50S ribosomal protein L1 - Escherichia coli (strain K12)

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P0A7L0 (RL1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 83. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
50S ribosomal protein L1

Gene names

Name:	rplA
Ordered Locus Names:	b3984, JW3947

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	234 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, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (Ref.16). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (Ref.16). Contacts the P and E site tRNAs. HAMAP-Rule MF_01318_B Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. HAMAP-Rule MF_01318_B
Subunit structure	Part of the 50S ribosomal subunit. Cross-links to the P and E site tRNAs. Ref.9
Sequence similarities	Belongs to the ribosomal protein L1P family.
Mass spectrometry	Molecular mass is 24598.9 Da from positions 2 - 234. Determined by MALDI. Ref.13

Ontologies

Keywords
Biological process	Translation regulation
Ligand	RNA-binding rRNA-binding tRNA-binding
Molecular function	Repressor Ribonucleoprotein Ribosomal protein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	negative regulation of translational initiation Inferred from direct assay PubMed 6354472. Source: EcoCyc translation Inferred from electronic annotation. Source: HAMAP
Cellular_component	large ribosomal subunit Inferred from electronic annotation. Source: InterPro
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...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
cspG	P0A978	2	EBI-543771,EBI-547581
thrS	P0A8M3	2	EBI-543771,EBI-551254

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5 Ref.7

Chain

2 – 234

233

50S ribosomal protein L1 HAMAP-Rule MF_01318_B

PRO_0000125654

Amino acid modifications

Modified residue

105

N6-succinyllysine Ref.15

Modified residue

154

N6-succinyllysine Ref.15

Modified residue

186

N6-succinyllysine Ref.15

Modified residue

197

N6-succinyllysine Ref.15

Experimental info

Sequence conflict

R → I AA sequence Ref.7

Secondary structure

234

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A7L0 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: D751704B34748D53
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FASTA

234

24,730

        10         20         30         40         50         60 
MAKLTKRMRV IREKVDATKQ YDINEAIALL KELATAKFVE SVDVAVNLGI DARKSDQNVR 

        70         80         90        100        110        120 
GATVLPHGTG RSVRVAVFTQ GANAEAAKAA GAELVGMEDL ADQIKKGEMN FDVVIASPDA 

       130        140        150        160        170        180 
MRVVGQLGQV LGPRGLMPNP KVGTVTPNVA EAVKNAKAGQ VRYRNDKNGI IHTTIGKVDF 

       190        200        210        220        230 
DADKLKENLE ALLVALKKAK PTQAKGVYIK KVSISTTMGA GVAVDQAGLS ASVN

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli." Post L.E., Strycharz G.D., Nomura M., Lewis H., Dennis P.P. Proc. Natl. Acad. Sci. U.S.A. 76:1697-1701(1979) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"The primary structure of protein L1 from the large ribosomal subunit of Escherichia coli." Brauer D., Oechsner I. FEBS Lett. 96:317-321(1978) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-234. Strain: K.
[6]	Erratum Brauer D., Oechsner I. FEBS Lett. 98:411-411(1979)
[7]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[8]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 199-203, CROSS-LINKING TO RRNA. Strain: MRE-600.
[9]	"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] [Europe PMC] [Abstract] Cited for: ASSEMBLY MAP OF THE 50S SUBUNIT. Strain: K12.
[10]	"Translational regulation of the L11 ribosomal protein operon of Escherichia coli: mutations that define the target site for repression by L1." Thomas M.S., Nomura M. Nucleic Acids Res. 15:3085-3096(1987) [PubMed] [Europe PMC] [Abstract] Cited for: MECHANISM OF TRANSLATION REGULATION. Strain: K12 / MC1061 / ATCC 53338 / DSM 7140.
[11]	"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] [Europe PMC] [Abstract] Cited for: CROSS-LINKING TO THE TRNA CENTRAL FOLD. Strain: MRE-600.
[12]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[13]	"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] [Europe PMC] [Abstract] Cited for: MASS SPECTROMETRY. Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[14]	"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] [Europe PMC] [Abstract] Cited for: 3D-STRUCTURE MODELING. Strain: MRE-600.
[15]	"Identification of lysine succinylation as a new post-translational modification." Zhang Z., Tan M., Xie Z., Dai L., Chen Y., Zhao Y. Nat. Chem. Biol. 7:58-63(2011) [PubMed] [Europe PMC] [Abstract] Cited for: SUCCINYLATION AT LYS-105; LYS-154; LYS-186 AND LYS-197. Strain: K12.
[16]	"Locking and unlocking of ribosomal motions." Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., Frank J. Cell 114:123-134(2003) [PubMed] [Europe PMC] [Abstract] Cited for: 3D-STRUCTURE MODELING OF RIBOSOMAL COMPLEXES IMPLYING THE INVOLVEMENT OF THE L1 STALK IN TRANSLOCATION OF TRNAS FROM THE P TO E SITE.
[17]	"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] [Europe PMC] [Abstract] Cited for: LOCALIZATION IN THE 3.5 ANGSTROM RIBOSOMAL STRUCTURES AND DISCUSSION OF ITS MOVEMENT. Strain: MRE-600.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V00339 Genomic DNA. Translation: CAA23622.1.
U00006 Genomic DNA. Translation: AAC43082.1.
U00096 Genomic DNA. Translation: AAC76958.1.
AP009048 Genomic DNA. Translation: BAE77336.1.

PIR

R5EC1. S12573.

RefSeq

NP_418411.1. NC_000913.2.
YP_491477.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EG0	electron microscopy	11.50	N	1-229	[»]
1ML5	electron microscopy	14.00	c	2-229	[»]
2GYA	electron microscopy	15.00	2	6-226	[»]
2GYC	electron microscopy	15.00	2	6-227	[»]
2RDO	electron microscopy	9.10	9	2-234	[»]
2WWQ	electron microscopy	5.80	5	1-234	[»]
3E1B	electron microscopy	9.00	Z	5-211	[»]
3E1D	electron microscopy	9.00	Z	5-211	[»]
3FIK	electron microscopy	6.70	5	1-234	[»]
3IZT	electron microscopy	-	C	1-234	[»]
3IZU	electron microscopy	-	C	1-234	[»]
3J01	electron microscopy	-	5	1-234	[»]
3J0T	electron microscopy	12.10	C	1-234	[»]
3J0W	electron microscopy	14.70	C	1-234	[»]
3J0Y	electron microscopy	13.50	C	1-234	[»]
3J11	electron microscopy	13.10	C	1-234	[»]
3J12	electron microscopy	11.50	C	1-234	[»]
3J14	electron microscopy	11.50	C	1-234	[»]
3KCR	electron microscopy	-	5	1-234	[»]
487D	electron microscopy	7.50	H	29-201	[»]

ProteinModelPortal

P0A7L0.

SMR

P0A7L0. Positions 1-234.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35746N.

IntAct

P0A7L0. 125 interactions.

MINT

MINT-1268287.

STRING

511145.b3984.

2D gel databases

SWISS-2DPAGE

P0A7L0.

Proteomic databases

PaxDb

P0A7L0.

PRIDE

P0A7L0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76958; AAC76958; b3984.
BAE77336; BAE77336; BAE77336.

GeneID

12930515.
948483.

KEGG

ecj:Y75_p3213.
eco:b3984.

PATRIC

32123489. VBIEscCol129921_4097.

Organism-specific databases

EchoBASE

EB0857.

EcoGene

EG10864. rplA.

Phylogenomic databases

eggNOG

COG0081.

HOGENOM

HOG000207015.

K02863.

OMA

AKGRYVK.

ProtClustDB

PRK05424.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10864-MONOMER.
ECOL316407:JW3947-MONOMER.

Gene expression databases

Genevestigator

P0A7L0.

Family and domain databases

Gene3D

3.30.190.20. 2 hits.
3.40.50.790. 1 hit.

HAMAP

MF_01318_B. Ribosomal_L1_B.

InterPro

IPR005878. Ribosom_L1_bac-type.
IPR002143. Ribosomal_L1.
IPR016094. Ribosomal_L1_2-a/b-sand.
IPR016095. Ribosomal_L1_3-a/b-sand.
IPR023673. Ribosomal_L1_CS.
IPR023674. Ribosomal_L1_SF.
[Graphical view]

Pfam

PF00687. Ribosomal_L1. 1 hit.
[Graphical view]

PIRSF

PIRSF002155. Ribosomal_L1. 1 hit.

SUPFAM

SSF56808. Ribosomal_L1. 1 hit.

TIGRFAMs

TIGR01169. rplA_bact. 1 hit.

PROSITE

PS01199. RIBOSOMAL_L1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A7L0.

Entry information

Entry name

RL1_ECOLI

Accession

Primary (citable) accession number: P0A7L0
Secondary accession number(s): P02384, Q2M8S0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 83 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

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents