Q5SHZ1 (RL25_THET8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
50S ribosomal protein L25
Short name=TL5

Gene names

Name:	rplY
Synonyms:	rpl25, rptL5
Ordered Locus Names:	TTHA1589

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	206 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. HAMAP-Rule MF_01334
Subunit structure	Part of the 50S ribosomal subunit. Contacts the 5S rRNA; has been isolated in a complex with 5S rRNA and RL5, 5S rRNA and DNA binding protein II; 5S rRNA and RL18; 5S rRNA, RL5 and DNA binding protein II (Ref.4).
Sequence similarities	Belongs to the ribosomal protein L25P family. Ctc subfamily.
Mass spectrometry	Molecular mass is 23207 Da from positions 1 - 206. Determined by MALDI. Ref.5

Ontologies

Keywords
Ligand	RNA-binding 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	ribosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	5S rRNA binding Inferred from electronic annotation. Source: InterPro 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

Chain

1 – 206

206

50S ribosomal protein L25 HAMAP-Rule MF_01334

PRO_0000181608

Experimental info

Sequence conflict

43 – 45

3

EFD → QRF AA sequence Ref.2

Sequence conflict

60 – 70

11

ELPDGQSLPTL → QLRRGTRLSPE AA sequence Ref.2

Secondary structure

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206

Helix Strand Turn

Details...

Beta strand

3 – 9

7

Beta strand

11 – 13

3

Helix

15 – 20

6

Beta strand

23 – 30

8

Beta strand

33 – 40

8

Helix

41 – 51

11

Turn

52 – 54

3

Beta strand

57 – 60

4

Beta strand

62 – 64

3

Beta strand

66 – 77

12

Turn

78 – 81

4

Beta strand

82 – 90

9

Beta strand

96 – 101

6

Beta strand

103 – 106

4

Turn

111 – 114

4

Beta strand

116 – 118

3

Beta strand

122 – 128

7

Beta strand

130 – 132

3

Beta strand

138 – 140

3

Beta strand

142 – 144

3

Beta strand

145 – 147

3

Beta strand

148 – 150

3

Beta strand

152 – 154

3

Beta strand

159 – 163

5

Beta strand

167 – 169

3

Beta strand

172 – 175

4

Helix

180 – 182

3

Helix

183 – 186

4

Beta strand

188 – 195

8

Beta strand

199 – 201

3

Sequences

	Sequence		Length	Mass (Da)
	Q5SHZ1 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: ACC20EC1279181CD	FASTA	206	23,205
	10 20 30 40 50 60 MEYRLKAYYR EGEKPSALRR AGKLPGVMYN RHLNRKVYVD LVEFDKVFRQ ASIHHVIVLE 70 80 90 100 110 120 LPDGQSLPTL VRQVNLDKRR RRPEHVDFFV LSDEPVEMYV PLRFVGTPAG VRAGGVLQEI 130 140 150 160 170 180 HRDILVKVSP RNIPEFIEVD VSGLEIGDSL HASDLKLPPG VELAVSPEET IAAVVPPEDV 190 200 EKLAEEAAAE VAEPEVIKKG KEEEEE

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]. Strain: HB8 / ATCC 27634 / DSM 579.
[2]	"The isolation and complete amino acid sequence of the ribosomal protein L36 from Thermus thermophilus and its zinc-binding motif." Boysen R.I., Lorenz S., Kim J.S., Schroeder W.F.K.J., Erdmann V.A. Endocyt. Cell Res. 11:41-58(1995) Cited for: PROTEIN SEQUENCE OF 1-70.
[3]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-30.
[4]	"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 1-22, ISOLATION OF 5S RRNA-ASSOCIATED COMPLEXES.
[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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AP008226 Genomic DNA. Translation: BAD71412.1.

