Reviewed, UniProtKB/Swiss-Prot Q9RXY1 (RL13_DEIRA)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L13

Gene names

Name:	rplM
Ordered Locus Names:	DR_0174

Organism

Deinococcus radiodurans [Complete proteome] [HAMAP]

Taxonomic identifier

1299 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	174 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	This protein is one of the early assembly proteins of the 50S ribosomal subunit By similarity. Binds to the 23S rRNA.
Subunit structure	Part of the 50S ribosomal subunit. Contacts proteins L3 and L20. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8
Sequence similarities	Belongs to the ribosomal protein L13P family.

Ontologies

Keywords
Ligand	RNA-binding rRNA-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
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 174

174

50S ribosomal protein L13 HAMAP MF_01366

PRO_0000133733

Secondary structure

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174

Helix Strand Turn

Details...

Beta strand

41 – 45

5

Helix

54 – 62

9

Beta strand

72 – 74

3

Beta strand

79 – 83

5

Beta strand

95 – 97

3

Beta strand

99 – 102

4

Beta strand

112 – 116

5

Turn

117 – 120

4

Helix

123 – 131

9

Turn

143 – 147

5

Helix

156 – 160

5

Sequences

	Sequence		Length	Mass (Da)
	Q9RXY1-1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 9F7B977882CB715E	FASTA	174	19,190
	10 20 30 40 50 60 MAFPDTDVSP PRGGPSSPAK SPLLRSFKVK TYIPKNDEQN WVVVDASGVP LGRLATLIAS 70 80 90 100 110 120 RIRGKHRPDF TPNMIQGDFV VVINAAQVAL TGKKLDDKVY TRYTGYQGGL KTETAREALS 130 140 150 160 170 KHPERVIEHA VFGMLPKGRQ GRAMHTRLKV YAGETHPHSA QKPQVLKTQP LEVK

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. , McDonald L.A., Utterback T.R., Zalewski C., Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D., Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C., 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 1-5, CONTACTS WITH 23S RRNA. 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

EMBLGenBankDDBJ

AE000513 Genomic DNA. Translation: AAF09760.1.

PIR

E75552.

RefSeq

NP_293898.2.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GS2	model	-	H	30-171	[»]
1NKW	X-ray	3.10	H	1-174	[»]
1NWX	X-ray	3.50	H	1-174	[»]
1NWY	X-ray	3.30	H	1-174	[»]
1PNU	X-ray	8.70	H	29-171	[»]
1PNY	X-ray	9.50	H	29-171	[»]
1SM1	X-ray	3.42	H	1-174	[»]
1XBP	X-ray	3.50	H	1-174	[»]
2ZJP	X-ray	3.70	G	1-174	[»]
2ZJQ	X-ray	3.30	G	1-174	[»]
2ZJR	X-ray	2.91	G	1-174	[»]
3CF5	X-ray	3.30	G	1-174	[»]
3DLL	X-ray	3.50	G	1-174	[»]

ModBase

Search...

Genome annotation databases

GeneID

1799575.

GenomeReviews

Gene locus DR_0174 in contig AE000513_GR.

KEGG

dra:DR_0174.

NMPDR

fig|243230.1.peg.357.

TIGR

DR_0174.

Phylogenomic databases

HOGENOM

Q9RXY1.

OMA

PKNKLAR.

Enzyme and pathway databases

BioCyc

DRAD243230:DR_0174-MON.

Family and domain databases

HAMAP

MF_01366.
[Tree]

InterPro

IPR005822. Ribosomal_L13.
IPR005823. Ribosomal_L13_bac-type.
[Graphical view]

Gene3D

G3DSA:3.90.1180.10. Ribosomal_L13. 1 hit.

PANTHER

PTHR11545:SF2. Ribosom_L13_bac. 1 hit.
PTHR11545. Ribosomal_L13. 1 hit.

Pfam

PF00572. Ribosomal_L13. 1 hit.
[Graphical view]

PIRSF

PIRSF002181. Ribosomal_L13. 1 hit.

ProDom

PD001791. Ribosomal_L13. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR01066. rplM_bact. 1 hit.

PROSITE

PS00783. RIBOSOMAL_L13. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL13_DEIRA

Accession

Primary (citable) accession number: Q9RXY1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	May 1, 2000
Last modified:	November 3, 2009
This is version 61 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)