P0A7S3 (RS12_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
30S ribosomal protein S12

Gene names

Name:	rpsL
Synonyms:	strA
Ordered Locus Names:	b3342, JW3304

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	124 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	With S4 and S5 plays an important role in translational accuracy. HAMAP-Rule MF_00403_B Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit By similarity. HAMAP-Rule MF_00403_B Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit. HAMAP-Rule MF_00403_B
Subunit structure	Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex By similarity.
Miscellaneous	At least 19 substitutions or deletions in 11 codons can promote streptomycin resistance, dependence or pseudodependence; all but one of the streptomycin resistant mutations (K42R) are associated with hyperaccurate translation and thus reduced translational efficiency. HAMAP-Rule MF_00403_B The streptomycin sensitive allele is dominant to resistant alleles. HAMAP-Rule MF_00403_B
Sequence similarities	Belongs to the ribosomal protein S12P family.
Mass spectrometry	Molecular mass is 13651.3 Da from positions 2 - 124. Determined by MALDI. Ref.12

Ontologies

Keywords
Biological process	Antibiotic resistance
Ligand	RNA-binding rRNA-binding tRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	Group I intron splicing Inferred from direct assay PubMed 7958841. Source: EcoCyc RNA folding Inferred from direct assay PubMed 7958841. Source: EcoCyc positive regulation of RNA splicing Inferred from direct assay PubMed 7958841. Source: EcoCyc response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW translation Inferred from mutant phenotype PubMed 321423. Source: EcoCyc
Cellular_component	cytosolic small ribosomal subunit Inferred from direct assay PubMed 4922286. Source: EcoCyc
Molecular_function	misfolded RNA binding Inferred from direct assay PubMed 7958841. Source: EcoCyc rRNA binding Inferred from direct assay PubMed 2459389. Source: EcoCyc structural constituent of ribosome Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1 Ref.8

Chain

2 – 124

123

30S ribosomal protein S12 HAMAP-Rule MF_00403_B

PRO_0000146219

Amino acid modifications

Modified residue

89

1

3-methylthioaspartic acid HAMAP-Rule MF_00403_B

Modified residue

108

1

N6-acetyllysine Ref.13

Natural variations

Natural variant

43

1

K → R Confers streptomycin resistance but not hyperaccurate translation.

Experimental info

Mutagenesis

57

1

L → H: Protein is not incorporated into ribosomes. Ref.10

Mutagenesis

88

1

K → Q: Confers low-level resistance to streptomycin and a 15% decrease in the translational elongation rate. Ref.10

Secondary structure

1

.

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.

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124

Helix Strand Turn

Details...

Helix

4 – 9

6

Turn

24 – 26

3

Beta strand

28 – 36

9

Beta strand

37 – 40

4

Beta strand

43 – 45

3

Beta strand

50 – 57

8

Turn

58 – 60

3

Beta strand

64 – 66

3

Beta strand

69 – 71

3

Beta strand

79 – 84

6

Beta strand

88 – 90

3

Beta strand

95 – 97

3

Beta strand

99 – 101

3

Turn

115 – 118

4

Sequences

	Sequence		Length	Mass (Da)
	P0A7S3 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 94A57F4C4FF0FC5E	FASTA	124	13,737
	10 20 30 40 50 60 MATVNQLVRK PRARKVAKSN VPALEACPQK RGVCTRVYTT TPKKPNSALR KVCRVRLTNG 70 80 90 100 110 120 FEVTSYIGGE GHNLQEHSVI LIRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Primary structure of protein S12 from the small Escherichia coli ribosomal subunit." Funatsu G., Yaguchi M., Wittmann-Liebold B. FEBS Lett. 73:12-17(1977) [PubMed] [Europe PMC] [Abstract] Cited for: PRELIMINARY PROTEIN SEQUENCE OF 2-124. Strain: K.
[2]	"DNA sequences from the str operon of Escherichia coli." Post L.E., Nomura M. J. Biol. Chem. 255:4660-4666(1980) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Mutant sequences in the rpsL gene of Escherichia coli B/r: mechanistic implications for spontaneous and ultraviolet light mutagenesis." Timms A.R., Steingrimsdottir H., Lehmann A.R., Bridges B.A. Mol. Gen. Genet. 232:89-96(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS STREPTOMYCIN RESISTANT. Strain: B/R WP2.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Nucleotide information of the rpsL150 allele of MC4100, strain of Escherichia coli." Kharat A.S., Blot M. Submitted (OCT-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT STREPTOMYCIN RESISTANT. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574 and K12 / W3110 / ZK126.
[6]	"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.
[7]	"DNA sequences of promoter regions for the str and spc ribosomal protein operons in E. coli." Post L.E., Arfsten A.E., Reusser F., Nomura M. Cell 15:215-229(1978) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-21. Strain: K12.
[8]	"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 2-11, CROSS-LINKING TO RRNA. Strain: MRE-600.
[9]	"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.
[10]	"Modelling in Escherichia coli of mutations in mitoribosomal protein S12: novel mutant phenotypes of rpsL." Toivonen J.M., Boocock M.R., Jacobs H.T. Mol. Microbiol. 31:1735-1746(1999) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LEU-57 AND LYS-88. Strain: K12.
[11]	"Beta-methylthio-aspartic acid: identification of a novel posttranslational modification in ribosomal protein S12 from Escherichia coli." Kowalak J.A., Walsh K.A. Protein Sci. 5:1625-1632(1996) [PubMed] [Europe PMC] [Abstract] Cited for: BETA-METHYLTHIOLATION AT ASP-89.
[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] [Europe PMC] [Abstract] Cited for: MASS SPECTROMETRY. Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[13]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-108, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[14]	"Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process." Valle M., Sengupta J., Swami N.K., Grassucci R.A., Burkhardt N., Nierhaus K.H., Agrawal R.K., Frank J. EMBO J. 21:3557-3567(2002) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (11 ANGSTROMS) OF KIRROMYCIN-STALLED RIBOSOMES COMPLEXED WITH EF-TU/AMINOACYL-TRNA/GTP.
[15]	"Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex." Stark H., Rodnina M.V., Wieden H.-J., Zemlin F., Wintermeyer W., Van Heel M. Nat. Struct. Biol. 9:849-854(2002) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (13 ANGSTROMS) OF KIRROMYCIN-STALLED RIBOSOMES COMPLEXED WITH EF-TU/AMINOACYL-TRNA/GTP. Strain: MRE-600.
[16]	"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.
[17]	"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.
[18]	"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.
[19]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V00355 Genomic DNA. Translation: CAA23648.1.
U18997 Genomic DNA. Translation: AAA58139.1.
U00096 Genomic DNA. Translation: AAC76367.1.
AP009048 Genomic DNA. Translation: BAE77949.1.
AF312716 Genomic DNA. Translation: AAG30936.1.
AF312717 Genomic DNA. Translation: AAG30937.1.
V00354 Genomic DNA. Translation: CAA23647.1.
J01688 Genomic DNA. Translation: AAA50988.1.

PIR

R3EC12. S13738.

RefSeq

NP_417801.1. NC_000913.2.
YP_492090.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1M5G	model	-	L	2-124	[»]
1MJ1	electron microscopy	13.00	O	5-123	[»]
1P6G	electron microscopy	12.30	L	2-124	[»]
1P87	electron microscopy	11.50	L	2-124	[»]
1VS5	X-ray	3.46	L	1-124	[»]
1VS7	X-ray	3.46	L	1-124	[»]
1ZN1	electron microscopy	14.10	L	28-123	[»]
2AVY	X-ray	3.46	L	2-124	[»]
2AW7	X-ray	3.46	L	2-124	[»]
2GY9	electron microscopy	15.00	L	23-122	[»]
2GYB	electron microscopy	15.00	L	23-122	[»]
2I2P	X-ray	3.22	L	2-123	[»]
2I2U	X-ray	3.22	L	2-123	[»]
2QAL	X-ray	3.21	L	2-124	[»]
2QAN	X-ray	3.21	L	2-124	[»]
2QB9	X-ray	3.54	L	2-124	[»]
2QBB	X-ray	3.54	L	2-124	[»]
2QBD	X-ray	3.30	L	2-124	[»]
2QBF	X-ray	3.30	L	2-124	[»]
2QBH	X-ray	4.00	L	2-124	[»]
2QBJ	X-ray	4.00	L	2-124	[»]
2QOU	X-ray	3.93	L	2-124	[»]
2QOW	X-ray	3.93	L	2-124	[»]
2QOY	X-ray	3.50	L	2-124	[»]
2QP0	X-ray	3.50	L	2-124	[»]
2VHO	X-ray	3.74	L	2-124	[»]
2VHP	X-ray	3.74	L	2-124	[»]
2WWL	electron microscopy	5.80	L	2-124	[»]
2YKR	electron microscopy	9.80	L	2-124	[»]
2Z4K	X-ray	4.45	L	2-124	[»]
2Z4M	X-ray	4.45	L	2-124	[»]
3DEG	electron microscopy	-	D	2-124	[»]
3DF1	X-ray	3.50	L	2-123	[»]
3DF3	X-ray	3.50	L	2-123	[»]
3E1A	electron microscopy	-	D	1-124	[»]
3E1C	electron microscopy	-	D	1-124	[»]
3EP2	electron microscopy	-	L	2-124	[»]
3EQ3	electron microscopy	-	L	2-124	[»]
3EQ4	electron microscopy	-	L	2-124	[»]
3FIH	electron microscopy	6.70	L	2-124	[»]
3I1M	X-ray	3.19	L	1-124	[»]
3I1O	X-ray	3.19	L	1-124	[»]
3I1Q	X-ray	3.81	L	1-124	[»]
3I1S	X-ray	3.81	L	1-124	[»]
3I1Z	X-ray	3.71	L	1-124	[»]
3I21	X-ray	3.71	L	1-124	[»]
3IZV	electron microscopy	-	P	1-124	[»]
3IZW	electron microscopy	-	P	1-124	[»]
3J00	electron microscopy	-	L	2-124	[»]
3J0D	electron microscopy	11.10	I	2-124	[»]
3J0E	electron microscopy	9.90	F	2-124	[»]
3J0U	electron microscopy	12.10	O	2-124	[»]
3J0V	electron microscopy	14.70	O	2-124	[»]
3J0X	electron microscopy	13.50	O	2-124	[»]
3J0Z	electron microscopy	11.50	O	2-124	[»]
3J10	electron microscopy	11.50	O	2-124	[»]
3J13	electron microscopy	13.10	N	2-124	[»]
3J18	electron microscopy	8.30	L	2-124	[»]
3J36	electron microscopy	9.80	L	2-124	[»]
3KC4	electron microscopy	-	L	1-124	[»]
3OAQ	X-ray	3.25	L	2-124	[»]
3OAR	X-ray	3.25	L	2-124	[»]
3OFA	X-ray	3.19	L	2-124	[»]
3OFB	X-ray	3.19	L	2-124	[»]
3OFO	X-ray	3.10	L	2-124	[»]
3OFP	X-ray	3.10	L	2-124	[»]
3OFX	X-ray	3.29	L	2-124	[»]
3OFY	X-ray	3.29	L	2-124	[»]
3OR9	X-ray	3.30	L	1-124	[»]
3ORA	X-ray	3.30	L	1-124	[»]
3SFS	X-ray	3.20	L	1-124	[»]
3UOQ	X-ray	3.70	L	1-124	[»]
4A2I	electron microscopy	16.50	L	2-124	[»]
4ADV	electron microscopy	13.50	L	2-124	[»]
4GAQ	X-ray	3.30	L	1-124	[»]
4GAS	X-ray	3.30	L	1-124	[»]
4GD1	X-ray	3.00	L	2-124	[»]
4GD2	X-ray	3.00	L	2-124	[»]

ProteinModelPortal

P0A7S3.

SMR

P0A7S3. Positions 2-124.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35806N.

IntAct

P0A7S3. 26 interactions.

STRING

511145.b3342.

Proteomic databases

PaxDb

P0A7S3.

PRIDE

P0A7S3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76367; AAC76367; b3342.
BAE77949; BAE77949; BAE77949.

GeneID

12932620.
947845.

KEGG

ecj:Y75_p3834.
eco:b3342.

PATRIC

32122116. VBIEscCol129921_3435.

Organism-specific databases

EchoBASE

EB0904.

EcoGene

EG10911. rpsL.

Phylogenomic databases

eggNOG

COG0048.

HOGENOM

HOG000040063.

KO

K02950.

OMA

SCPERRG.

ProtClustDB

PRK05163.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10911-MONOMER.
ECOL316407:JW3304-MONOMER.

Gene expression databases

Genevestigator

P0A7S3.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

HAMAP

MF_00403_B. Ribosomal_S12_B.

InterPro

IPR012340. NA-bd_OB-fold.
IPR006032. Ribosomal_S12/S23.
IPR005679. Ribosomal_S12_bac.
[Graphical view]

PANTHER

PTHR11652. PTHR11652. 1 hit.

Pfam

PF00164. Ribosomal_S12. 1 hit.
[Graphical view]

PIRSF

PIRSF002133. Ribosomal_S12/S23. 1 hit.

PRINTS

PR01034. RIBOSOMALS12.

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.

TIGRFAMs

TIGR00981. rpsL_bact. 1 hit.

PROSITE

PS00055. RIBOSOMAL_S12. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00479. Amikacin.
DB00452. Framycetin.
DB00798. Gentamicin.
DB01172. Kanamycin.
DB00994. Neomycin.
DB00955. Netilmicin.
DB00919. Spectinomycin.
DB01082. Streptomycin.
DB00684. Tobramycin.

EvolutionaryTrace

P0A7S3.

Entry information

Entry name

RS12_ECOLI

Accession

Primary (citable) accession number: P0A7S3
Secondary accession number(s): P02367, Q2M707, Q9F5N3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	May 29, 2013
This is version 96 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program