50S ribosomal protein L5 - Deinococcus radiodurans

Contribute

Send feedback

Read comments (?) or add your own

Q9RXJ0 (RL5_DEIRA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 73. History...

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

Documents (3) |

Third-party data

text xml rdf/xml gff fasta

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 L5

Gene names

Name:	rplE
Ordered Locus Names:	DR_0323

Organism

Deinococcus radiodurans

Taxonomic identifier

1299 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	180 AA.
Sequence status	Complete.
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 (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement By similarity. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. HAMAP MF_01333_B
Subunit structure	Forms a bridge to the 30S subunit in the 70S ribosome By similarity. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 (CTC) subcomplex. Is known to contact the 5S rRNA, 23S rRNA and the P site tRNA. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8
Sequence similarities	Belongs to the ribosomal protein L5P family.

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	rRNA binding Inferred from electronic annotation. Source: UniProtKB-KW 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 – 180

180

50S ribosomal protein L5 HAMAP MF_01333_B

PRO_0000124923

Secondary structure

180

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9RXJ0 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: 755B760BA0E90F5B
Show »

FASTA

180

20,350

        10         20         30         40         50         60 
MQQLKTKYND QVRPALMQQF GYSSVMAVPR IEKIVVNEGL GSSKEDSKAI DKAAKELALI 

        70         80         90        100        110        120 
TLQKPIITKA KKSISNFKLR QGMPVGIKVT LRGERMYVFL EKLINIGLPR IRDFRGINPN 

       130        140        150        160        170        180 
AFDGRGNYNL GIKEQLIFPE ITYDMVDKTR GMDITIVTTA KTDEEARALL QSMGLPFRKQ

« 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]	"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.
[3]	"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.
[4]	"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.
[5]	"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.
[6]	"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.
[7]	"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.
[8]	"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: AAF09904.1.

PIR

C75535.

RefSeq

NP_294046.1. NC_001263.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NKW	X-ray	3.10	D	1-180	[»]
1NWX	X-ray	3.50	D	1-180	[»]
1NWY	X-ray	3.30	D	1-180	[»]
1PNU	X-ray	8.70	D	2-179	[»]
1PNY	X-ray	9.50	D	2-179	[»]
1SM1	X-ray	3.42	D	1-180	[»]
1XBP	X-ray	3.50	D	1-180	[»]
2ZJP	X-ray	3.70	D	1-180	[»]
2ZJQ	X-ray	3.30	D	1-180	[»]
2ZJR	X-ray	2.91	D	1-180	[»]
3CF5	X-ray	3.30	D	1-180	[»]
3DLL	X-ray	3.50	D	1-180	[»]
3PIO	X-ray	3.25	D	1-180	[»]
3PIP	X-ray	3.45	D	1-180	[»]

ProteinModelPortal

Q9RXJ0.

SMR

Q9RXJ0. Positions 2-179.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1798348.

GenomeReviews

Gene locus DR_0323 in contig AE000513_GR.

KEGG

dra:DR_0323.

NMPDR

fig|243230.1.peg.505.

PATRIC

21628144. VBIDeiRad64572_0489.

TIGR

DR_0323.

Phylogenomic databases

HOGENOM

HBG592167.

OMA

RQGMPIG.

PhylomeDB

Q9RXJ0.

ProtClustDB

PRK00010.

Enzyme and pathway databases

BioCyc

DRAD243230:DR_0323-MONOMER.

Family and domain databases

HAMAP

MF_01333_B. Ribosomal_L5_B.
[Tree]

InterPro

IPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR022803. Ribosomal_L5_domain.
[Graphical view]

Gene3D

G3DSA:3.30.1440.10. Ribosomal_L5. 1 hit.

K02931.

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.

SUPFAM

SSF55282. Ribosomal_L5. 1 hit.

PROSITE

PS00358. RIBOSOMAL_L5. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL5_DEIRA

Accession

Primary (citable) accession number: Q9RXJ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	May 1, 2000
Last modified:	January 25, 2012
This is version 73 of the entry and version 1 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

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