Reviewed, UniProtKB/Swiss-Prot P60422 (RL2_ECOLI)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L2

Gene names

Name:	rplB
Ordered Locus Names:	b3317, JW3279

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	273 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. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial. HAMAP MF_01320 In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, Ref.14); these contacts are broken in the model with bound EF-G. HAMAP MF_01320
Subunit structure	Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome, contacting the 16S rRNA. Interacts weakly with S6 in one of the 3.5 A resolved structures. Ref.6 Ref.10 Ref.14
Miscellaneous	This protein can be partially replaced in vivo by its H.marismortui (HmaL2) or human (L8, from the 60S cytoplasmic ribosome) homolog. HAMAP MF_01320
Sequence similarities	Belongs to the ribosomal protein L2P family.
Mass spectrometry	Molecular mass is 29732.3 Da from positions 2 - 273. Determined by MALDI. Ref.11

Ontologies

Keywords
Ligand	RNA-binding rRNA-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	large ribosomal subunit Inferred from electronic annotation. Source: InterPro
Molecular function	protein binding Inferred from physical interaction. Source: IntAct rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro transferase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
gspE	P45759	1	EBI-543515,EBI-1132437
intA	P32053	1	EBI-543515,EBI-552967
ispB	P0AD57	1	EBI-543515,EBI-1131851
metG	P00959	1	EBI-543515,EBI-909268
ppsA	P23538	1	EBI-543515,EBI-1114517
rfaB	P27127	1	EBI-543515,EBI-1133312
torR	P38684	1	EBI-543515,EBI-557598
ydcF	P34209	1	EBI-543515,EBI-1123957
yfdP	P76512	1	EBI-543515,EBI-1119667
ygcF	P64554	1	EBI-543515,EBI-1126335
yhbJ	P0A894	1	EBI-543515,EBI-559087
yliJ	P0ACA7	1	EBI-543515,EBI-1120568

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 273

272

50S ribosomal protein L2 HAMAP MF_01320

PRO_0000129559

Amino acid modifications

Modified residue

242

1

N6-acetyllysine Ref.12

Experimental info

Mutagenesis

230

1

H → Q: Loss of peptidyltransferase activity in reconstituted ribosomes. No change in rRNA binding or assembly into ribosomes. Ref.7 Ref.9

Sequence conflict

232 – 235

4

HGGG → GGGH AA sequence Ref.4

Secondary structure

1

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273

Helix Strand Turn

Details...

Beta strand

6 – 8

3

Beta strand

15 – 18

4

Beta strand

47 – 49

3

Beta strand

76 – 78

3

Beta strand

85 – 87

3

Beta strand

119 – 121

3

Beta strand

124 – 128

5

Helix

132 – 134

3

Beta strand

146 – 149

4

Helix

199 – 201

3

Turn

209 – 215

7

Beta strand

229 – 232

4

Beta strand

235 – 237

3

Beta strand

258 – 260

3

Sequences

	Sequence		Length	Mass (Da)
	P60422-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 1010BDE8D8C68B9B	FASTA	273	29,860
	10 20 30 40 50 60 MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ 70 80 90 100 110 120 AYRIVDFKRN KDGIPAVVER LEYDPNRSAN IALVLYKDGE RRYILAPKGL KAGDQIQSGV 130 140 150 160 170 180 DAAIKPGNTL PMRNIPVGST VHNVEMKPGK GGQLARSAGT YVQIVARDGA YVTLRLRSGE 190 200 210 220 230 240 MRKVEADCRA TLGEVGNAEH MLRVLGKAGA ARWRGVRPTV RGTAMNPVDH PHGGGEGRNF 250 260 270 GKHPVTPWGV QTKGKKTRSN KRTDKFIVRR RSK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure of the Escherichia coli S10 ribosomal protein operon." Zurawski G., Zurawski S.M. Nucleic Acids Res. 13:4521-4526(1985) [PubMed: 3892488] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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 protein L2 from the Escherichia coli ribosome." Kimura M., Mende L., Wittmann-Liebold B. FEBS Lett. 149:304-312(1982) Cited for: PROTEIN SEQUENCE OF 2-273.
[5]	"Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies." Urlaub H., Kruft V., Bischof O., Mueller E.-C., Wittmann-Liebold B. EMBO J. 14:4578-4588(1995) [PubMed: 7556101] [Abstract] Cited for: PROTEIN SEQUENCE OF 60-71 AND 200-208, CROSS-LINKING TO RRNA. Strain: MRE-600.
[6]	"Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes." Herold M., Nierhaus K.H. J. Biol. Chem. 262:8826-8833(1987) [PubMed: 3298242] [Abstract] Cited for: ASSEMBLY MAP OF THE 50S SUBUNIT. Strain: K12.
[7]	"Histidine 229 in protein L2 is apparently essential for 50S peptidyl transferase activity." Cooperman B.S., Wooten T., Romero D.P., Traut R.R. Biochem. Cell Biol. 73:1087-1094(1995) [PubMed: 8722025] [Abstract] Cited for: MUTAGENESIS OF HIS-230.
[8]	"Functional implications of ribosomal protein L2 in protein biosynthesis as shown by in vivo replacement studies." Uehlein M., Wegloehner W., Urlaub H., Wittmann-Liebold B. Biochem. J. 331:423-430(1998) [PubMed: 9531480] [Abstract] Cited for: PROTEIN REPLACEMENT STUDIES.
[9]	"Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transfer." Diedrich G., Spahn C.M.T., Stelzl U., Schaefer M.A., Wooten T., Bochkariov D.E., Cooperman B.S., Traut R.R., Nierhaus K.H. EMBO J. 19:5241-5250(2000) [PubMed: 11013226] [Abstract] Cited for: REQUIREMENT FOR 70S RIBOSOME FORMATION, TRNA-BINDING, MUTAGENESIS OF CONSERVED RESIDUES.
[10]	"Localization of the protein L2 in the 50 S subunit and the 70 S E. coli ribosome." Willumeit R., Forthmann S., Beckmann J., Diedrich G., Ratering R., Stuhrmann H.B., Nierhaus K.H. J. Mol. Biol. 305:167-177(2001) [PubMed: 11114255] [Abstract] Cited for: POSITION IN THE 50S SUBUNIT AND 70S RIBOSOME. Strain: MRE-600.
[11]	"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.
[12]	"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-242, MASS SPECTROMETRY.
[13]	"The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution." Mueller F., Sommer I., Baranov P., Matadeen R., Stoldt M., Woehnert J., Goerlach M., van Heel M., Brimacombe R. J. Mol. Biol. 298:35-59(2000) [PubMed: 10756104] [Abstract] Cited for: 3D-STRUCTURE MODELING.
[14]	"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.
[15]	"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. Strain: MRE-600.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X02613 Genomic DNA. Translation: CAA26463.1.
U18997 Genomic DNA. Translation: AAA58114.1.
U00096 Genomic DNA. Translation: AAC76342.1.
AP009048 Genomic DNA. Translation: BAE77974.1.

