Reviewed, UniProtKB/Swiss-Prot P0A7W1 (RS5_ECOLI)

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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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.9 Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Ref.9 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.9
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. HAMAP MF_01307
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 MF_01307
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 MF_01307 Some mutants in this protein can partially suppress an alanyl-tRNA synthetase mutant. HAMAP MF_01307
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.10

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
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	protein binding Inferred from physical interaction. Source: IntAct rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
lexA	P0A7C2	1	EBI-543949,EBI-553416
rnb	P30850	1	EBI-543949,EBI-557325
rplW	P0ADZ0	1	EBI-543949,EBI-542264
yjaB	P09163	1	EBI-543949,EBI-1134402

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 MF_01307

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. HAMAP MF_01307

Natural variant

21

1

V → E in strain: SPCR7; spectinomycin resistant. Not a ram mutation. HAMAP MF_01307

Natural variant

22

1

S → P in strain: SPCR13 and SPCR15; spectinomycin resistant. Not a ram mutation. HAMAP MF_01307

Natural variant

104

1

G → R in strain: N-660; suppresses S12 streptomycin dependence. HAMAP MF_01307

Natural variant

112

1

R → G in strain: NEA-314; neamycin resistant. HAMAP MF_01307

Natural variant

112

1

R → L in strain: N-421 and D-1023; suppresses S12 streptomycin-dependence. HAMAP MF_01307

Natural variant

112

1

R → S in strain: NEA-319; neamycin resistant. HAMAP MF_01307

Natural variant

151

1

E → S in strain: B. HAMAP MF_01307

Natural variant

162 – 167

6

EEILGK → G in strain: 0-1; suppresses an alanyl-tRNA synthetase mutation. Blocks ribosome assembly below 25 degrees Celsius. HAMAP MF_01307

Experimental info

Mutagenesis

20 – 29

10

RVSKTVKGGR → AVSKTVKGGA: No effect on mRNA unwinding ability of the ribosome. HAMAP MF_01307

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

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.

.

.

.

.

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167

Helix Strand Turn

Details...

Beta strand

12 – 17

6

Beta strand

22 – 24

3

Beta strand

26 – 31

6

Beta strand

36 – 41

6

Turn

42 – 44

3

Beta strand

45 – 50

6

Helix

56 – 68

13

Beta strand

77 – 80

4

Beta strand

86 – 89

4

Beta strand

92 – 95

4

Helix

110 – 118

9

Beta strand

122 – 124

3

Helix

133 – 144

12

Beta strand

150 – 152

3

Helix

153 – 156

4

Sequences

	Sequence		Length	Mass (Da)
	P0A7W1-1 [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: 6222285] [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]	"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: 363452] [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: 4273819] [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: 4346030] [Abstract] Cited for: INVOLVEMENT IN FORMATION OF THE EF-G/RIBOSOME COMPLEX. Strain: B/2.
[7]	"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: 2138078] [Abstract] Cited for: CHARACTERIZATION OF VARIANTS. Strain: O17.
[8]	"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: 1712292] [Abstract] Cited for: CROSS-LINKING TO MRNA.
[9]	"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.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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

EMBLGenBankDDBJ

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

AP_004487.1.
NP_417762.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
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	-	E	10-156	[»]
2GYB	electron microscopy	-	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	[»]
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	[»]
3FIH	electron microscopy	-	E	10-159	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A7W1. 189 interactions.

2-D gel databases

ECO2DBASE

I014.4. 6TH EDITION.

Genome annotation databases

GeneID

947795.

GenomeReviews

Gene locus JW3265 in contig AP009048_GR.
Gene locus b3303 in contig U00096_GR.

KEGG

ecj:JW3265.
eco:b3303.

Organism-specific databases

EchoBASE

EB0897.

EcoGene

EG10904. rpsE.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A7W1.

OMA

P0A7W1. INRTAKV.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10904-MON.

Family and domain databases

HAMAP

MF_01307.
[Tree]

InterPro

IPR014720. dsRNA-bd-like.
IPR000851. Ribosomal_S5.
IPR005712. Ribosomal_S5_bac-type.
IPR005324. Ribosomal_S5_C.
IPR014721. Ribosomal_S5_D2-type_fold.
IPR013810. Ribosomal_S5_N.
IPR018192. Ribosomal_S5_N_CS.
[Graphical view]

Gene3D

G3DSA:3.30.160.20. dsRNA-bd-like. 1 hit.
G3DSA:3.30.230.10. Ribosomal_S5_D2-type_fold. 1 hit.

PANTHER

PTHR13718. Ribosomal_S5. 1 hit.

Pfam

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

TIGRFAMs

TIGR01021. rpsE_bact. 1 hit.

PROSITE

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

ProtoNet

Search...

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:	June 16, 2009
This is version 54 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)