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P0A7V8 (RS4_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

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) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

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

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4 Ref.5
Chain2 – 20620530S ribosomal protein S4 HAMAP-Rule MF_01306_B
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 AA sequence Ref.4
Sequence conflict911Missing AA sequence Ref.5
Sequence conflict951E → Q AA sequence Ref.4
Sequence conflict951E → Q AA sequence Ref.5
Sequence conflict138 – 1447SPNDVVS → DPNSVV AA sequence Ref.4
Sequence conflict138 – 1447SPNDVVS → DPNSVV AA sequence Ref.5
Sequence conflict1521Q → E AA sequence Ref.4
Sequence conflict1521Q → E AA sequence Ref.5
Sequence conflict1661E → Q AA sequence Ref.4
Sequence conflict1661E → Q AA sequence Ref.5

Secondary structure

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

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A7V8 [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

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] [Europe PMC] [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 277:1453-1462(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]"The primary structure of ribosomal protein S4 from Escherichia coli."
Reinbolt J., Schiltz E.
FEBS Lett. 36:250-252(1973) [PubMed] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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, IDENTIFICATION BY 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.46 ANGSTROMS) OF 2 DIFFERENT RIBOSOME STRUCTURES.
Strain: MRE-600.
+Additional computationally mapped references.

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.
RefSeqNP_417755.1. NC_000913.3.
YP_492136.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EG0electron microscopy11.50A43-200[»]
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[»]
2VHPX-ray3.74D2-206[»]
2WWLelectron microscopy5.80D2-206[»]
2YKRelectron microscopy9.80D2-206[»]
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[»]
3IZVelectron microscopy-H1-206[»]
3IZWelectron microscopy-H1-206[»]
3J00electron microscopy-D2-206[»]
3J0Uelectron microscopy12.10G2-206[»]
3J0Velectron microscopy14.70G2-206[»]
3J0Xelectron microscopy13.50G2-206[»]
3J0Zelectron microscopy11.50G2-206[»]
3J10electron microscopy11.50G2-206[»]
3J13electron microscopy13.10F2-206[»]
3J18electron microscopy8.30D2-206[»]
3J36electron microscopy9.80D2-206[»]
3J4Velectron microscopy12.00D1-206[»]
3J4Welectron microscopy12.00D1-206[»]
3J4Yelectron microscopy17.00D1-206[»]
3J4Zelectron microscopy20.00D1-206[»]
3J53electron microscopy13.00D1-206[»]
3J55electron microscopy15.00D1-206[»]
3J57electron microscopy17.00D1-206[»]
3J59electron microscopy12.00D1-206[»]
3J5Belectron microscopy17.00D1-206[»]
3J5Delectron microscopy17.00D1-206[»]
3J5Felectron microscopy20.00D1-206[»]
3J5Helectron microscopy15.00D1-206[»]
3J5Jelectron microscopy9.00D1-206[»]
3J5Nelectron microscopy6.80D1-206[»]
3J5Telectron microscopy7.60D2-206[»]
3J5Xelectron microscopy7.60D2-206[»]
3KC4electron microscopy-D1-206[»]
3OAQX-ray3.25D2-206[»]
3OARX-ray3.25D2-206[»]
3OFAX-ray3.19D2-206[»]
3OFBX-ray3.19D2-206[»]
3OFOX-ray3.10D2-206[»]
3OFPX-ray3.10D2-206[»]
3OFXX-ray3.29D2-206[»]
3OFYX-ray3.29D2-206[»]
3OR9X-ray3.30D1-206[»]
3ORAX-ray3.30D1-206[»]
3SFSX-ray3.20D1-206[»]
3UOQX-ray3.70D1-206[»]
4A2Ielectron microscopy16.50D2-206[»]
4ADVelectron microscopy13.50D2-206[»]
4GAQX-ray3.30D1-206[»]
4GASX-ray3.30D1-206[»]
4GD1X-ray3.00D2-206[»]
4GD2X-ray3.00D2-206[»]
4KIYX-ray2.90D1-206[»]
4KJ0X-ray2.90D1-206[»]
4KJ2X-ray2.90D1-206[»]
4KJ4X-ray2.90D1-206[»]
4KJ6X-ray2.90D1-206[»]
4KJ8X-ray2.90D1-206[»]
4KJAX-ray2.90D1-206[»]
4KJCX-ray2.90D1-206[»]
ProteinModelPortalP0A7V8.
SMRP0A7V8. Positions 2-206.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid852105. 1 interaction.
DIPDIP-35794N.
IntActP0A7V8. 214 interactions.
MINTMINT-6478162.
STRING511145.b3296.

Chemistry

ChEMBLCHEMBL2363135.
DrugBankDB00453. Clomocycline.
DB00618. Demeclocycline.
DB00254. Doxycycline.
DB00256. Lymecycline.
DB01017. Minocycline.
DB00595. Oxytetracycline.
DB00759. Tetracycline.
DB00560. Tigecycline.

Proteomic databases

PaxDbP0A7V8.
PRIDEP0A7V8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76321; AAC76321; b3296.
BAE77995; BAE77995; BAE77995.
GeneID12934394.
947793.
KEGGecj:Y75_p3880.
eco:b3296.
PATRIC32122024. VBIEscCol129921_3389.

Organism-specific databases

EchoBASEEB0896.
EcoGeneEG10903. rpsD.

Phylogenomic databases

eggNOGCOG0522.
HOGENOMHOG000221003.
KOK02986.
OMATHGHILV.
OrthoDBEOG6N3CXM.
ProtClustDBPRK05327.

Enzyme and pathway databases

BioCycEcoCyc:EG10903-MONOMER.
ECOL316407:JW3258-MONOMER.

Gene expression databases

GenevestigatorP0A7V8.

Family and domain databases

Gene3D1.10.1050.10. 1 hit.
3.10.290.10. 1 hit.
HAMAPMF_01306_B. Ribosomal_S4_B.
InterProIPR022801. Ribosomal_S4/S9.
IPR001912. Ribosomal_S4/S9_N.
IPR005709. Ribosomal_S4_bac-type.
IPR018079. Ribosomal_S4_CS.
IPR002942. S4_RNA-bd.
[Graphical view]
PANTHERPTHR11831. PTHR11831. 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

EvolutionaryTraceP0A7V8.
PROP0A7V8.

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: April 16, 2014
This is version 103 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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