PIR

R5EC2. E23129.

RefSeq

AP_004473.1.
NP_417776.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1P85	electron microscopy	12.30	A	2-273	[»]
1P86	electron microscopy	11.50	A	2-273	[»]
1VS6	X-ray	3.46	C	1-273	[»]
1VS8	X-ray	3.46	C	1-273	[»]
2AW4	X-ray	3.46	C	1-273	[»]
2AWB	X-ray	3.46	C	1-273	[»]
2GYA	electron microscopy	15.00	A	39-264	[»]
2GYC	electron microscopy	15.00	A	39-265	[»]
2I2T	X-ray	3.22	C	2-272	[»]
2I2V	X-ray	3.22	C	2-272	[»]
2J28	electron microscopy	8.00	C	4-269	[»]
2QAM	X-ray	3.21	C	2-273	[»]
2QAO	X-ray	3.21	C	2-273	[»]
2QBA	X-ray	3.54	C	2-273	[»]
2QBC	X-ray	3.54	C	2-273	[»]
2QBE	X-ray	3.30	C	2-273	[»]
2QBG	X-ray	3.30	C	2-273	[»]
2QBI	X-ray	4.00	C	2-273	[»]
2QBK	X-ray	4.00	C	2-273	[»]
2QOV	X-ray	3.93	C	2-273	[»]
2QOX	X-ray	3.93	C	2-273	[»]
2QOZ	X-ray	3.50	C	2-273	[»]
2QP1	X-ray	3.50	C	2-273	[»]
2RDO	electron microscopy	9.10	C	2-273	[»]
2VHM	X-ray	3.74	C	1-273	[»]
2VHN	X-ray	3.74	C	1-273	[»]
2Z4L	X-ray	4.45	C	2-273	[»]
2Z4N	X-ray	4.45	C	2-273	[»]
3BBX	electron microscopy	10.00	C	1-273	[»]
3DF2	X-ray	3.50	C	1-273	[»]
3DF4	X-ray	3.50	C	1-273	[»]
3FIK	electron microscopy	6.70	C	2-272	[»]
487D	electron microscopy	7.50	I	62-172	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P60422. 359 interactions.

STRING

P60422.

2-D gel databases

ECO2DBASE

I030.2. 6TH EDITION.

Genome annotation databases

GeneID

947820.

GenomeReviews

Gene locus JW3279 in contig AP009048_GR.
Gene locus b3317 in contig U00096_GR.

KEGG

ecj:JW3279.
eco:b3317.

Organism-specific databases

EchoBASE

EB0858.

EcoGene

EG10865. rplB.

CMR

Search...

Phylogenomic databases

HOGENOM

P60422.

OMA

ASIEYDP.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10865-MON.

Gene expression databases

Genevestigator

P60422.

Family and domain databases

HAMAP

MF_01320.
[Tree]

InterPro

IPR012340. NA-bd_OB-fold.
IPR002171. Ribosomal_L2.
IPR005880. Ribosomal_L2_bac-type.
IPR014722. Transl_SH3-like_sub.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
G3DSA:2.30.30.30. Ribosomal_L2. 1 hit.

PANTHER

PTHR13691:SF5. Ribosom_L2_bac. 1 hit.
PTHR13691. Ribosomal_L2. 1 hit.

Pfam

PF00181. Ribosomal_L2. 1 hit.
PF03947. Ribosomal_L2_C. 1 hit.
[Graphical view]

PIRSF

PIRSF002158. Ribosomal_L2. 1 hit.

TIGRFAMs

TIGR01171. rplB_bact. 1 hit.

PROSITE

PS00467. RIBOSOMAL_L2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL2_ECOLI

Accession

Primary (citable) accession number: P60422
Secondary accession number(s): P02387, Q2M6Y2

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 79 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)