment(s):EBI-881486 | ||
|
Protein |
rplK |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsJ |
LCMS(ID Probability):99.6 MALDI(Z-score):2.499464 | ||
|
Protein |
acpP |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpmB |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsN |
LCMS(ID Probability):99.6 | ||
|
Protein |
dnaJ |
LCMS(ID Probability):99.4 MALDI(Z-score):18.261563 | ||
|
Protein |
hupB |
LCMS(ID Probability):99.6 MALDI(Z-score):3.082768 | ||
|
Protein |
rplP |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsP |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplU |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplS |
LCMS(ID Probability):99.6 MALDI(Z-score):7.700577 | ||
|
Protein |
hupA |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsT |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplM |
LCMS(ID Probability):99.6 MALDI(Z-score):15.678591 | ||
|
Protein |
rpsK |
LCMS(ID Probability):99.6 MALDI(Z-score):2.007437 | ||
|
Protein |
rpsA |
LCMS(ID Probability):99.6 MALDI(Z-score):26.788003 | ||
|
Protein |
rplI |
LCMS(ID Probability):99.6 MALDI(Z-score):27.484300 | ||
|
Protein |
rpsH |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsI |
LCMS(ID Probability):99.6 MALDI(Z-score):6.833274 | ||
|
Protein |
rplE |
LCMS(ID Probability):99.6 MALDI(Z-score):13.589053 | ||
|
Protein |
rpsS |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsO |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsF |
LCMS(ID Probability):99.6 MALDI(Z-score):9.114247 | ||
|
Protein |
rpsD |
LCMS(ID Probability):99.6 MALDI(Z-score):35.503180 | ||
|
Protein |
rplW |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpmA |
LCMS(ID Probability):99.4 | ||
|
Protein |
rpsL |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsC |
LCMS(ID Probability):99.6 MALDI(Z-score):33.439795 | ||
|
Protein |
rplB |
LCMS(ID Probability):99.6 MALDI(Z-score):38.065302 | ||
|
Protein |
rpsM |
LCMS(ID Probability):99.6 MALDI(Z-score):25.836351 | ||
|
Protein |
rplA |
LCMS(ID Probability):99.6 MALDI(Z-score):49.766331 | ||
|
Protein |
rplT |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplX |
LCMS(ID Probability):99.6 MALDI(Z-score):13.018295 | ||
|
Protein |
rpsR |
LCMS(ID Probability):99.6 | ||
|
Protein |
dacA |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplO |
LCMS(ID Probability):99.6 MALDI(Z-score):4.899346 | ||
|
Protein |
rpsU |
LCMS(ID Probability):99.6 MALDI(Z-score):17.053160 | ||
|
Protein |
sufC |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplR |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplD |
LCMS(ID Probability):99.6 MALDI(Z-score):21.709148 | ||
|
Protein |
yphE |
LCMS(ID Probability):99.6 | ||
|
Protein |
cspC |
LCMS(ID Probability):99.6 MALDI(Z-score):28.434341 | ||
|
Protein |
rpsQ |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplF |
LCMS(ID Probability):99.6 MALDI(Z-score):10.782348 | ||
|
Protein |
rplQ |
LCMS(ID Probability):99.5 | ||
|
Protein |
srmB |
MALDI(Z-score):28.361090 | ||
|
Protein |
yfiF |
LCMS(ID Probability):99.6 MALDI(Z-score):38.920449 | ||
|
Protein |
rluB |
LCMS(ID Probability):99.2 MALDI(Z-score):37.368522 | ||
|
Protein |
ygiF |
MALDI(Z-score):39.147611 | ||
|
Protein |
pssA |
MALDI(Z-score):26.949774 | ||
|
Protein |
rnr |
LCMS(ID Probability):99.2 MALDI(Z-score):28.380982 | ||
|
Protein |
yibL |
LCMS(ID Probability):99.6 | ||
|
Protein |
hcp |
LCMS(ID Probability):99.4 | ||
|
Protein |
hrpA |
MALDI(Z-score):18.737310 | ||
|
Protein |
rluC |
LCMS(ID Probability):95.6 MALDI(Z-score):36.951557 | ||
| edit table |
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Notes
Localization
See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
