30S ribosomal protein S5 - Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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Reviewed, UniProtKB/Swiss-Prot Q5SHQ5 (RS5_THET8)

Last modified November 3, 2009. Version 49. History...

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

Names and origin

Protein names

Recommended name:
30S ribosomal protein S5

Gene names

Name:	rpsE
Ordered Locus Names:	TTHA1675

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	162 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 By similarity. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation. HAMAP MF_01307
Subunit structure	Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. Ref.4 Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.14 Ref.15
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	Is positioned such that it could physically interact with spectinomycin. HAMAP MF_01307
Sequence similarities	Belongs to the ribosomal protein S5P family. Contains 1 S5 DRBM domain.
Mass spectrometry	Molecular mass is 17428 Da from positions 2 - 162. Determined by MALDI. Ref.3

Ontologies

Keywords
Ligand	RNA-binding rRNA-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	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: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

Removed Ref.2

Chain

161

30S ribosomal protein S5 HAMAP MF_01307

PRO_0000131621

Regions

Domain

64

S5 DRBM

Secondary structure

1

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162

Helix Strand Turn

Sequences

Sequence

Length

Mass (Da)

Tools

Q5SHQ5-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: BE3367CB619E68D2
Show »

162

17,557

        10         20         30         40         50         60 
MPETDFEEKM ILIRRTARMQ AGGRRFRFGA LVVVGDRQGR VGLGFGKAPE VPLAVQKAGY 

        70         80         90        100        110        120 
YARRNMVEVP LQNGTIPHEI EVEFGASKIV LKPAAPGTGV IAGAVPRAIL ELAGVTDILT 

       130        140        150        160 
KELGSRNPIN IAYATMEALR QLRTKADVER LRKGEAHAQA QG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of Thermus thermophilus HB8." Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S. Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	"Purification and characterization of the 30S ribosomal proteins from the bacterium Thermus thermophilus." Tsiboli P., Herfurth E., Choli T. Eur. J. Biochem. 226:169-177(1994) [PubMed: 7957245] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-44.
[3]	"Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry." Suh M.-J., Hamburg D.M., Gregory S.T., Dahlberg A.E., Limbach P.A. Proteomics 5:4818-4831(2005) [PubMed: 16287167] [Abstract] Cited for: MASS SPECTROMETRY.
[4]	"Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution." Clemons W.M. Jr., May J.L.C., Wimberly B.T., McCutcheon J.P., Capel M.S., Ramakrishnan V. Nature 400:833-840(1999) [PubMed: 10476960] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE 30S SUBUNIT.
[5]	"The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site." Tocilj A., Schluenzen F., Janell D., Gluehmann M., Hansen H.A., Harms J., Bashan A., Bartels H., Agmon I., Franceschi F., Yonath A. Proc. Natl. Acad. Sci. U.S.A. 96:14252-14257(1999) [PubMed: 10588692] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).
[6]	"Structure of the 30S ribosomal subunit." Wimberly B.T., Brodersen D.E., Clemons W.M. Jr., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., Ramakrishnan V. Nature 407:327-339(2000) [PubMed: 11014182] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.05 ANGSTROMS) OF THE 30S SUBUNIT.
[7]	"Structure of functionally activated small ribosomal subunit at 3.3 A resolution." Schluenzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., Yonath A. Cell 102:615-623(2000) [PubMed: 11007480] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 30S SUBUNIT.
[8]	"The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit." Brodersen D.E., Clemons W.M. Jr., Carter A.P., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Cell 103:1143-1154(2000) [PubMed: 11163189] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 30S SUBUNIT.
[9]	"Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics." Carter A.P., Clemons W.M. Jr., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Nature 407:340-348(2000) [PubMed: 11014183] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 30S SUBUNIT.
[10]	"The path of messenger RNA through the ribosome." Yusupova G.Z., Yusupov M.M., Cate J.H.D., Noller H.F. Cell 106:233-241(2001) [PubMed: 11511350] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.0 ANGSTROMS) OF THE RIBOSOME.
[11]	"Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3." Pioletti M., Schluenzen F., Harms J., Zarivach R., Gluehmann M., Avila H., Bashan A., Bartels H., Auerbach T., Jacobi C., Hartsch T., Yonath A., Franceschi F. EMBO J. 20:1829-1839(2001) [PubMed: 11296217] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF THE 30S SUBUNIT.
[12]	"Crystal structure of an initiation factor bound to the 30S ribosomal subunit." Carter A.P., Clemons W.M. Jr., Brodersen D.E., Morgan-Warren R.J., Hartsch T., Wimberly B.T., Ramakrishnan V. Science 291:498-501(2001) [PubMed: 11228145] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF THE 30S SUBUNIT.
[13]	"Crystal structure of the ribosome at 5.5 A resolution." Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H.D., Noller H.F. Science 292:883-896(2001) [PubMed: 11283358] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.
[14]	"Recognition of cognate transfer RNA by the 30S ribosomal subunit." Ogle J.M., Brodersen D.E., Clemons W.M. Jr., Tarry M.J., Carter A.P., Ramakrishnan V. Science 292:897-902(2001) [PubMed: 11340196] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.11 ANGSTROMS) OF THE 30S SUBUNIT.
[15]	"Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA." Brodersen D.E., Clemons W.M. Jr., Carter A.P., Wimberly B.T., Ramakrishnan V. J. Mol. Biol. 316:725-768(2002) [PubMed: 11866529] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.05 ANGSTROMS) OF THE 30S SUBUNIT.
+	Additional computationally mapped references.

Web resources

T.thermophilus ribosome structure and function

Cross-references

Sequence databases

AP008226 Genomic DNA. Translation: BAD71498.1.

RefSeq

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FJG	X-ray	3.00	E	1-162	[»]
1FKA	X-ray	3.30	E	1-162	[»]
1GIX	X-ray	5.50	H	1-162	[»]
1HNW	X-ray	3.40	E	1-162	[»]
1HNX	X-ray	3.40	E	1-162	[»]
1HNZ	X-ray	3.30	E	1-162	[»]
1HR0	X-ray	3.20	E	1-162	[»]
1I94	X-ray	3.20	E	2-162	[»]
1I95	X-ray	4.50	E	2-162	[»]
1I96	X-ray	4.20	E	2-162	[»]
1I97	X-ray	4.50	E	2-162	[»]
1IBK	X-ray	3.31	E	1-162	[»]
1IBL	X-ray	3.11	E	1-162	[»]
1IBM	X-ray	3.31	E	1-162	[»]
1J5E	X-ray	3.05	E	2-162	[»]
1JGO	X-ray	5.60	H	1-162	[»]
1JGP	X-ray	7.00	H	1-162	[»]
1JGQ	X-ray	5.00	H	1-162	[»]
1L1U	model	-	E	5-154	[»]
1N32	X-ray	3.00	E	2-162	[»]
1N33	X-ray	3.35	E	2-162	[»]
1N34	X-ray	3.80	E	2-162	[»]
1N36	X-ray	3.65	E	2-162	[»]
1PNS	X-ray	8.70	E	5-154	[»]
1PNX	X-ray	9.50	E	5-154	[»]
1QD7	X-ray	5.50	D	22-130	[»]
1XMO	X-ray	3.25	E	1-162	[»]
1XMQ	X-ray	3.00	E	1-162	[»]
1XNQ	X-ray	3.05	E	1-162	[»]
1XNR	X-ray	3.10	E	1-162	[»]
1YL4	X-ray	5.50	H	1-162	[»]
2B64	X-ray	5.90	E	1-162	[»]
2B9O	X-ray	6.46	E	1-162	[»]
2E5L	X-ray	3.30	E	2-162	[»]
2HGI	X-ray	5.00	H	1-162	[»]
2HGP	X-ray	5.50	H	1-162	[»]
2HGR	X-ray	4.51	H	1-162	[»]
2J00	X-ray	2.80	E	2-161	[»]
2J02	X-ray	2.80	E	2-161	[»]
2OW8	X-ray	3.71	f	-	[»]
2UU9	X-ray	3.10	E	2-161	[»]
2UUA	X-ray	2.90	E	2-161	[»]
2UUB	X-ray	2.90	E	2-161	[»]
2UUC	X-ray	3.10	E	2-161	[»]
2UXB	X-ray	3.10	E	2-161	[»]
2UXC	X-ray	2.90	E	2-161	[»]
2UXD	X-ray	3.20	E	2-161	[»]
2V46	X-ray	3.80	E	2-161	[»]
2V48	X-ray	3.80	E	2-161	[»]
2VQE	X-ray	2.50	E	1-162	[»]
2VQF	X-ray	2.90	E	1-162	[»]
2WDG	X-ray	3.30	E	1-162	[»]
2WDH	X-ray	3.30	E	1-162	[»]
2WDK	X-ray	3.50	E	1-162	[»]
2WDM	X-ray	3.50	E	1-162	[»]
2WH1	X-ray	3.45	E	1-162	[»]
2WH3	X-ray	3.45	E	1-162	[»]
2ZM6	X-ray	3.30	E	2-162	[»]
3FIC	electron microscopy	6.40	E	5-155	[»]

ModBase

Protein-protein interaction databases

STRING

Genome annotation databases

GeneID

GenomeReviews

Gene locus TTHA1675 in contig AP008226_GR.

KEGG

Organism-specific databases

CMR

Phylogenomic databases

HOGENOM

OMA

Enzyme and pathway databases

BioCyc

TTHE300852:TTHA1675-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-typ_fold_subgr.
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

Entry information

Entry name

RS5_THET8

Accession

Primary (citable) accession number: Q5SHQ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 49 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Ribosomal proteins

Ribosomal proteins families and list of entries

SIMILARITY comments

Index of protein domains and families

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