50S ribosomal protein L16 - Deinococcus radiodurans

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Reviewed, UniProtKB/Swiss-Prot Q9RXJ5 (RL16_DEIRA)

Last modified February 9, 2010. Version 65. History...

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

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein names

Recommended name:
50S ribosomal protein L16

Gene names

Name:	rplP
Ordered Locus Names:	DR_0318

Organism

Deinococcus radiodurans [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

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

Protein attributes

Sequence length	141 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	Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center. HAMAP MF_01342
Subunit structure	Part of the 50S ribosomal subunit. Contacts the CTC protein (RL25). Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8
Sequence similarities	Belongs to the ribosomal protein L16P family.

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: 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

Initiator methionine

1

Removed HAMAP MF_01342

Chain

140

50S ribosomal protein L16 HAMAP MF_01342

PRO_0000062093

Secondary structure

1

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141

Helix Strand Turn

Sequences

Sequence

Length

Mass (Da)

Tools

Q9RXJ5-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: F6666E00FF79FA5B
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141

16,095

        10         20         30         40         50         60 
MLLPKRTKFR KQFRGRMTGD AKGGDYVAFG DYGLIAMEPA WIKSNQIEAC RIVMSRHFRR 

        70         80         90        100        110        120 
GGKIYIRIFP DKPVTKKPAE TRMGKGKGAV EYWVSVVKPG RVMFEVAGVT EEQAKEAFRL 

       130        140 
AGHKLPIQTK MVKREVYDEA Q

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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 1-6. Strain: ATCC 13939 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[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 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000513 Genomic DNA. Translation: AAF09899.1. Different initiation.

PIR

RefSeq

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GS2	model	-	K	6-135	[»]
1NJM	X-ray	3.60	K	1-141	[»]
1NJP	X-ray	3.50	K	1-141	[»]
1NKW	X-ray	3.10	K	1-141	[»]
1NWX	X-ray	3.50	K	1-141	[»]
1NWY	X-ray	3.30	K	1-141	[»]
1PNU	X-ray	8.70	K	7-130	[»]
1PNY	X-ray	9.50	K	7-130	[»]
1SM1	X-ray	3.42	K	1-141	[»]
1XBP	X-ray	3.50	K	1-141	[»]
1Y69	X-ray	3.33	K	1-141	[»]
2ZJP	X-ray	3.70	J	1-141	[»]
2ZJQ	X-ray	3.30	J	1-141	[»]
2ZJR	X-ray	2.91	J	1-141	[»]
3CF5	X-ray	3.30	J	1-141	[»]
3DLL	X-ray	3.50	J	1-141	[»]

ModBase

Genome annotation databases

GeneID

GenomeReviews

Gene locus DR_0318 in contig AE000513_GR.

KEGG

NMPDR

fig|243230.1.peg.500.

TIGR

Phylogenomic databases

HOGENOM

OMA

Enzyme and pathway databases

BioCyc

DRAD243230:DR_0318-MONOMER.

Family and domain databases

HAMAP

MF_01342. Ribosomal_L16.
[Tree]

InterPro

IPR016180. Ribosomal_L10e/L16.
IPR000114. Ribosomal_L16.
IPR020798. Ribosomal_L16_CS.
[Graphical view]

PANTHER

PTHR12220. Ribosomal_L16. 1 hit.

Pfam

PF00252. Ribosomal_L16. 1 hit.
[Graphical view]

PRINTS

PR00060. RIBOSOMALL16.

TIGRFAMs

TIGR01164. rplP_bact. 1 hit.

PROSITE

PS00586. RIBOSOMAL_L16_1. 1 hit.
PS00701. RIBOSOMAL_L16_2. 1 hit.
[Graphical view]

ProtoNet

Entry information

Entry name

RL16_DEIRA

Accession

Primary (citable) accession number: Q9RXJ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	January 23, 2007
Last modified:	February 9, 2010
This is version 65 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)

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Ribosomal proteins

Ribosomal proteins families and list of entries

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents