P68919 (RL25_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
50S ribosomal protein L25

Gene names

Name:	rplY
Ordered Locus Names:	b2185, JW2173

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	94 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA. HAMAP MF_01336
Subunit structure	Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Ref.11
Sequence similarities	Belongs to the ribosomal protein L25P family.
Mass spectrometry	Molecular mass is 10693.4 Da from positions 1 - 94. Determined by MALDI. Ref.14

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	5S rRNA binding Inferred from electronic annotation. Source: InterPro structural constituent of ribosome Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaK	P0A6Y8	1	EBI-553087,EBI-542092

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 94

94

50S ribosomal protein L25 HAMAP MF_01336

PRO_0000181478

Experimental info

Sequence conflict

86 – 94

9

LQHIDFVRA → CSTSTSFALNC in AAA16413. Ref.6

Secondary structure

1

.

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.

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94

Helix Strand Turn

Details...

Beta strand

3 – 5

3

Helix

14 – 22

9

Beta strand

25 – 31

7

Beta strand

33 – 35

3

Beta strand

38 – 43

6

Helix

44 – 50

7

Helix

54 – 57

4

Beta strand

61 – 65

5

Beta strand

72 – 79

8

Beta strand

81 – 84

4

Beta strand

86 – 93

8

Sequences

	Sequence		Length	Mass (Da)
	P68919 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 85DAF5ACBA1C5F86	FASTA	94	10,693
	10 20 30 40 50 60 MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV 70 80 90 LTIVVDGKEI KVKAQDVQRH PYKPKLQHID FVRA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The primary structure of the 5S RNA binding protein L25 from Escherichia coli ribosomes." Dovgas N.V., Markova L.F., Mednikova T.A., Vinokurov L.M., Alakhov Y.B., Ovchinnikov Y.A. FEBS Lett. 53:351-354(1975) [PubMed: 1093874] [Abstract] Cited for: PROTEIN SEQUENCE. Strain: MRE-600.
[2]	Erratum Dovgas N.V., Markova L.F., Mednikova T.A., Vinokurov L.M., Alakhov Y.B., Ovchinnikov Y.A. FEBS Lett. 57:305-305(1975) Cited for: SEQUENCE REVISION.
[3]	"The primary structure of the 5s rRNA binding protein L25 of Escherichia coli ribosomes." Bitar K.G., Wittmann-Liebold B. Hoppe-Seyler's Z. Physiol. Chem. 356:1343-1352(1975) [PubMed: 1100506] [Abstract] Cited for: PROTEIN SEQUENCE. Strain: K12.
[4]	"Primary structure of the protein L25 from the ribosomes of E. coli MRE-600 forming part of the 5S-RNA-protein complex." Alakhov Y.B., Vinokurov L.M., Dovgas N.V., Markova L.F., Mednikova T.A., Motuz L.P., Kashparov I.A., Ovchinnikov Y.A. Bioorg. Khim. 2:5-18(1976) Cited for: PROTEIN SEQUENCE. Strain: MRE-600.
[5]	"Cloning, characterization, and physical location of the rplY gene which encodes ribosomal protein L25 in Escherichia coli K12." Uemura Y., Isono S., Isono K. Mol. Gen. Genet. 226:341-344(1991) [PubMed: 2034228] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[6]	"Automated multiplex sequencing of the E.coli genome." Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / BHB2600.
[7]	"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.
[8]	"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.
[9]	"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: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[10]	"Small genes/gene-products in Escherichia coli K-12." Wasinger V.C., Humphery-Smith I. FEMS Microbiol. Lett. 169:375-382(1998) [PubMed: 9868784] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-10. Strain: K12.
[11]	"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, BINDING TO 5S RRNA. Strain: K12.
[12]	"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.
[13]	"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 THE 5S RRNA/L5/L18/L25 SUBCOMPLEX. Strain: K12 / A19.
[14]	"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.
[15]	"The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases." Stoldt M., Woehnert J., Goerlach M., Brown L.R. EMBO J. 17:6377-6384(1998) [PubMed: 9799245] [Abstract] Cited for: STRUCTURE BY NMR IN COMPLEX WITH A FRAGMENT OF 5S RRNA. Strain: MRE-600.
[16]	"The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition." Stoldt M., Woehnert J., Ohlenschlaeger O., Goerlach M., Brown L.R. EMBO J. 18:6508-6521(1999) [PubMed: 10562563] [Abstract] Cited for: STRUCTURE BY NMR IN COMPLEX WITH A FRAGMENT OF 5S RRNA.
[17]	"Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution." Lu M., Steitz T.A. Proc. Natl. Acad. Sci. U.S.A. 97:2023-2028(2000) [PubMed: 10696113] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) BOUND TO A FRAGMENT OF 5S RRNA.
[18]	"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.
[19]	"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). Strain: MRE-600.
[20]	"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

EMBL
GenBank
DDBJ

D13326 Genomic DNA. Translation: BAA02585.1.
U00008 Genomic DNA. Translation: AAA16413.1.
U00096 Genomic DNA. Translation: AAC75246.1.
AP009048 Genomic DNA. Translation: BAE76650.1.

PIR

R5EC25. S16002.

RefSeq

NP_416690.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B75	NMR	-	A	1-94	[»]
1D6K	NMR	-	A	1-94	[»]
1DFU	X-ray	1.80	P	1-94	[»]
1ML5	electron microscopy	14.00	v	1-94	[»]
1P85	electron microscopy	12.30	T	1-94	[»]
1P86	electron microscopy	11.50	T	1-94	[»]
1VS6	X-ray	3.46	V	1-94	[»]
1VS8	X-ray	3.46	V	1-94	[»]
1VT2	X-ray	3.30	V	1-94	[»]
2AW4	X-ray	3.46	V	1-94	[»]
2AWB	X-ray	3.46	V	1-94	[»]
2GYA	electron microscopy	15.00	T	1-94	[»]
2GYC	electron microscopy	15.00	T	1-94	[»]
2I2T	X-ray	3.22	V	1-94	[»]
2I2V	X-ray	3.22	V	1-94	[»]
2J28	electron microscopy	8.00	V	1-94	[»]
2QAM	X-ray	3.21	V	1-94	[»]
2QAO	X-ray	3.21	V	1-94	[»]
2QBA	X-ray	3.54	V	1-94	[»]
2QBC	X-ray	3.54	V	1-94	[»]
2QBE	X-ray	3.30	V	1-94	[»]
2QBG	X-ray	3.30	V	1-94	[»]
2QBI	X-ray	4.00	V	1-94	[»]
2QBK	X-ray	4.00	V	1-94	[»]
2QOV	X-ray	3.93	V	1-94	[»]
2QOX	X-ray	3.93	V	1-94	[»]
2QOZ	X-ray	3.50	V	1-94	[»]
2QP1	X-ray	3.50	V	1-94	[»]
2RDO	electron microscopy	9.10	V	1-94	[»]
2VHM	X-ray	3.74	V	1-94	[»]
2VHN	X-ray	3.74	V	1-94	[»]
2WWQ	electron microscopy	5.80	W	1-94	[»]
2Z4L	X-ray	4.45	V	1-94	[»]
2Z4N	X-ray	4.45	V	1-94	[»]
3BBX	electron microscopy	10.00	V	1-94	[»]
3DF2	X-ray	3.50	V	1-94	[»]
3DF4	X-ray	3.50	V	1-94	[»]
3E1B	electron microscopy	-	C	1-94	[»]
3E1D	electron microscopy	-	C	1-94	[»]
3FIK	electron microscopy	6.70	V	1-94	[»]
3I1N	X-ray	3.19	V	1-94	[»]
3I1P	X-ray	3.19	V	1-94	[»]
3I1R	X-ray	3.81	V	1-94	[»]
3I1T	X-ray	3.81	V	1-94	[»]
3I20	X-ray	3.71	V	1-94	[»]
3I22	X-ray	3.71	V	1-94	[»]
3IZT	electron microscopy	-	W	1-94	[»]
3IZU	electron microscopy	-	W	1-94	[»]
3J01	electron microscopy	-	V	1-94	[»]
3KCR	electron microscopy	-	V	1-94	[»]
3OAS	X-ray	3.25	V	1-94	[»]
3OAT	X-ray	3.25	V	1-94	[»]
3OFC	X-ray	3.19	V	1-94	[»]
3OFD	X-ray	3.19	V	1-94	[»]
3OFQ	X-ray	3.10	V	1-94	[»]
3OFR	X-ray	3.10	V	1-94	[»]
3OFZ	X-ray	3.29	V	1-94	[»]
3OG0	X-ray	3.29	V	1-94	[»]
3ORB	X-ray	3.30	V	1-94	[»]
3R8S	X-ray	3.00	V	1-94	[»]
3R8T	X-ray	3.00	V	1-94	[»]
487D	electron microscopy	7.50	N	1-94	[»]

ProteinModelPortal

P68919.

SMR

P68919. Positions 1-94.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35885N.

IntAct

P68919. 13 interactions.

MINT

MINT-1261165.

2D gel databases

SWISS-2DPAGE

P68919.

ECO2DBASE

I011.8. 6TH EDITION.

Proteomic databases

PRIDE

P68919.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000004867; EBESCP00000004867; EBESCG00000003972.
EBESCT00000017264; EBESCP00000016555; EBESCG00000016323.

GeneID

945618.

GenomeReviews

Gene locus JW2173 in contig AP009048_GR.
Gene locus b2185 in contig U00096_GR.

KEGG

ecj:JW2173.
eco:b2185.

PATRIC

32119725. VBIEscCol129921_2273.

Organism-specific databases

EchoBASE

EB0878.

EcoGene

EG10885. rplY.

Phylogenomic databases

eggNOG

COG1825.

GeneTree

EBGT00050000010534.

HOGENOM

HBG289682.

OMA

SIELDHD.

PhylomeDB

P68919.

ProtClustDB

PRK05943.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10885-MONOMER.

Gene expression databases

Genevestigator

P68919.

Family and domain databases

HAMAP

MF_01336. Ribosomal_L25.
[Tree]

InterPro

IPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020055. Ribosomal_L25_short.
[Graphical view]

Gene3D

G3DSA:2.40.240.10. Rbsml_L25/Gln-tRNA_synth_b-brl. 1 hit.

KO

K02897.

Pfam

PF01386. Ribosomal_L25p. 1 hit.
[Graphical view]

ProDom

PD012503. Ribosomal_L25. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF50715. Ribosomal_L25rel. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RL25_ECOLI

Accession

Primary (citable) accession number: P68919
Secondary accession number(s): P02426, Q2MAQ6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	January 25, 2012
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program