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Reviewed, UniProtKB/Swiss-Prot P0A7V8 (RS4_ECOLI)

Last modified February 9, 2010. Version 61. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    30S ribosomal protein S4
Gene names
Name: rpsD
Synonyms: ramA
Ordered Locus Names: b3296, JW3258
OrganismEscherichia coli (strain K12) [Complete proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length206 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. Ref.10 Ref.15 Ref.16

With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations). Ref.10 Ref.15 Ref.16

Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp. Ref.10 Ref.15 Ref.16

Protein S4 is also a translational repressor protein, it controls the translation of the alpha-operon (which codes for S13, S11, S4, RNA polymerase alpha subunit, and L17) by binding to its mRNA. Ref.10 Ref.15 Ref.16

Also functions as a rho-dependent antiterminator of rRNA transcription, increasing the synthesis of rRNA under conditions of excess protein, allowing a more rapid return to homeostasis. Binds directly to RNA polymerase. Ref.10 Ref.15 Ref.16

Subunit structure

Part of the 30S ribosomal subunit. Contacts protein S5. With proteins S3 and S5 encircles the mRNA as it enters the ribosome, which may play a role in mRNA helicase processivity. Some nascent polypeptide chains are able to cross-link to this protein in situ. Ref.10

Sequence similarities

Belongs to the ribosomal protein S4P family.

Contains 1 S4 RNA-binding domain.

Mass spectrometry

Molecular mass is 23339.5 Da from positions 2 - 206. Determined by MALDI. Ref.17

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4 Ref.5
Chain2 – 20620530S ribosomal protein S4 HAMAP MF_01306
PRO_0000132380

Regions

Domain96 – 15661S4 RNA-binding

Natural variations

Natural variant511Y → D in rpsD101; suppresses a temperature-sensitive mutant of release factor 1, R137P. Not a ram mutation.
Natural variant170 – 20637Missing in rpsD16; suppresses streptomycin dependence in protein S12. A ram mutation.
Natural variant177 – 20630KMEGT…ELYSK → GRYV in rpsD12; suppresses streptomycin dependence in protein S12. A ram mutation.
Natural variant179 – 20628EGTFK…ELYSK → ARYV in rpsD14; suppresses streptomycin dependence in protein S12. A ram mutation.

Experimental info

Mutagenesis44 – 474RKPR → AKPA: Decreases mRNA unwinding ability of the ribosome.
Sequence conflict911Missing Ref.4
Sequence conflict911Missing Ref.5
Sequence conflict951E → Q Ref.4
Sequence conflict951E → Q Ref.5
Sequence conflict138 – 1447SPNDVVS → DPNSVV Ref.4
Sequence conflict138 – 1447SPNDVVS → DPNSVV Ref.5
Sequence conflict1521Q → E Ref.4
Sequence conflict1521Q → E Ref.5
Sequence conflict1661E → Q Ref.4
Sequence conflict1661E → Q Ref.5

Secondary structure

1 ........................................... 206
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P0A7V8-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 4015969DF8E582BB

FASTA20623,469
        10         20         30         40         50         60 
MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK 

        70         80         90        100        110        120 
VRRIYGVLER QFRNYYKEAA RLKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH 

       130        140        150        160        170        180 
KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE LAEQREKPTW LEVDAGKMEG 

       190        200 
TFKRKPERSD LSADINEHLI VELYSK

« Hide

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References

« Hide 'large scale' references
[1]"Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli."
Bedwell D.M., Davis G.R., Gosink M., Post L.E., Nomura M., Kestler H., Zengel J.M., Lindahl L.
Nucleic Acids Res. 13:3891-3903(1985) [PubMed: 2989779] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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: 9278503] [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: 16738553] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The primary structure of ribosomal protein S4 from Escherichia coli."
Reinbolt J., Schiltz E.
FEBS Lett. 36:250-252(1973) [PubMed: 4587210] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-206.
Strain: AB774.
[5]"Determination of the complete amino-acid sequence of protein S4 from Escherichia coli ribosomes."
Schiltz E., Reinbolt J.
Eur. J. Biochem. 56:467-481(1975) [PubMed: 1100394] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-206.
Strain: K.
[6]"Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies."
Urlaub H., Kruft V., Bischof O., Mueller E.-C., Wittmann-Liebold B.
EMBO J. 14:4578-4588(1995) [PubMed: 7556101] [Abstract]
Cited for: PROTEIN SEQUENCE OF 78-91, CROSS-LINKING TO RRNA.
Strain: MRE-600.
[7]Bienvenut W.V., Barblan J., Quadroni M.
Submitted (JAN-2004) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 84-97 AND 129-146, MASS SPECTROMETRY.
[8]"Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli."
Post L.E., Nomura M.
J. Biol. Chem. 254:10604-10606(1979) [PubMed: 387752] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 147-206.
[9]"Regulation of alpha operon gene expression in Escherichia coli. A novel form of translational coupling."
Thomas M.S., Bedwell D.M., Nomura M.
J. Mol. Biol. 196:333-345(1987) [PubMed: 3309351] [Abstract]
Cited for: MECHANISM OF TRANSLATION REGULATION.
[10]"Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7."
Nowotny V., Nierhaus K.H.
Biochemistry 27:7051-7055(1988) [PubMed: 2461734] [Abstract]
Cited for: ROLE IN SUBUNIT ASSEMBLY.
Strain: K12 / D10.
[11]"Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA."
Allen P.N., Noller H.F.
J. Mol. Biol. 208:457-468(1989) [PubMed: 2477554] [Abstract]
Cited for: EFFECT OF MUTATIONS ON RRNA FOLDING.
Strain: UD1A1.
[12]"Messenger RNA recognition by fragments of ribosomal protein S4."
Baker A.M., Draper D.E.
J. Biol. Chem. 270:22939-22945(1995) [PubMed: 7559430] [Abstract]
Cited for: BINDING TO MRNA.
[13]"Flexibility of the nascent polypeptide chain within the ribosome --contacts from the peptide N-terminus to a specific region of the 30S subunit."
Choi K.M., Atkins J.F., Gesteland R.F., Brimacombe R.
Eur. J. Biochem. 255:409-413(1998) [PubMed: 9716382] [Abstract]
Cited for: CROSS-LINKING TO NASCENT POLYPEPTIDE CHAINS.
[14]"A novel mutation in ribosomal protein S4 that affects the function of a mutated RF1."
Dahlgren A., Ryden-Aulin M.
Biochimie 82:683-691(2000) [PubMed: 11018284] [Abstract]
Cited for: VARIANT THAT AFFECTS TERMINATION.
Strain: K12 / MG1655 / ATCC 47076.
[15]"Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination."
Torres M., Condon C., Balada J.-M., Squires C., Squires C.L.
EMBO J. 20:3811-3820(2001) [PubMed: 11447122] [Abstract]
Cited for: RHO-DEPENDENT RIBOSOMAL RNA ANTITERMINATION FUNCTION.
[16]"mRNA helicase activity of the ribosome."
Takyar S., Hickerson R.P., Noller H.F.
Cell 120:49-58(2005) [PubMed: 15652481] [Abstract]
Cited for: ROLE IN MRNA HELICASE ACTIVITY, MUTAGENESIS.
Strain: MRE-600.
[17]"Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry."
Arnold R.J., Reilly J.P.
Anal. Biochem. 269:105-112(1999) [PubMed: 10094780] [Abstract]
Cited for: MASS SPECTROMETRY.
Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[18]"All-atom homology model of the Escherichia coli 30S ribosomal subunit."
Tung C.-S., Joseph S., Sanbonmatsu K.Y.
Nat. Struct. Biol. 9:750-755(2002) [PubMed: 12244297] [Abstract]
Cited for: 3D-STRUCTURE MODELING.
[19]"Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement."
Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J.
Cell 113:789-801(2003) [PubMed: 12809609] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (11.50 ANGSTROMS).
Strain: MRE-600.
[20]"Limitations of translational accuracy."
Kurland C.G., Hughes D., Ehrenberg M.
(In) Neidhardt F.C., Curtiss R. III, Ingraham J.L., Lin E.C.C., Low K.B. Magasanik B., Reznikoff W.S., Riley M., Schaechter M., Umbarger H.E. (eds.); Escherichia coli and Salmonella: Cellular and molecular biology (2nd ed.), pp.979-1004, American Society for Microbiology Press, Washington D.C. (1996)
Cited for: REVIEW ON TRANSLATIONAL ACCURACY.
[21]"Structures of the bacterial ribosome at 3.5 A resolution."
Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., Cate J.H.D.
Science 310:827-834(2005) [PubMed: 16272117] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.46 ANGSTROMS) OF 2 DIFFERENT RIBOSOME STRUCTURES.
Strain: MRE-600.
+Additional computationally mapped references.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X02543 Genomic DNA. Translation: CAA26394.1.
U18997 Genomic DNA. Translation: AAA58094.1.
U00096 Genomic DNA. Translation: AAC76321.1.
AP009048 Genomic DNA. Translation: BAE77995.1.
V00353 Genomic DNA. Translation: CAA23645.1.
J01685 Genomic DNA. Translation: AAA24576.1.
PIRR3EC4. C23807.
RefSeqAP_004494.1.
NP_417755.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1M5Gmodel-D2-206[»]
1P6Gelectron microscopy12.30D2-206[»]
1P87electron microscopy11.50D2-206[»]
1VS5X-ray3.46D1-206[»]
1VS7X-ray3.46D1-206[»]
2AVYX-ray3.46D2-206[»]
2AW7X-ray3.46D2-206[»]
2GY9electron microscopy15.00D3-205[»]
2GYBelectron microscopy15.00D3-205[»]
2I2PX-ray3.22D2-205[»]
2I2UX-ray3.22D2-205[»]
2QALX-ray3.21D2-206[»]
2QANX-ray3.21D2-206[»]
2QB9X-ray3.54D2-206[»]
2QBBX-ray3.54D2-206[»]
2QBDX-ray3.30D2-206[»]
2QBFX-ray3.30D2-206[»]
2QBHX-ray4.00D2-206[»]
2QBJX-ray4.00D2-206[»]
2QOUX-ray3.93D2-206[»]
2QOWX-ray3.93D2-206[»]
2QOYX-ray3.50D2-206[»]
2QP0X-ray3.50D2-206[»]
2Z4KX-ray4.45D2-206[»]
2Z4MX-ray4.45D2-206[»]
3DF1X-ray3.50D2-205[»]
3DF3X-ray3.50D2-205[»]
3E1Aelectron microscopy-R1-206[»]
3E1Celectron microscopy-R1-206[»]
3FIHelectron microscopy6.70D2-206[»]
3I1MX-ray3.19D1-206[»]
3I1OX-ray3.19D1-206[»]
3I1QX-ray3.81D1-206[»]
3I1SX-ray3.81D1-206[»]
3I1ZX-ray3.71D1-206[»]
3I21X-ray3.71D1-206[»]
ModBaseSearch...

