50S ribosomal protein L4 - Deinococcus radiodurans

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Q9RXK1 (RL4_DEIRA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 72. 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 L4

Gene names

Name:	rplD
Ordered Locus Names:	DR_0312

Organism

Deinococcus radiodurans

Taxonomic identifier

1299 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	205 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

One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly By similarity. HAMAP MF_01328_B

Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit. HAMAP MF_01328_B

This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel. HAMAP MF_01328_B

Subunit structure

Part of the 50S ribosomal subunit. Contacts proteins L15 and L34. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8

Sequence similarities

Belongs to the ribosomal protein L4P family.

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

Initiator methionine

Removed HAMAP MF_01328_B

Chain

2 – 205

204

50S ribosomal protein L4 HAMAP MF_01328_B

PRO_0000129214

Secondary structure

205

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9RXK1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 760A6C160912477B
Show »

FASTA

205

22,278

        10         20         30         40         50         60 
MAQINVIGQN GGRTIELPLP EVNSGVLHEV VTWQLASRRR GTASTRTRAQ VSKTGRKMYG 

        70         80         90        100        110        120 
QKGTGNARHG DRSVPTFVGG GVAFGPKPRS YDYTLPRQVR QLGLAMAIAS RQEGGKLVAV 

       130        140        150        160        170        180 
DGFDIADAKT KNFISWAKQN GLDGTEKVLL VTDDENTRRA ARNVSWVSVL PVAGVNVYDI 

       190        200 
LRHDRLVIDA AALEIVEEEA GEEQQ

« 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 1-6. 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: AAF09893.1.

PIR

H75533.

RefSeq

NP_294035.1. NC_001263.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J5A	X-ray	3.50	K	1-205	[»]
1JZX	X-ray	3.10	K	1-205	[»]
1JZY	X-ray	3.50	K	1-205	[»]
1JZZ	X-ray	3.80	K	1-205	[»]
1K01	X-ray	3.50	K	1-205	[»]
1NKW	X-ray	3.10	C	1-205	[»]
1NWX	X-ray	3.50	C	2-205	[»]
1NWY	X-ray	3.30	C	2-205	[»]
1PNU	X-ray	8.70	C	2-198	[»]
1PNY	X-ray	9.50	C	2-198	[»]
1SM1	X-ray	3.42	C	1-205	[»]
1XBP	X-ray	3.50	C	2-205	[»]
2ZJP	X-ray	3.70	C	1-205	[»]
2ZJQ	X-ray	3.30	C	1-205	[»]
2ZJR	X-ray	2.91	C	1-205	[»]
3CF5	X-ray	3.30	C	1-205	[»]
3DLL	X-ray	3.50	C	1-205	[»]
3PIO	X-ray	3.25	C	1-205	[»]
3PIP	X-ray	3.45	C	1-205	[»]

ProteinModelPortal

Q9RXK1.

SMR

Q9RXK1. Positions 2-198.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1799571.

GenomeReviews

Gene locus DR_0312 in contig AE000513_GR.

KEGG

dra:DR_0312.

NMPDR

fig|243230.1.peg.494.

PATRIC

21628122. VBIDeiRad64572_0478.

TIGR

DR_0312.

Phylogenomic databases

HOGENOM

HBG545479.

OMA

QAHSRQG.

ProtClustDB

PRK05319.

Enzyme and pathway databases

BioCyc

DRAD243230:DR_0312-MONOMER.

Family and domain databases

HAMAP

MF_01328_B. Ribosomal_L4_B.
[Tree]

InterPro

IPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
IPR023574. Ribosomal_L4_dom.
[Graphical view]

Gene3D

G3DSA:3.40.1370.10. G3DSA:3.40.1370.10. 1 hit.

K02926.

PANTHER

PTHR10746. Ribos_L4_L1E_bac. 1 hit.

Pfam

PF00573. Ribosomal_L4. 1 hit.
[Graphical view]

SUPFAM

SSF52166. Ribosomal_L4/L1E. 1 hit.

TIGRFAMs

TIGR03953. RplD_bact. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RL4_DEIRA

Accession

Primary (citable) accession number: Q9RXK1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 72 of the entry and version 3 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