50S ribosomal protein L6 - Deinococcus radiodurans

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Q9RSL3 (RL6_DEIRA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 74. 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 L6

Gene names

Name:	rplF
Ordered Locus Names:	DR_2111

Organism

Deinococcus radiodurans

Taxonomic identifier

1299 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	185 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center By similarity. This protein binds to the 23S rRNA, and is important in its secondary structure. HAMAP MF_01365_B
Subunit structure	Part of the 50S ribosomal subunit. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8
Sequence similarities	Belongs to the ribosomal protein L6P family.
Sequence caution	The sequence AAF11660.1 differs from that shown. Reason: Erroneous initiation.

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: 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
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 185

185

50S ribosomal protein L6 HAMAP MF_01365_B

PRO_0000131047

Secondary structure

185

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9RSL3 [UniParc].

Last modified March 15, 2004. Version 2.
Checksum: 00E39D11826B4C1D
Show »

FASTA

185

19,582

        10         20         30         40         50         60 
MSRIGKQPIA VPSGVTVNAQ DGVFKVKGPK GELTVPYNTE LTVRQDGDQL LVERPSDAQK 

        70         80         90        100        110        120 
HRALHGLTRT LVANAVKGVS DGYTINLELR GVGFRAKLTG KALEMNIGYS HPVIIEPPAG 

       130        140        150        160        170        180 
VTFAVPEPTR IDVSGIDKQL VGQVAANVRK VRKPDAYHGK GVRFVGEQIA LKAGKAGATG 


GKGKK

« 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: AAF11660.1. Different initiation.

PIR

B75314.

RefSeq

NP_295834.2. NC_001263.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NKW	X-ray	3.10	E	1-185	[»]
1NWX	X-ray	3.50	E	1-185	[»]
1NWY	X-ray	3.30	E	1-185	[»]
1PNU	X-ray	8.70	E	5-181	[»]
1PNY	X-ray	9.50	E	5-181	[»]
1SM1	X-ray	3.42	E	1-185	[»]
1XBP	X-ray	3.50	E	1-185	[»]
2ZJP	X-ray	3.70	E	1-185	[»]
2ZJQ	X-ray	3.30	E	1-185	[»]
2ZJR	X-ray	2.91	E	1-185	[»]
3CF5	X-ray	3.30	E	1-185	[»]
3DLL	X-ray	3.50	E	1-185	[»]
3PIO	X-ray	3.25	E	1-185	[»]
3PIP	X-ray	3.45	E	1-185	[»]

ProteinModelPortal

Q9RSL3.

SMR

Q9RSL3. Positions 5-181.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1800121.

GenomeReviews

Gene locus DR_2111 in contig AE000513_GR.

KEGG

dra:DR_2111.

NMPDR

fig|243230.1.peg.2293.

PATRIC

21631898. VBIDeiRad64572_2334.

TIGR

DR_2111.

Phylogenomic databases

HOGENOM

HBG606796.

OMA

ALINNMV.

PhylomeDB

Q9RSL3.

ProtClustDB

PRK05498.

Enzyme and pathway databases

BioCyc

DRAD243230:DR_2111-MONOMER.

Family and domain databases

HAMAP

MF_01365_B. Ribosomal_L6_B.
[Tree]

InterPro

IPR000702. Ribosomal_L6.
IPR020040. Ribosomal_L6_a/b-dom.
IPR019906. Ribosomal_L6_bac-type.
[Graphical view]

Gene3D

G3DSA:3.90.930.12. Ribosomal_L6. 2 hits.

K02933.

PANTHER

PTHR11655:SF6. PTHR11655:SF6. 1 hit.
PTHR11655. Ribosomal_L6. 1 hit.

Pfam

PF00347. Ribosomal_L6. 2 hits.
[Graphical view]

PIRSF

PIRSF002162. Ribosomal_L6. 1 hit.

PRINTS

PR00059. RIBOSOMALL6.

SUPFAM

SSF56053. Ribosomal_L6. 2 hits.

TIGRFAMs

TIGR03654. L6_bact. 1 hit.

PROSITE

PS00525. RIBOSOMAL_L6_1. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL6_DEIRA

Accession

Primary (citable) accession number: Q9RSL3

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	March 15, 2004
Last modified:	January 25, 2012
This is version 74 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

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