P80373 (RS4_THET8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
30S ribosomal protein S4

Gene names

Name:	rpsD
Synonyms:	rps4
Ordered Locus Names:	TTHA1665

Organism

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

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus › Thermus thermophilus

Protein attributes

Sequence length	209 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	One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation. HAMAP-Rule MF_01306_B
Cofactor	Binds 1 zinc ion per subunit Probable.
Subunit structure	Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.14 Ref.15
Sequence similarities	Belongs to the ribosomal protein S4P family. Contains 1 S4 RNA-binding domain.
Mass spectrometry	Molecular mass is 24192 Da from positions 2 - 209. Determined by MALDI. Ref.4

Ontologies

Keywords
Domain	Zinc-finger
Ligand	Metal-binding RNA-binding Zinc rRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
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	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW 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

1

Removed Ref.3

Chain

2 – 209

208

30S ribosomal protein S4 HAMAP-Rule MF_01306_B

PRO_0000132483

Regions

Domain

99 – 161

63

S4 RNA-binding

Zinc finger

9 – 31

23

C4-type HAMAP-Rule MF_01306_B

Sites

Metal binding

9

1

Zinc Probable

Metal binding

12

1

Zinc Probable

Metal binding

26

1

Zinc Probable

Metal binding

31

1

Zinc Probable

Experimental info

Sequence conflict

12

1

C → S AA sequence Ref.3

Sequence conflict

26

1

C → D AA sequence Ref.3

Secondary structure

1

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209

Helix Strand Turn

Details...

Helix

9 – 15

7

Beta strand

21 – 23

3

Beta strand

26 – 28

3

Helix

33 – 35

3

Turn

42 – 45

4

Helix

53 – 68

16

Helix

72 – 84

13

Beta strand

85 – 87

3

Helix

89 – 98

10

Helix

101 – 107

7

Beta strand

110 – 113

4

Helix

114 – 122

9

Turn

123 – 125

3

Beta strand

126 – 128

3

Beta strand

129 – 131

3

Beta strand

145 – 148

4

Helix

150 – 152

3

Beta strand

153 – 155

3

Helix

156 – 164

9

Turn

165 – 167

3

Beta strand

174 – 176

3

Turn

178 – 181

4

Beta strand

182 – 184

3

Helix

191 – 193

3

Helix

200 – 206

7

Sequences

	Sequence		Length	Mass (Da)
	P80373 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 0FF3911816971236	FASTA	209	24,324
	10 20 30 40 50 60 MGRYIGPVCR LCRREGVKLY LKGERCYSPK CAMERRPYPP GQHGQKRARR PSDYAVRLRE 70 80 90 100 110 120 KQKLRRIYGI SERQFRNLFE EASKKKGVTG SVFLGLLESR LDNVVYRLGF AVSRRQARQL 130 140 150 160 170 180 VRHGHITVNG RRVDLPSYRV RPGDEIAVAE KSRNLELIRQ NLEAMKGRKV GPWLSLDVEG 190 200 MKGKFLRLPD REDLALPVNE QLVIEFYSR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning of the RNA polymerase alpha subunit gene from Thermus thermophilus HB8 and characterization of the protein." Wada T., Yamazaki T., Kuramitsu S., Kyogoku Y. J. Biochem. 125:143-150(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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]. Strain: HB8 / ATCC 27634 / DSM 579.
[3]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-27.
[4]	"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] [Europe PMC] [Abstract] Cited for: MASS SPECTROMETRY.
[5]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE 30S SUBUNIT.
[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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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

EMBL
GenBank
DDBJ

AB024328 Genomic DNA. Translation: BAA75548.1.
AP008226 Genomic DNA. Translation: BAD71488.1.

RefSeq

YP_144931.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FJG	X-ray	3.00	D	1-209	[»]
1FKA	X-ray	3.30	D	1-209	[»]
1GIX	X-ray	5.50	G	1-209	[»]
1HNW	X-ray	3.40	D	1-209	[»]
1HNX	X-ray	3.40	D	1-209	[»]
1HNZ	X-ray	3.30	D	1-209	[»]
1HR0	X-ray	3.20	D	1-209	[»]
1I94	X-ray	3.20	D	2-209	[»]
1I95	X-ray	4.50	D	2-209	[»]
1I96	X-ray	4.20	D	2-209	[»]
1I97	X-ray	4.50	D	2-209	[»]
1IBK	X-ray	3.31	D	1-209	[»]
1IBL	X-ray	3.11	D	1-209	[»]
1IBM	X-ray	3.31	D	1-209	[»]
1J5E	X-ray	3.05	D	2-209	[»]
1JGO	X-ray	5.60	F	95-98	[»]
			G	1-209	[»]
1JGP	X-ray	7.00	F	95-98	[»]
			G	1-209	[»]
1JGQ	X-ray	5.00	F	95-98	[»]
			G	1-209	[»]
1L1U	model	-	D	1-209	[»]
1N32	X-ray	3.00	D	2-209	[»]
1N33	X-ray	3.35	D	2-209	[»]
1N34	X-ray	3.80	D	2-209	[»]
1N36	X-ray	3.65	D	2-209	[»]
1QD7	X-ray	5.50	C	60-155	[»]
1TWT	model	-	G	2-209	[»]
1XMO	X-ray	3.25	D	1-209	[»]
1XMQ	X-ray	3.00	D	1-209	[»]
1XNQ	X-ray	3.05	D	1-209	[»]
1XNR	X-ray	3.10	D	1-209	[»]
1YL4	X-ray	5.50	G	1-209	[»]
2B64	X-ray	5.90	D	1-209	[»]
2B9M	X-ray	6.76	D	1-209	[»]
2B9O	X-ray	6.46	D	1-209	[»]
2E5L	X-ray	3.30	D	2-209	[»]
2F4V	X-ray	3.80	D	1-209	[»]
2HGI	X-ray	5.00	G	1-209	[»]
2HGP	X-ray	5.50	G	1-209	[»]
2HGR	X-ray	4.51	G	1-209	[»]
2HHH	X-ray	3.35	D	1-209	[»]
2J00	X-ray	2.80	D	2-208	[»]
2J02	X-ray	2.80	D	2-208	[»]
2OW8	X-ray	3.71	e	-	[»]
2UU9	X-ray	3.10	D	2-208	[»]
2UUA	X-ray	2.90	D	1-209	[»]
2UUB	X-ray	2.90	D	2-208	[»]
2UUC	X-ray	3.10	D	2-208	[»]
2UXB	X-ray	3.10	D	1-209	[»]
2UXC	X-ray	2.90	D	1-209	[»]
2UXD	X-ray	3.20	D	1-209	[»]
2V46	X-ray	3.80	D	2-208	[»]
2V48	X-ray	3.50	D	1-209	[»]
2VQE	X-ray	2.50	D	1-209	[»]
2VQF	X-ray	2.90	D	1-209	[»]
2WDG	X-ray	3.30	D	1-209	[»]
2WDH	X-ray	3.30	D	1-209	[»]
2WDK	X-ray	3.50	D	1-209	[»]
2WDM	X-ray	3.50	D	1-209	[»]
2WH1	X-ray	3.45	D	1-209	[»]
2WH3	X-ray	3.45	D	1-209	[»]
2WRI	X-ray	3.60	D	1-209	[»]
2WRK	X-ray	3.60	D	1-209	[»]
2WRN	X-ray	3.60	D	1-209	[»]
2WRQ	X-ray	3.60	D	1-209	[»]
2X9R	X-ray	3.10	D	1-209	[»]
2X9T	X-ray	3.10	D	1-209	[»]
2XFZ	X-ray	3.20	D	1-209	[»]
2XG1	X-ray	3.20	D	1-209	[»]
2XQD	X-ray	3.10	D	1-209	[»]
2XSY	electron microscopy	7.80	D	1-209	[»]
2XUY	electron microscopy	7.60	D	1-209	[»]
2Y0U	X-ray	3.10	D	1-209	[»]
2Y0W	X-ray	3.10	D	1-209	[»]
2Y0Y	X-ray	3.10	D	1-209	[»]
2Y10	X-ray	3.10	D	1-209	[»]
2Y12	X-ray	3.10	D	1-209	[»]
2Y14	X-ray	3.10	D	1-209	[»]
2Y16	X-ray	3.10	D	1-209	[»]
2Y18	X-ray	3.10	D	1-209	[»]
2ZM6	X-ray	3.30	D	2-209	[»]
3FIC	electron microscopy	6.40	D	2-209	[»]
3HUW	X-ray	3.10	D	1-209	[»]
3HUY	X-ray	3.10	D	1-209	[»]
3I8G	X-ray	3.10	G	1-209	[»]
3I8H	X-ray	3.10	G	1-209	[»]
3I9B	X-ray	3.50	G	1-209	[»]
3I9D	X-ray	3.50	G	1-209	[»]
3KIQ	X-ray	3.30	d	1-209	[»]
3KIS	X-ray	3.30	d	1-209	[»]
3KIU	X-ray	3.60	d	1-209	[»]
3KIX	X-ray	3.60	d	1-209	[»]
3KNH	X-ray	3.00	D	1-209	[»]
3KNJ	X-ray	3.15	D	1-209	[»]
3KNL	X-ray	3.45	D	1-209	[»]
3KNN	X-ray	3.45	D	1-209	[»]
3OGE	X-ray	3.00	D	1-209	[»]
3OGY	X-ray	3.00	D	1-209	[»]
3OHC	X-ray	3.00	D	1-209	[»]
3OHD	X-ray	3.00	D	1-209	[»]
3OHY	X-ray	3.00	D	1-209	[»]
3OI0	X-ray	3.00	D	1-209	[»]
3OI2	X-ray	3.10	D	1-209	[»]
3OI4	X-ray	3.10	D	1-209	[»]
3OTO	X-ray	3.69	D	1-209	[»]
3T1H	X-ray	3.11	D	1-209	[»]
3T1Y	X-ray	2.80	D	1-209	[»]
3TVF	X-ray	3.10	G	2-209	[»]
3TVG	X-ray	3.10	G	2-209	[»]
3UXS	X-ray	3.20	D	1-209	[»]
3UXT	X-ray	3.20	D	1-209	[»]
3UYD	X-ray	3.00	G	2-209	[»]
3UYF	X-ray	3.00	G	2-209	[»]
3UZ3	X-ray	3.30	G	2-209	[»]
3UZ4	X-ray	3.30	G	2-209	[»]
3UZ6	X-ray	3.00	G	2-209	[»]
3UZ7	X-ray	3.00	G	2-209	[»]
3UZG	X-ray	3.30	G	2-209	[»]
3UZI	X-ray	3.30	G	2-209	[»]
3UZL	X-ray	3.30	G	2-209	[»]
3UZM	X-ray	3.30	G	2-209	[»]
3V22	X-ray	3.00	D	1-209	[»]
3V24	X-ray	3.00	D	1-209	[»]
3V26	X-ray	3.10	D	1-209	[»]
3V28	X-ray	3.10	D	1-209	[»]
3V2C	X-ray	2.70	D	1-209	[»]
3V2E	X-ray	2.70	D	1-209	[»]
3ZN7	X-ray	3.10	D	1-209	[»]
3ZND	X-ray	3.10	D	1-209	[»]
3ZVO	X-ray	3.80	D	1-209	[»]
4ABR	X-ray	3.10	D	1-209	[»]
4AQY	X-ray	3.50	D	2-209	[»]
4B8F	X-ray	3.70	D	1-209	[»]
4B8H	X-ray	3.70	D	1-209	[»]
4DH9	X-ray	3.20	D	1-209	[»]
4DHB	X-ray	3.20	D	1-209	[»]
4DR1	X-ray	3.60	D	1-209	[»]
4DR2	X-ray	3.25	D	1-209	[»]
4DR3	X-ray	3.35	D	1-209	[»]
4DR4	X-ray	3.97	D	1-209	[»]
4DR5	X-ray	3.45	D	1-209	[»]
4DR6	X-ray	3.30	D	1-209	[»]
4DR7	X-ray	3.75	D	1-209	[»]
4DUY	X-ray	3.39	D	1-209	[»]
4DUZ	X-ray	3.65	D	1-209	[»]
4DV0	X-ray	3.85	D	1-209	[»]
4DV1	X-ray	3.85	D	1-209	[»]
4DV2	X-ray	3.65	D	1-209	[»]
4DV3	X-ray	3.55	D	1-209	[»]
4DV4	X-ray	3.65	D	1-209	[»]
4DV5	X-ray	3.68	D	1-209	[»]
4DV6	X-ray	3.30	D	1-209	[»]
4DV7	X-ray	3.29	D	1-209	[»]
4G5K	X-ray	3.30	G	2-209	[»]
4G5M	X-ray	3.30	G	2-209	[»]
4G5T	X-ray	3.10	G	2-209	[»]
4G5V	X-ray	3.10	G	2-209	[»]

ProteinModelPortal

P80373.

SMR

P80373. Positions 2-209.

ModBase

Search...

Protein-protein interaction databases

STRING

300852.TTHA1665.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD71488; BAD71488; BAD71488.

GeneID

3168006.

KEGG

ttj:TTHA1665.

PATRIC

23958285. VBITheThe93045_1635.

Phylogenomic databases

eggNOG

COG0522.

HOGENOM

HOG000221004.

KO

K02986.

OMA

THGHILV.

ProtClustDB

PRK05327.

Enzyme and pathway databases

BioCyc

TTHE300852:GH8R-1704-MONOMER.

Family and domain databases

Gene3D

1.10.1050.10. 1 hit.
3.10.290.10. 1 hit.

HAMAP

MF_01306_B. Ribosomal_S4_B.

InterPro

IPR022801. Ribosomal_S4/S9.
IPR001912. Ribosomal_S4/S9_N.
IPR005709. Ribosomal_S4_bac-type.
IPR018079. Ribosomal_S4_CS.
IPR002942. S4_RNA-bd.
[Graphical view]

PANTHER

PTHR11831. PTHR11831. 1 hit.

Pfam

PF00163. Ribosomal_S4. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]

SMART

SM00363. S4. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01017. rpsD_bact. 1 hit.

PROSITE

PS00632. RIBOSOMAL_S4. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P80373.

Entry information

Entry name

RS4_THET8

Accession

Primary (citable) accession number: P80373
Secondary accession number(s): Q5SHR5, Q9Z9H7

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	January 23, 2007
Last modified:	May 29, 2013
This is version 118 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program