| Compartment | Description | Evidence | Reference/Source | Notes |
|---|---|---|---|---|
|
cytoplasm |
From EcoCyc[3] |
| ||
| edit table |
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Notes
Structure and Physical Properties
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Physical Properties
See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MMSYVDWPPL ILRHTYYMAE FETTFADLGL KAPILEALND LGYEKPSPIQ AECIPHLLNG RDVLGMAQTG SGKTAAFSLP LLQNLDPELK APQILVLAPT RELAVQVAEA MTDFSKHMRG VNVVALYGGQ RYDVQLRALR QGPQIVVGTP GRLLDHLKRG TLDLSKLSGL VLDEADEMLR MGFIEDVETI MAQIPEGHQT ALFSATMPEA IRRITRRFMK EPQEVRIQSS VTTRPDISQS YWTVWGMRKN EALVRFLEAE DFDAAIIFVR TKNATLEVAE ALERNGYNSA ALNGDMNQAL REQTLERLKD GRLDILIATD VAARGLDVER ISLVVNYDIP MDSESYVHRI GRTGRAGRAG RALLFVENRE RRLLRNIERT MKLTIPEVEL PNAELLGKRR LEKFAAKVQQ QLESSDLDQY RALLSKIQPT AEGEELDLET LAAALLKMAQ GERTLIVPPD APMRPKREFR DRDDRGPRDR NDRGPRGDRE DRPRRERRDV GDMQLYRIEV GRDDGVEVRH IVGAIANEGD ISSRYIGNIK LFASHSTIEL PKGMPGEVLQ HFTRTRILNK PMNMQLLGDA QPHTGGERRG GGRGFGGERR EGGRNFSGER REGGRGDGRR FSGERREGRA PRRDDSTGRR RFGGDA |
| Length |
646 |
| Mol. Wt |
72.715 kDa |
| pI |
9.0 (calculated) |
| Extinction coefficient |
35,870 - 35,995 (calc based on 13 Y, 3 W, and 1 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
| </protect>
Structure figures<protect> | ||||||
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| edit table |
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 2.3 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ Charollais, J et al. (2004) CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Res. 32 2751-9 PubMed
- ↑ 6.0 6.1 6.2 Jones, PG et al. (1996) Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 93 76-80 PubMed
- ↑ Bizebard, T et al. (2004) Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases. Biochemistry 43 7857-66 PubMed
- ↑ Turner, AM et al. (2007) Mutational analysis of the Escherichia coli DEAD box protein CsdA. J. Bacteriol. 189 2769-76 PubMed
- ↑ Raynal, LC & Carpousis, AJ (1999) Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation. Mol. Microbiol. 32 765-75 PubMed
- ↑ Sato, A et al. (2005) The GTP binding protein Obg homolog ObgE is involved in ribosome maturation. Genes Cells 10 393-408 PubMed
- ↑ Prud'homme-Généreux, A et al. (2004) Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'. Mol. Microbiol. 54 1409-21 PubMed
- ↑ 12.00 12.01 12.02 12.03 12.04 12.05 12.06 12.07 12.08 12.09 12.10 12.11 12.12 12.13 12.14 12.15 12.16 12.17 12.18 12.19 12.20 12.21 12.22 12.23 12.24 12.25 12.26 12.27 12.28 12.29 12.30 12.31 12.32 12.33 12.34 12.35 12.36 12.37 12.38 12.39 12.40 12.41 12.42 12.43 12.44 12.45 12.46 12.47 12.48 12.49 12.50 12.51 12.52 12.53 12.54 12.55 12.56 12.57 12.58 12.59 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ 13.00 13.01 13.02 13.03 13.04 13.05 13.06 13.07 13.08 13.09 13.10 13.11 13.12 13.13 13.14 13.15 13.16 13.17 13.18 13.19 13.20 13.21 13.22 13.23 13.24 13.25 13.26 13.27 13.28 13.29 13.30 13.31 13.32 13.33 13.34 13.35 13.36 13.37 13.38 13.39 13.40 13.41 13.42 13.43 13.44 13.45 13.46 13.47 13.48 13.49 13.50 13.51 13.52 13.53 13.54 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
- ↑ 14.0 14.1 14.2 14.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
Categories
- GO:0000027 ! ribosomal large subunit assembly
- GO:0000166 ! nucleotide binding
- GO:0003676 ! nucleic acid binding
- GO:0003723 ! RNA binding
- GO:0003724 ! RNA helicase activity
- GO:0004004 ! ATP-dependent RNA helicase activity
- GO:0005515 ! protein binding
- GO:0005524 ! ATP binding
- GO:0005737 ! cytoplasm
- GO:0006401 ! RNA catabolic process
- GO:0070417 ! cellular response to cold
- Proteins
