50S ribosomal protein L25 - Deinococcus radiodurans

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Q9RX88 (RL25_DEIRA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 82. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
50S ribosomal protein L25

Alternative name(s):
General stress protein CTC

Gene names

Name:	rplY
Synonyms:	ctc
Ordered Locus Names:	DR_0427

Organism

Deinococcus radiodurans

Taxonomic identifier

1299 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Deinococcales › Deinococcaceae › Deinococcus

Protein attributes

Sequence length	237 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. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding. HAMAP MF_01334
Subunit structure	Part of the 50S ribosomal subunit. Contacts proteins L11 and L16, the A site tRNA, and the 5S and 23S rRNAs. Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9
Sequence similarities	Belongs to the ribosomal protein L25P family. Ctc subfamily.
Sequence caution	The sequence AAF10004.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Ligand	RNA-binding rRNA-binding tRNA-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: InterPro
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 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

Chain

1 – 237

237

50S ribosomal protein L25 HAMAP MF_01334

PRO_0000181543

Regions

Region

1 – 104

104

N-terminal domain HAMAP MF_01334

Region

105 – 189

Middle domain HAMAP MF_01334

Region

190 – 237

C-terminal domain HAMAP MF_01334

Secondary structure

237

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9RX88 [UniParc].

Last modified March 15, 2004. Version 2.
Checksum: 1B67F7DD4D385C21
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FASTA

237

25,390

        10         20         30         40         50         60 
MELTAKPRTP KQKLDESMIA AVAYNKENNV SFALDRKAFD RAFRQQSTTG LFDITVEGGE 

        70         80         90        100        110        120 
TFPALVKAVQ MDKRKRAPIH VDFYMVTYGE PVEVSVPVHT TGRSQGEVQG GLVDIVVHNL 

       130        140        150        160        170        180 
QIVAPGPRRI PQELVVDVTK MNIGDHITAG DIKLPEGCTL AADPELTVVS VLPPRLTAEE 

       190        200        210        220        230 
LEAEVQAAQV AGLVAAGELS EEAAEAVLEG DASLEEVKAE ASEDNAGTDS EDNSDAQ

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1." White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D., Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L., Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M., Vamathevan J.J., Lam P. Fraser C.M. Science 286:1571-1577(1999) [PubMed: 10567266] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[2]	"Protein recycling is a major component of post-irradiation recovery in Deinococcus radiodurans strain R1." Joshi B.S., Schmid R., Altendorf K., Apte S.K. Biochem. Biophys. Res. Commun. 320:1112-1117(2004) [PubMed: 15249204] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-22. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[3]	"High resolution structure of the large ribosomal subunit from a mesophilic eubacterium." Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., Yonath A. Cell 107:679-688(2001) [PubMed: 11733066] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT, PROTEIN SEQUENCE OF 1-5. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[4]	"Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria." Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R., Yonath A., Franceschi F. Nature 413:814-821(2001) [PubMed: 11677599] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FIVE ANTIBIOTICS. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[5]	"Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression." Bashan A., Agmon I., Zarivach R., Schluenzen F., Harms J., Berisio R., Bartels H., Franceschi F., Auerbach T., Hansen H.A., Kossoy E., Kessler M., Yonath A. Mol. Cell 11:91-102(2003) [PubMed: 12535524] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TRNA MIMICS. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[6]	"Structural basis for the antibiotic activity of ketolides and azalides." Schluenzen F., Harms J.M., Franceschi F., Hansen H.A., Bartels H., Zarivach R., Yonath A. Structure 11:329-338(2003) [PubMed: 12623020] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH MODIFIED MACROLIDE ANTIBIOTICS. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[7]	"Structural insight into the role of the ribosomal tunnel in cellular regulation." Berisio R., Schluenzen F., Harms J., Bashan A., Auerbach T., Baram D., Yonath A. Nat. Struct. Biol. 10:366-370(2003) [PubMed: 12665853] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TROLEANDOMYCIN. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[8]	"Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin." Harms J.M., Schluenzen F., Fucini P., Bartels H., Yonath A. BMC Biol. 2:4-4(2004) [PubMed: 15059283] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH THE STREPTOGRAMINS QUINUPRISTIN AND DALFOPRISTIN. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
[9]	"Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin." Schluenzen F., Pyetan E., Fucini P., Yonath A., Harms J.M. Mol. Microbiol. 54:1287-1294(2004) [PubMed: 15554968] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TIAMULIN. Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000513 Genomic DNA. Translation: AAF10004.1. Different initiation.

PIR

A75521.

RefSeq

NP_294150.1. NC_001263.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NJM	X-ray	3.60	T	1-237	[»]
1NJP	X-ray	3.50	T	1-237	[»]
1NKW	X-ray	3.10	T	1-237	[»]
1NWX	X-ray	3.50	T	1-237	[»]
1NWY	X-ray	3.30	T	1-237	[»]
1PNU	X-ray	8.70	T	1-173	[»]
1PNY	X-ray	9.50	T	1-173	[»]
1SM1	X-ray	3.42	T	1-237	[»]
1XBP	X-ray	3.50	T	1-237	[»]
2ZJP	X-ray	3.70	S	1-237	[»]
2ZJQ	X-ray	3.30	S	1-237	[»]
2ZJR	X-ray	2.91	S	1-237	[»]
3CF5	X-ray	3.30	S	1-237	[»]
3DLL	X-ray	3.50	S	1-237	[»]
3PIO	X-ray	3.25	S	1-237	[»]
3PIP	X-ray	3.45	S	1-237	[»]

ProteinModelPortal

Q9RX88.

SMR

Q9RX88. Positions 1-177.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1798774.

GenomeReviews

Gene locus DR_0427 in contig AE000513_GR.

KEGG

dra:DR_0427.

NMPDR

fig|243230.1.peg.609.

PATRIC

21628370. VBIDeiRad64572_0601.

TIGR

DR_0427.

Phylogenomic databases

HOGENOM

HBG731986.

OMA

ELIMKKG.

ProtClustDB

PRK05618.

Enzyme and pathway databases

BioCyc

DRAD243230:DR_0427-MONOMER.

Family and domain databases

HAMAP

MF_01334. Ribosomal_L25_CTC.
[Tree]

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]

Gene3D

G3DSA:2.40.240.10. Rbsml_L25/Gln-tRNA_synth_b-brl. 1 hit.
G3DSA:2.170.120.20. Ribosomal_L25_b-dom. 1 hit.

K02897.

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...

Entry information

Entry name

RL25_DEIRA

Accession

Primary (citable) accession number: Q9RX88

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	March 15, 2004
Last modified:	January 25, 2012
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents