50S ribosomal protein L5 - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P62399 (RL5_ECOLI)

Last modified January 19, 2010. Version 69. History...

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

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Names and origin

Protein names

Recommended name:
50S ribosomal protein L5

Gene names

Name:	rplE
Ordered Locus Names:	b3308, JW3270

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	179 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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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. Its 5S rRNA binding is significantly enhanced in the presence of L18. HAMAP MF_01333 In the 70S ribosome in the initiation state (Ref.12) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (Ref.12 and Ref.11). In the two 3.5 A resolved ribosome structures (Ref.14) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction. HAMAP MF_01333 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
Subunit structure	Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA; cross-links to the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome, contacting protein S13 and S19. Ref.7 Ref.12 Ref.14
Sequence similarities	Belongs to the ribosomal protein L5P family.
Mass spectrometry	Molecular mass is 20169.8 Da from positions 2 - 179. Determined by MALDI. Ref.10

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Ontologies

Keywords
Ligand	RNA-binding rRNA-binding tRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Acetylation
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: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4

Chain

2 – 179

178

50S ribosomal protein L5 HAMAP MF_01333

PRO_0000124925

Amino acid modifications

Modified residue

N6-acetyllysine Ref.11

Experimental info

Sequence conflict

E → Q AA sequence Ref.4

Sequence conflict

127

N → D AA sequence Ref.4

Secondary structure

179

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P62399-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: B2E95A8BE4B8D2A7
Show »

FASTA

179

20,302

        10         20         30         40         50         60 
MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI 

        70         80         90        100        110        120 
SGQKPLITKA RKSVAGFKIR QGYPIGCKVT LRGERMWEFF ERLITIAVPR IRDFRGLSAK 

       130        140        150        160        170 
SFDGRGNYSM GVREQIIFPE IDYDKVDRVR GLDITITTTA KSDEEGRALL AAFDFPFRK

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene." Cerretti D.P., Dean D., Davis G.R., Bedwell D.M., Nomura M. Nucleic Acids Res. 11:2599-2616(1983) [PubMed: 6222285] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The primary structure of the 5 S RNA binding protein L5 of Escherichia coli ribosomes." Chen R., Ehrke G. FEBS Lett. 69:240-245(1976) [PubMed: 791672] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-179. Strain: K.
[5]	"Translational regulation by ribosomal protein S8 in Escherichia coli: structural homology between rRNA binding site and feedback target on mRNA." Olins P.O., Nomura M. Nucleic Acids Res. 9:1757-1764(1981) [PubMed: 6262737] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-18. Strain: K12 / JM105 / ATCC 47016.
[6]	"Stoichiometry, cooperativity, and stability of interactions between 5S RNA and proteins L5, L18, and L25 from the 50S ribosomal subunit of Escherichia coli." Spierer P., Zimmermann R.A. Biochemistry 17:2474-2479(1978) [PubMed: 354687] [Abstract] Cited for: FORMATION OF THE 5S RRNA/L5/L18/L25 SUBCOMPLEX. Strain: MRE-600.
[7]	"Assembly map of the large subunit (50S) of Escherichia coli ribosomes." Rohl R., Nierhaus K.H. Proc. Natl. Acad. Sci. U.S.A. 79:729-733(1982) [PubMed: 7038683] [Abstract] Cited for: REQUIREMENT FOR INCORPORATION OF 5S RRNA INTO THE 50S SUBUNIT. Strain: MRE-600.
[8]	"The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site." Osswald M., Doering T., Brimacombe R. Nucleic Acids Res. 23:4635-4641(1995) [PubMed: 8524654] [Abstract] Cited for: CROSS-LINKING TO THE TRNA CENTRAL FOLD. Strain: MRE-600.
[9]	"5S rRNA sugar-phosphate backbone protection in complexes with specific ribosomal proteins." Shpanchenko O.V., Zvereva M.I., Dontsova O.A., Nierhaus K.H., Bogdanov A.A. FEBS Lett. 394:71-75(1996) [PubMed: 8925931] [Abstract] Cited for: CHARACTERIZATION OF A 5S RRNA/L5/L18/L25 SUBCOMPLEX. Strain: K12 / A19.
[10]	"Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry." Arnold R.J., Reilly J.P. Anal. Biochem. 269:105-112(1999) [PubMed: 10094780] [Abstract] Cited for: MASS SPECTROMETRY. Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[11]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-3, MASS SPECTROMETRY.
[12]	"Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement." Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J. Cell 113:789-801(2003) [PubMed: 12809609] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (11.50 ANGSTROMS), INTERSUBUNIT BRIDGE FORMATION. Strain: MRE-600.
[13]	"Locking and unlocking of ribosomal motions." Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., Frank J. Cell 114:123-134(2003) [PubMed: 12859903] [Abstract] Cited for: 3D-STRUCTURE MODELING OF RIBOSOMAL COMPLEXES INCLUDING BRIDGE CHANGES UPPON TRANSLOCATION.
[14]	"Structures of the bacterial ribosome at 3.5 A resolution." Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., Cate J.H.D. Science 310:827-834(2005) [PubMed: 16272117] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.46 ANGSTROMS) OF 2 DIFFERENT RIBOSOME STRUCTURES INCLUDING 2 CONFORMATIONS OF INTERSUBUNIT BRIDGE B1B.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X01563 Genomic DNA. Translation: CAA25717.1.
U18997 Genomic DNA. Translation: AAA58105.1.
U00096 Genomic DNA. Translation: AAC76333.1.
AP009048 Genomic DNA. Translation: BAE77983.1.
M10195 Genomic DNA. Translation: AAA24051.1.

PIR

R5EC5. G65123.

RefSeq

AP_004482.1.
NP_417767.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1P85	electron microscopy	12.30	D	2-179	[»]
1P86	electron microscopy	11.50	D	2-179	[»]
1VS6	X-ray	3.46	F	1-179	[»]
1VS8	X-ray	3.46	F	1-179	[»]
2AW4	X-ray	3.46	F	2-179	[»]
2AWB	X-ray	3.46	F	2-179	[»]
2GYA	electron microscopy	15.00	D	3-178	[»]
2GYC	electron microscopy	15.00	D	3-179	[»]
2I2T	X-ray	3.22	F	2-178	[»]
2I2V	X-ray	3.22	F	2-178	[»]
2J28	electron microscopy	8.00	F	2-178	[»]
2QAM	X-ray	3.21	F	2-179	[»]
2QAO	X-ray	3.21	F	2-179	[»]
2QBA	X-ray	3.54	F	2-179	[»]
2QBC	X-ray	3.54	F	2-179	[»]
2QBE	X-ray	3.30	F	2-179	[»]
2QBG	X-ray	3.30	F	2-179	[»]
2QBI	X-ray	4.00	F	2-179	[»]
2QBK	X-ray	4.00	F	2-179	[»]
2QOV	X-ray	3.93	F	2-179	[»]
2QOX	X-ray	3.93	F	2-179	[»]
2QOZ	X-ray	3.50	F	2-179	[»]
2QP1	X-ray	3.50	F	2-179	[»]
2RDO	electron microscopy	9.10	F	2-179	[»]
2VHM	X-ray	3.74	F	2-179	[»]
2VHN	X-ray	3.74	F	2-179	[»]
2Z4L	X-ray	4.45	F	2-179	[»]
2Z4N	X-ray	4.45	F	2-179	[»]
3BBX	electron microscopy	10.00	F	2-179	[»]
3DF2	X-ray	3.50	F	2-178	[»]
3DF4	X-ray	3.50	F	2-178	[»]
3E1B	electron microscopy	-	2	2-179	[»]
3E1D	electron microscopy	-	2	2-179	[»]
3FIK	electron microscopy	6.70	F	2-179	[»]
3I1N	X-ray	3.19	F	1-179	[»]
3I1P	X-ray	3.19	F	1-179	[»]
3I1R	X-ray	3.81	F	1-179	[»]
3I1T	X-ray	3.81	F	1-179	[»]
3I20	X-ray	3.71	F	1-179	[»]
3I22	X-ray	3.71	F	1-179	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P62399.

2-D gel databases

ECO2DBASE

I016.4. 6TH EDITION.

Proteomic databases

PRIDE

P62399.

Genome annotation databases

GeneID

947800.

GenomeReviews

Gene locus JW3270 in contig AP009048_GR.
Gene locus b3308 in contig U00096_GR.

KEGG

ecj:JW3270.
eco:b3308.

Organism-specific databases

EchoBASE

EB0861.

EcoGene

EG10868. rplE.

CMR

Search...

Phylogenomic databases

eggNOG

COG0094.

HOGENOM

HBG592167.

OMA

NIHQVPK.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10868-MONOMER.
ECOL168927:B3308-MONOMER.

Gene expression databases

Genevestigator

P62399.

Family and domain databases

HAMAP

MF_01333_B. Ribosomal_L5_B.
[Tree]

InterPro

IPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR020929. Ribosomal_L5_CS.
[Graphical view]

PANTHER

PTHR11994. Ribosomal_L5. 1 hit.

PIRSF

PIRSF002161. Ribosomal_L5. 1 hit.

PROSITE

PS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

RL5_ECOLI

Accession

Primary (citable) accession number: P62399
Secondary accession number(s): P02389, Q2M6X3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	January 19, 2010
This is version 69 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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

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