Reviewed, UniProtKB/Swiss-Prot Q5SHQ0 (RL5_THET8)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L5

Gene names

Name:	rplE
Ordered Locus Names:	TTHA1680

Organism

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

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	182 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	This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (forming bridge B1b) connecting the head of the 30S subunit to the top of the 50S subunit. The bridge itself contacts the P site tRNA and is implicated in movement during ribosome translocation. Also contacts the P site tRNA independently of the intersubunit bridge; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. HAMAP MF_01333
Subunit structure	Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 (TL5) subcomplex; has also been isolated as a complex with 5S rRNA, RL25 (TL5) and DNA binding protein II. Forms a bridge to the 30S subunit in the 70S ribosome, contacting protein S13; this bridge is straddled by the 5S rRNA. Contacts the P site tRNA. Ref.7
Sequence similarities	Belongs to the ribosomal protein L5P family.
Caution	Note that in Ref.3 it was shown that the initiator methionine is not removed, in Ref.4 it was shown the initiator methionine is removed, and the mass determined in Ref.5 is compatible with initiator methionine removal. In Ref.4 there is uncertainty about the number of Arg residues at position 10 and whether position 25 is Pro or Tyr.
Mass spectrometry	Molecular mass is 20900 Da from positions 2 - 182. Determined by MALDI. Ref.5

Ontologies

Keywords
Ligand	RNA-binding rRNA-binding tRNA-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	ribosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
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 Ref.4

Chain

2 – 182

181

50S ribosomal protein L5 HAMAP MF_01333

PRO_0000125014

Secondary structure

1

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182

Helix Strand Turn

Details...

Helix

6 – 12

7

Helix

15 – 22

8

Turn

28 – 30

3

Beta strand

34 – 40

7

Turn

48 – 50

3

Helix

55 – 63

9

Helix

96 – 106

11

Turn

107 – 109

3

Turn

122 – 125

4

Beta strand

131 – 133

3

Turn

146 – 148

3

Beta strand

156 – 162

7

Helix

166 – 175

10

Sequences

	Sequence		Length	Mass (Da)
	Q5SHQ0-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 69A3361F6825929B	FASTA	182	21,030
	10 20 30 40 50 60 MPLDVALKRK YYEEVRPELI RRFGYQNVWE VPRLEKVVIN QGLGEAKEDA RILEKAAQEL 70 80 90 100 110 120 ALITGQKPAV TRAKKSISNF KLRKGMPIGL RVTLRRDRMW IFLEKLLNVA LPRIRDFRGL 130 140 150 160 170 180 NPNSFDGRGN YNLGLREQLI FPEITYDMVD ALRGMDIAVV TTAETDEEAR ALLELLGFPF RK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Comparative analysis of ribosomal protein L5 sequences from bacteria of the genus Thermus." Jahn O., Hartmann R.K., Boeckh T., Erdmann V.A. Biochimie 73:669-678(1991) [PubMed: 1764514] [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].
[3]	"Identification, purification and partial sequence of four Thermus thermophilus 5S rRNA binding proteins." Kim J.-S., Boysen R.I., Schroeder W., Erdmann V.A., Gessner R.V. Endocyt. Cell Res. 11:177-194(1996) Cited for: PROTEIN SEQUENCE OF 2-44, ISOLATION OF 5S RRNA-ASSOCIATED COMPLEXES.
[4]	"Identification of the 50S ribosomal proteins from the eubacterium Thermus thermophilus." Katsani K.R., Tsiboli P., Anagnostopoulos K., Urlaub H., Choli-Papadopoulou T. Biol. Chem. 381:1079-1087(2000) [PubMed: 11154066] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-28.
[5]	"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.
[6]	"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.
[7]	"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, INTERSUBUNIT BRIDGE FORMATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AP008226 Genomic DNA. Translation: BAD71503.1.

RefSeq

YP_144946.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GIY	X-ray	5.50	G	-	[»]
1YL3	X-ray	5.50	G	32-38	[»]
2HGJ	X-ray	5.00	G	1-182	[»]
2HGQ	X-ray	5.50	G	1-182	[»]
2HGU	X-ray	4.51	G	1-182	[»]
2J01	X-ray	2.80	G	2-181	[»]
2J03	X-ray	2.80	G	2-181	[»]
2V47	X-ray	3.80	G	2-181	[»]
2V49	X-ray	3.80	G	2-181	[»]
2WDI	X-ray	3.30	G	1-182	[»]
2WDJ	X-ray	3.30	G	1-182	[»]
2WDL	X-ray	3.50	G	1-182	[»]
2WDN	X-ray	3.50	G	1-182	[»]
2WH2	X-ray	3.45	G	1-182	[»]
2WH4	X-ray	3.45	G	1-182	[»]
3FIN	electron microscopy	6.40	G	2-182	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q5SHQ0.

Genome annotation databases

GeneID

3169803.

GenomeReviews

Gene locus TTHA1680 in contig AP008226_GR.

KEGG

ttj:TTHA1680.

NMPDR

fig|300852.3.peg.744.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q5SHQ0.

OMA

ATITGQK.

Enzyme and pathway databases

BioCyc

TTHE300852:TTHA1680-MON.

Family and domain databases

HAMAP

MF_01333.
[Tree]

InterPro

IPR002132. Ribosomal_L5.
[Graphical view]

Gene3D

G3DSA:3.30.1440.10. Ribosomal_L5. 1 hit.

PANTHER

PTHR11994. Ribosomal_L5. 1 hit.

Pfam

PF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]

PIRSF

PIRSF002161. Ribosomal_L5. 1 hit.

ProDom

PD013434. Ribosomal_L5_mit. 1 hit.
[Graphical view] [Entries sharing at least one domain]

PROSITE

PS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL5_THET8

Accession

Primary (citable) accession number: Q5SHQ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 50 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)