30S ribosomal protein S13 - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P0A7S9 (RS13_ECOLI)

Last modified June 16, 2009. Version 50. History...

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

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Names and origin

Protein names

Recommended name:
30S ribosomal protein S13

Gene names

Name:	rpsM
Ordered Locus Names:	b3298, JW3260

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	118 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. Ref.11 In the E.coli 70S ribosome in the initiation state (Ref.14) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (Ref.14). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (Ref.15), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (Ref.16) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder. Ref.11 Contacts the tRNAs in the A and P sites. Ref.11 The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Ref.11
Subunit structure	Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Cross-links to the P site tRNA and weakly to the A site tRNA. Forms two bridges to the 50S subunit in the 70S ribosome, contacting the 16S rRNA and proteins S19 and L5. Ref.14 Ref.15
Sequence similarities	Belongs to the ribosomal protein S13P family.
Mass spectrometry	Molecular mass is 12968.1 Da from positions 2 - 118. Determined by MALDI. Ref.12

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Ontologies

Keywords
Ligand	RNA-binding rRNA-binding tRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: HAMAP
Cellular component	ribosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4

Chain

2 – 118

117

30S ribosomal protein S13 HAMAP MF_01315

PRO_0000132089

Natural variations

Natural variant

89 – 99

Missing in PW118; partially suppresses a rimM deletion. HAMAP MF_01315

Natural variant

100 – 118

Missing in rpsM413; pseudorevertant of streptomycin resistance. A strong antisuppressor of two tRNA suppressors, decreases translation step time and growth rate. HAMAP MF_01315

Natural variant

105

N → H in PW095; partially suppresses a rimM deletion. HAMAP MF_01315

Natural variant

105

N → K in PW097; partially suppresses a rimM deletion. HAMAP MF_01315

Experimental info

Mutagenesis

83 – 118

Missing: Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro. HAMAP MF_01315

Mutagenesis

114 – 118

Missing: Decreased growth rate at all temperatures. Decreased affinity of the 30S subunit P site for tRNA in vitro. HAMAP MF_01315

Secondary structure

118

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0A7S9-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 6277C365EBE4F732
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FASTA

118

13,099

        10         20         30         40         50         60 
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV 

        70         80         90        100        110 
AKFVVEGDLR REISMSIKRL MDLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKPIKK

« Hide

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References

	« Hide 'large scale' referencesShow '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]. Strain: K12.
[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]	"Primary structure of protein S13 from the small subunit of Escherichia coli ribosomes." Lindemann H., Wittmann-Liebold B. Hoppe-Seyler's Z. Physiol. Chem. 358:843-863(1977) [PubMed: 330375] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-118. Strain: K.
[5]	"DNA sequence of the promoter region for the alpha ribosomal protein operon in Escherichia coli." Post L.E., Arfsten A.E., Davis G.R., Nomura M. J. Biol. Chem. 255:4653-4659(1980) [PubMed: 6154696] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-36.
[6]	"Growth-rate-dependent regulation of ribosome synthesis in E. coli: expression of the lacZ and galK genes fused to ribosomal promoters." Miura A., Krueger J.H., Itoh S., de Boer H.A., Nomura M. Cell 25:773-782(1981) [PubMed: 6793240] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-36.
[7]	"Identification of a cross-link in the Escherichia coli ribosomal protein pair S13-S19 at the amino acid level." Pohl T., Wittmann-Liebold B. J. Biol. Chem. 263:4293-4301(1988) [PubMed: 3279034] [Abstract] Cited for: PROTEIN SEQUENCE OF 83-85, CROSS-LINKING TO S19. Strain: K12 / A19.
[8]	"Antisuppression by a mutation in rpsM(S13) giving a shortened ribosomal protein S13." Faxen M., Walles-Granberg A., Isaksson L.A. Biochim. Biophys. Acta 1218:27-34(1994) [PubMed: 8193163] [Abstract] Cited for: CHARACTERIZATION OF VARIANT RPSM413. Strain: K12.
[9]	"The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site." Osswald M., Doering T., Brimacombe R. Nucleic Acids Res. 23:4635-4641(1995) [PubMed: 8524654] [Abstract] Cited for: CROSS-LINKING TO THE TRNA CENTRAL FOLD. Strain: MRE-600.
[10]	"A novel ribosome-associated protein is important for efficient translation in Escherichia coli." Bylund G.O., Persson B.C., Lundberg L.A., Wikstroem P.M. J. Bacteriol. 179:4567-4574(1997) [PubMed: 9226267] [Abstract] Cited for: ABILITY OF VARIANTS PW118; PW097 AND PW095 TO PARTIALLY SUPPRESS A RIMM DELETION. Strain: MW100.
[11]	"Creating ribosomes with an all-RNA 30S subunit P site." Hoang L., Fredrick K., Noller H.F. Proc. Natl. Acad. Sci. U.S.A. 101:12439-12443(2004) [PubMed: 15308780] [Abstract] Cited for: ROLE IN P SITE TRNA BINDING, MUTAGENESIS. Strain: CSH142.
[12]	"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.
[13]	"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.
[14]	"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), INTERSUBUNIT BRIDGE FORMATION. Strain: MRE-600.
[15]	"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 INCLUDING THE INTERSUBUNIT BRIDGE B1B. Strain: MRE-600.
[16]	"Locking and unlocking of ribosomal motions." Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., Frank J. Cell 114:123-134(2003) [PubMed: 12859903] [Abstract] Cited for: 3D-STRUCTURE MODELING OF RIBOSOMAL COMPLEXES INCLUDING BRIDGE CHANGES UPPON TRANSLOCATION.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

X02543 Genomic DNA. Translation: CAA26392.1.
U18997 Genomic DNA. Translation: AAA58093.1.
U00096 Genomic DNA. Translation: AAC76323.1.
AP009048 Genomic DNA. Translation: BAE77993.1.
M12432 Genomic DNA. Translation: AAA83903.1.
M10213 Genomic DNA. Translation: AAA72457.1.

PIR

R3EC13. A23807.

RefSeq

AP_004492.1.
NP_417757.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1M5G	model	-	M	2-118	[»]
1P6G	electron microscopy	12.30	M	2-118	[»]
1P87	electron microscopy	11.50	M	2-118	[»]
1VS5	X-ray	3.46	M	1-118	[»]
1VS7	X-ray	3.46	M	1-118	[»]
2AVY	X-ray	3.46	M	2-118	[»]
2AW7	X-ray	3.46	M	2-118	[»]
2GY9	electron microscopy	-	M	2-115	[»]
2GYB	electron microscopy	-	M	2-115	[»]
2I2P	X-ray	3.22	M	2-117	[»]
2I2U	X-ray	3.22	M	2-117	[»]
2QAL	X-ray	3.21	M	2-118	[»]
2QAN	X-ray	3.21	M	2-118	[»]
2QB9	X-ray	3.54	M	2-118	[»]
2QBB	X-ray	3.54	M	2-118	[»]
2QBD	X-ray	3.30	M	2-118	[»]
2QBF	X-ray	3.30	M	2-118	[»]
2QBH	X-ray	4.00	M	2-118	[»]
2QBJ	X-ray	4.00	M	2-118	[»]
2QOU	X-ray	3.93	M	2-118	[»]
2QOW	X-ray	3.93	M	2-118	[»]
2QOY	X-ray	3.50	M	2-118	[»]
2QP0	X-ray	3.50	M	2-118	[»]
2VHO	X-ray	3.74	M	2-118	[»]
2VHP	X-ray	3.74	M	2-118	[»]
2Z4K	X-ray	4.45	M	2-118	[»]
2Z4M	X-ray	4.45	M	2-118	[»]
3DF1	X-ray	3.50	M	2-117	[»]
3DF3	X-ray	3.50	M	2-117	[»]
3FIH	electron microscopy	-	M	2-114	[»]

ModBase

Search...

Genome annotation databases

GeneID

947791.

GenomeReviews

Gene locus JW3260 in contig AP009048_GR.
Gene locus b3298 in contig U00096_GR.

KEGG

ecj:JW3260.
eco:b3298.

Organism-specific databases

EchoBASE

EB0905.

EcoGene

EG10912. rpsM.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A7S9.

OMA

P0A7S9. RRQEGMA.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10912-MON.

Family and domain databases

HAMAP

MF_01315.
[Tree]

InterPro

IPR001892. Ribosomal_S13.
IPR019980. Ribosomal_S13_bac-type.
IPR018269. Ribosomal_S13_CS.
[Graphical view]

Pfam

PF00416. Ribosomal_S13. 1 hit.
[Graphical view]

PIRSF

PIRSF002134. Ribosomal_S13. 1 hit.

ProDom

PD001363. Ribosomal_S13. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR03631. Bact_S13. 1 hit.

PROSITE

PS00646. RIBOSOMAL_S13_1. 1 hit.
PS50159. RIBOSOMAL_S13_2. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

RS13_ECOLI

Accession

Primary (citable) accession number: P0A7S9
Secondary accession number(s): P02369, Q2M6W3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 50 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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