RefSeq

YP_144855.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GIY	X-ray	5.50	V	1-206	[»]
2HGJ	X-ray	5.00	Y	1-206	[»]
2HGQ	X-ray	5.50	Y	1-206	[»]
2HGU	X-ray	4.51	Y	1-206	[»]
2J01	X-ray	2.80	Z	1-206	[»]
2J03	X-ray	2.80	Z	1-206	[»]
2V47	X-ray	3.80	Z	1-206	[»]
2V49	X-ray	3.80	Z	1-206	[»]
2WDI	X-ray	3.30	Z	1-206	[»]
2WDJ	X-ray	3.30	Z	1-206	[»]
2WDL	X-ray	3.50	Z	1-206	[»]
2WDN	X-ray	3.50	Z	1-206	[»]
2WH2	X-ray	3.45	Z	1-206	[»]
2WH4	X-ray	3.45	Z	1-206	[»]
2WRJ	X-ray	3.60	Z	1-206	[»]
2WRL	X-ray	3.60	Z	1-206	[»]
2WRO	X-ray	3.60	Z	1-206	[»]
2WRR	X-ray	3.60	Z	1-206	[»]
2X9S	X-ray	3.10	Z	1-206	[»]
2X9U	X-ray	3.10	Z	1-206	[»]
2XG0	X-ray	3.20	Z	1-206	[»]
2XG2	X-ray	3.20	Z	1-206	[»]
2XQE	X-ray	3.10	Z	1-206	[»]
2XTG	electron microscopy	7.80	Z	1-206	[»]
2XUX	electron microscopy	7.60	Z	1-206	[»]
2Y0V	X-ray	3.10	Z	1-206	[»]
2Y0X	X-ray	3.10	Z	1-206	[»]
2Y0Z	X-ray	3.10	Z	1-206	[»]
2Y11	X-ray	3.10	Z	1-206	[»]
2Y13	X-ray	3.10	Z	1-206	[»]
2Y15	X-ray	3.10	Z	1-206	[»]
2Y17	X-ray	3.10	Z	1-206	[»]
2Y19	X-ray	3.10	Z	1-206	[»]
3FIN	electron microscopy	6.40	Z	3-179	[»]
3HUX	X-ray	3.10	Z	1-206	[»]
3HUZ	X-ray	3.10	Z	1-206	[»]
3I8F	X-ray	3.10	V	1-206	[»]
3I8I	X-ray	3.10	V	1-206	[»]
3I9C	X-ray	3.50	V	1-206	[»]
3I9E	X-ray	3.50	V	1-206	[»]
3KIR	X-ray	3.30	Z	1-206	[»]
3KIT	X-ray	3.30	Z	1-206	[»]
3KIW	X-ray	3.60	Z	1-206	[»]
3KIY	X-ray	3.60	Z	1-206	[»]
3KNI	X-ray	3.00	Z	1-206	[»]
3KNK	X-ray	3.00	Z	1-206	[»]
3KNM	X-ray	3.45	Z	1-206	[»]
3KNO	X-ray	3.45	Z	1-206	[»]
3TVE	X-ray	3.10	V	1-175	[»]
3TVH	X-ray	3.10	V	1-179	[»]
3UXQ	X-ray	3.20	Z	1-206	[»]
3UXR	X-ray	3.20	Z	1-206	[»]
3UYE	X-ray	3.00	V	1-206	[»]
3UYG	X-ray	3.00	V	1-206	[»]
3UZ1	X-ray	3.30	V	1-206	[»]
3UZ2	X-ray	3.30	V	1-206	[»]
3UZ8	X-ray	3.00	V	1-206	[»]
3UZ9	X-ray	3.00	V	1-206	[»]
3UZF	X-ray	3.30	V	1-206	[»]
3UZH	X-ray	3.30	V	1-206	[»]
3UZK	X-ray	3.30	V	1-206	[»]
3UZN	X-ray	3.30	V	1-206	[»]
3V23	X-ray	3.00	Z	1-206	[»]
3V25	X-ray	3.00	Z	1-206	[»]
3V27	X-ray	3.10	Z	1-206	[»]
3V29	X-ray	3.10	Z	1-206	[»]
3V2D	X-ray	2.70	Z	1-206	[»]
3V2F	X-ray	2.70	Z	1-206	[»]
3ZVP	X-ray	3.80	Z	1-206	[»]
4ABS	X-ray	3.10	Z	1-206	[»]
4DHA	X-ray	3.20	Z	1-206	[»]
4DHC	X-ray	3.20	Z	1-206	[»]
4G5L	X-ray	3.30	V	1-206	[»]
4G5N	X-ray	3.30	V	1-206	[»]
4G5U	X-ray	3.10	V	1-206	[»]
4G5W	X-ray	3.10	V	1-206	[»]

ProteinModelPortal

Q5SHZ1.

SMR

Q5SHZ1. Positions 1-185.

ModBase

Search...

Protein-protein interaction databases

STRING

300852.TTHA1589.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD71412; BAD71412; BAD71412.

GeneID

3169859.

KEGG

ttj:TTHA1589.

PATRIC

23958133. VBITheThe93045_1559.

Phylogenomic databases

eggNOG

COG1825.

HOGENOM

HOG000214906.

KO

K02897.

OMA

ELIMKKG.

ProtClustDB

PRK05618.

Family and domain databases

Gene3D

2.170.120.20. 1 hit.
2.40.240.10. 1 hit.

HAMAP

MF_01334. Ribosomal_L25_CTC.

InterPro

IPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020057. Ribosomal_L25_b-dom.
IPR001021. Ribosomal_L25_long.
IPR020055. Ribosomal_L25_short.
[Graphical view]

Pfam

PF01386. Ribosomal_L25p. 1 hit.
[Graphical view]

ProDom

PD012503. Ribosomal_L25. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF50715. Ribosomal_L25rel. 1 hit.

TIGRFAMs

TIGR00731. ctc_TL5. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q5SHZ1.

Entry information

Entry name

RL25_THET8

Accession

Primary (citable) accession number: Q5SHZ1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	December 21, 2004
Last modified:	May 1, 2013
This is version 74 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program