Protein-protein interaction databases

IntActP0A7V8. 212 interactions.
STRINGP0A7V8.

Proteomic databases

PRIDEP0A7V8.

Genome annotation databases

GeneID947793.
GenomeReviewsGene locus JW3258 in contig AP009048_GR.
Gene locus b3296 in contig U00096_GR.
KEGGecj:JW3258.
eco:b3296.

Organism-specific databases

EchoBASEEB0896.
EcoGeneEG10903. rpsD.
CMRSearch...

Phylogenomic databases

eggNOGCOG0522.
HOGENOMHBG285740.
OMAQLVVELY.

Enzyme and pathway databases

BioCycEcoCyc:EG10903-MONOMER.
ECOL168927:B3296-MONOMER.

Gene expression databases

GenevestigatorP0A7V8.

Family and domain databases

HAMAPMF_01306_B. Ribosomal_S4_B.
[Tree]
InterProIPR001912. Ribosomal_S4.
IPR005709. Ribosomal_S4_bac-type.
IPR018079. Ribosomal_S4_CS.
IPR002942. S4_RNA_bd.
[Graphical view]
PANTHERPTHR11831. Ribosomal_S4. 1 hit.
PfamPF00163. Ribosomal_S4. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]
SMARTSM00363. S4. 1 hit.
[Graphical view]
TIGRFAMsTIGR01017. rpsD_bact. 1 hit.
PROSITEPS00632. RIBOSOMAL_S4. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

DrugBankDB00453. Clomocycline.
DB00618. Demeclocycline.
DB00254. Doxycycline.
DB00256. Lymecycline.
DB01017. Minocycline.
DB00595. Oxytetracycline.
DB00759. Tetracycline.
DB00560. Tigecycline.

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Entry information

Entry nameRS4_ECOLI
AccessionPrimary (citable) accession number: P0A7V8
Secondary accession number(s): P02354, Q2M6W1
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: February 9, 2010
This is version 61 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Escherichia coli

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Ribosomal proteins

Ribosomal proteins families and list of entries

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents