P0A7W1 (RS5_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
30S ribosomal protein S5

Gene names

Name:	rpsE
Synonyms:	spc
Ordered Locus Names:	b3303, JW3265

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	167 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 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 Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Ref.10 The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp. Ref.10
Subunit structure	Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. With proteins S4 and S5 encircles the mRNA as it enters the ribosome, which may play a role in mRNA helicase processivity. Can be cross-linked to mRNA.
Domain	The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. HAMAP-Rule MF_01307_B
Miscellaneous	Altered S5 proteins have been identified in a number of mutants. Some mutations in S5 have been shown to increase translational error frequencies. HAMAP-Rule MF_01307_B Some mutants in this protein can partially suppress an alanyl-tRNA synthetase mutant. HAMAP-Rule MF_01307_B
Sequence similarities	Belongs to the ribosomal protein S5P family. Contains 1 S5 DRBM domain.
Mass spectrometry	Molecular mass is 17514.8 Da from positions 2 - 167. Determined by MALDI. Ref.11

Ontologies

Keywords
Biological process	Antibiotic resistance
Ligand	RNA-binding rRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW translation Inferred from electronic annotation. Source: HAMAP
Cellular_component	small ribosomal subunit Inferred from electronic annotation. Source: InterPro
Molecular_function	rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome 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.4

Chain

2 – 167

166

30S ribosomal protein S5 HAMAP-Rule MF_01307_B

PRO_0000131511

Regions

Domain

11 – 74

64

S5 DRBM

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.4

Natural variations

Natural variant

20

1

R → L in strain: SPCR9; spectinomycin resistant. Not a ram mutation.

Natural variant

21

1

V → E in strain: SPCR7; spectinomycin resistant. Not a ram mutation.

Natural variant

22

1

S → P in strain: SPCR13 and SPCR15; spectinomycin resistant. Not a ram mutation.

Natural variant

104

1

G → R in strain: N-660; suppresses S12 streptomycin dependence.

Natural variant

112

1

R → G in strain: NEA-314; neamycin resistant.

Natural variant

112

1

R → L in strain: N-421 and D-1023; suppresses S12 streptomycin-dependence.

Natural variant

112

1

R → S in strain: NEA-319; neamycin resistant.

Natural variant

151

1

E → S in strain: B.

Natural variant

162 – 167

6

EEILGK → G in strain: 0-1; suppresses an alanyl-tRNA synthetase mutation. Blocks ribosome assembly below 25 degrees Celsius.

Experimental info

Mutagenesis

20 – 29

10

RVSKTVKGGR → AVSKTVKGGA: No effect on mRNA unwinding ability of the ribosome.

Secondary structure

1

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167

Helix Strand Turn

Details...

Beta strand

13 – 20

8

Beta strand

22 – 24

3

Beta strand

26 – 28

3

Beta strand

33 – 40

8

Beta strand

42 – 44

3

Beta strand

46 – 49

4

Beta strand

52 – 55

4

Helix

56 – 68

13

Beta strand

69 – 72

4

Beta strand

77 – 80

4

Beta strand

85 – 89

5

Beta strand

92 – 97

6

Beta strand

102 – 104

3

Turn

109 – 111

3

Helix

112 – 117

6

Beta strand

120 – 123

4

Beta strand

124 – 129

6

Helix

133 – 146

14

Helix

152 – 156

5

Sequences

	Sequence		Length	Mass (Da)
	P0A7W1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 0B7EA2CB34018CAB	FASTA	167	17,603
	10 20 30 40 50 60 MAHIEKQAGE LQEKLIAVNR VSKTVKGGRI FSFTALTVVG DGNGRVGFGY GKAREVPAAI 70 80 90 100 110 120 QKAMEKARRN MINVALNNGT LQHPVKGVHT GSRVFMQPAS EGTGIIAGGA MRAVLEVAGV 130 140 150 160 HNVLAKAYGS TNPINVVRAT IDGLENMNSP EMVAAKRGKS VEEILGK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene." Cerretti D.P., Dean D., Davis G.R., Bedwell D.M., Nomura M. Nucleic Acids Res. 11:2599-2616(1983) [PubMed] [Europe PMC] [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] [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 protein S5 from the small subunit of the Escherichia coli ribosome." Wittmann-Liebold B., Greuer B. FEBS Lett. 95:91-98(1978) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-167, ACETYLATION AT ALA-2, VARIANTS, MUTANTS. Strain: B and K.
[5]	"Localization of the amino-acid exchange in protein S5 from an Escherichia coli mutant resistant to spectinomycin." DeWilde M., Wittmann-Liebold B. Mol. Gen. Genet. 127:273-276(1973) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 15-23, VARIANT SPECTINOMYCIN RESISTANT. Strain: B.
[6]	"Requirement of proteins S5 and S9 from 30S subunits for the ribosome-dependent GTPase activity of elongation factor G." Marsh R.C., Parmeggiani A. Proc. Natl. Acad. Sci. U.S.A. 70:151-155(1973) [PubMed] [Europe PMC] [Abstract] Cited for: INVOLVEMENT IN FORMATION OF THE EF-G/RIBOSOME COMPLEX. Strain: B/2.
[7]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[8]	"Ribosomal RNA and protein mutants resistant to spectinomycin." Bilgin N., Richter A.A., Ehrenberg M., Dahlberg A.E., Kurland C.G. EMBO J. 9:735-739(1990) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF VARIANTS. Strain: O17.
[9]	"The path of mRNA through the Escherichia coli ribosome; site-directed cross-linking of mRNA analogues carrying a photo-reactive label at various points 3' to the decoding site." Rinke-Appel J., Juenke N., Stade K., Brimacombe R. EMBO J. 10:2195-2202(1991) [PubMed] [Europe PMC] [Abstract] Cited for: CROSS-LINKING TO MRNA.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.
[15]	"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

X01563 Genomic DNA. Translation: CAA25722.1.
U18997 Genomic DNA. Translation: AAA58100.1.
U00096 Genomic DNA. Translation: AAC76328.1.
AP009048 Genomic DNA. Translation: BAE77988.1.

PIR

R3EC5. B65123.

RefSeq

NP_417762.1. NC_000913.2.
YP_492129.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EG0	electron microscopy	11.50	B	1-148	[»]
1M5G	model	-	E	10-159	[»]
1P6G	electron microscopy	12.30	E	2-167	[»]
1P87	electron microscopy	11.50	E	2-167	[»]
1VS5	X-ray	3.46	E	1-167	[»]
1VS7	X-ray	3.46	E	1-167	[»]
2AVY	X-ray	3.46	E	2-167	[»]
2AW7	X-ray	3.46	E	2-167	[»]
2GY9	electron microscopy	15.00	E	10-156	[»]
2GYB	electron microscopy	15.00	E	10-156	[»]
2I2P	X-ray	3.22	E	2-166	[»]
2I2U	X-ray	3.22	E	2-166	[»]
2QAL	X-ray	3.21	E	2-167	[»]
2QAN	X-ray	3.21	E	2-167	[»]
2QB9	X-ray	3.54	E	2-167	[»]
2QBB	X-ray	3.54	E	2-167	[»]
2QBD	X-ray	3.30	E	2-167	[»]
2QBF	X-ray	3.30	E	2-167	[»]
2QBH	X-ray	4.00	E	2-167	[»]
2QBJ	X-ray	4.00	E	2-167	[»]
2QOU	X-ray	3.93	E	2-167	[»]
2QOW	X-ray	3.93	E	2-167	[»]
2QOY	X-ray	3.50	E	2-167	[»]
2QP0	X-ray	3.50	E	2-167	[»]
2VHO	X-ray	3.74	E	2-167	[»]
2VHP	X-ray	3.74	E	2-167	[»]
2WWL	electron microscopy	5.80	E	10-159	[»]
2Z4K	X-ray	4.45	E	2-167	[»]
2Z4M	X-ray	4.45	E	2-167	[»]
3DF1	X-ray	3.50	E	2-166	[»]
3DF3	X-ray	3.50	E	2-166	[»]
3E1A	electron microscopy	-	S	1-159	[»]
3E1C	electron microscopy	-	S	1-159	[»]
3FIH	electron microscopy	6.70	E	10-159	[»]
3I1M	X-ray	3.19	E	1-167	[»]
3I1O	X-ray	3.19	E	1-167	[»]
3I1Q	X-ray	3.81	E	1-167	[»]
3I1S	X-ray	3.81	E	1-167	[»]
3I1Z	X-ray	3.71	E	1-167	[»]
3I21	X-ray	3.71	E	1-167	[»]
3IZV	electron microscopy	-	I	1-167	[»]
3IZW	electron microscopy	-	I	1-167	[»]
3J00	electron microscopy	-	E	2-167	[»]
3J0U	electron microscopy	12.10	H	2-167	[»]
3J0V	electron microscopy	14.70	H	2-167	[»]
3J0X	electron microscopy	13.50	H	2-167	[»]
3J0Z	electron microscopy	11.50	H	2-167	[»]
3J10	electron microscopy	11.50	H	2-167	[»]
3J13	electron microscopy	13.10	G	2-167	[»]
3J18	electron microscopy	8.30	E	10-159	[»]
3KC4	electron microscopy	-	E	1-167	[»]
3OAQ	X-ray	3.25	E	10-159	[»]
3OAR	X-ray	3.25	E	10-159	[»]
3OFA	X-ray	3.19	E	10-159	[»]
3OFB	X-ray	3.19	E	10-159	[»]
3OFO	X-ray	3.10	E	10-159	[»]
3OFP	X-ray	3.10	E	10-159	[»]
3OFX	X-ray	3.29	E	10-159	[»]
3OFY	X-ray	3.29	E	10-159	[»]
3OR9	X-ray	3.30	E	1-167	[»]
3ORA	X-ray	3.30	E	1-167	[»]
3SFS	X-ray	3.20	E	1-167	[»]
3UOQ	X-ray	3.70	E	1-167	[»]
4A2I	electron microscopy	16.50	E	10-159	[»]
4ADV	electron microscopy	13.50	E	2-167	[»]
4GAQ	X-ray	3.30	E	1-167	[»]
4GAS	X-ray	3.30	E	1-167	[»]
4GD1	X-ray	3.00	E	10-159	[»]
4GD2	X-ray	3.00	E	10-159	[»]

ProteinModelPortal

P0A7W1.

SMR

P0A7W1. Positions 10-159.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A7W1. 189 interactions.

STRING

511145.b3303.

Proteomic databases

PaxDb

P0A7W1.

PRIDE

P0A7W1.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76328; AAC76328; b3303.
BAE77988; BAE77988; BAE77988.

GeneID

12934414.
947795.

KEGG

ecj:Y75_p3873.
eco:b3303.

PATRIC

32122038. VBIEscCol129921_3396.

Organism-specific databases

EchoBASE

EB0897.

EcoGene

EG10904. rpsE.

Phylogenomic databases

eggNOG

COG0098.

HOGENOM

HOG000072595.

KO

K02988.

OMA

HNVVKAT.

ProtClustDB

PRK00550.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10904-MONOMER.
ECOL316407:JW3265-MONOMER.

Gene expression databases

Genevestigator

P0A7W1.

Family and domain databases

Gene3D

3.30.160.20. 1 hit.
3.30.230.10. 1 hit.

HAMAP

MF_01307_B. Ribosomal_S5_B.

InterPro

IPR014720. dsRNA-bd-like_dom.
IPR000851. Ribosomal_S5.
IPR005712. Ribosomal_S5_bac-type.
IPR005324. Ribosomal_S5_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR013810. Ribosomal_S5_N.
IPR018192. Ribosomal_S5_N_CS.
[Graphical view]

PANTHER

PTHR13718. PTHR13718. 1 hit.

Pfam

PF00333. Ribosomal_S5. 1 hit.
PF03719. Ribosomal_S5_C. 1 hit.
[Graphical view]

SUPFAM

SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

TIGRFAMs

TIGR01021. rpsE_bact. 1 hit.

PROSITE

PS00585. RIBOSOMAL_S5. 1 hit.
PS50881. S5_DSRBD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A7W1.

Entry information

Entry name

RS5_ECOLI

Accession

Primary (citable) accession number: P0A7W1
Secondary accession number(s): O54299, P02356, Q2M6W8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 93 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program