PDBsum entry 1b75

RNA binding protein

PDB id

1b75

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Contents

			Protein chain

					94 a.a. *

* Residue conservation analysis

PDB id:

1b75

Links

Name:

RNA binding protein

Title:

Solution structure of ribosomal protein l25 from escherichia coli

Structure:

Protein (50s ribosomal protein l25). Chain: a

Source:

Escherichia coli. Organism_taxid: 562. Strain: mre 600

NMR struc:

10 models

Authors:

M.Stoldt,J.Woehnert,M.Goerlach,L.R.Brown

Key ref:

M.Stoldt et al. (1998). The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases. Embo J, 17, 6377-6384. PubMed id: 9799245

Date:

27-Jan-99

Release date:

26-Jan-00

PROCHECK

	Headers

	References

Protein chain

P68919 (RL25_ECOLI) - Large ribosomal subunit protein bL25 from Escherichia coli (strain K12)

Seq: Struc:					94 a.a. 94 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	Embo J 17:6377-6384 (1998)
PubMed id: 9799245

The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
M.Stoldt, J.Wöhnert, M.Görlach, L.R.Brown.

ABSTRACT

The structure of the Escherichia coli ribosomal protein L25 has been determined to an r.m.s. displacement of backbone heavy atoms of 0.62 +/- 0.14 A by multi-dimensional heteronuclear NMR spectroscopy on protein samples uniformly labeled with 15N or 15N/13C. L25 shows a new topology for RNA-binding proteins consisting of a six-stranded beta-barrel and two alpha-helices. A putative RNA-binding surface for L25 has been obtained by comparison of backbone 15N chemical shifts for L25 with and without a bound cognate RNA containing the eubacterial E-loop that is the site for binding of L25 to 5S ribosomal RNA. Sequence comparisons with related proteins, including the general stress protein, CTC, show that the residues involved in RNA binding are highly conserved, thereby providing further confirmation of the binding surface. Tertiary structure comparisons indicate that the six-stranded beta-barrels of L25 and of the tRNA anticodon-binding domain of glutaminyl-tRNA synthetase are similar.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20544375

C.Richter, H.Kovacs, J.Buck, A.Wacker, B.Fürtig, W.Bermel, and H.Schwalbe (2010).
13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides.

J Biomol NMR, 47, 259-269.

18298371

A.V.Korobeinikova, G.M.Gongadze, A.P.Korepanov, B.D.Eliseev, M.V.Bazhenova, and M.B.Garber (2008).
5S rRNA-recognition module of CTC family proteins and its evolution.

Biochemistry (Mosc), 73, 156-163.

17605815

A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.

Biol Direct, 2, 18.

17407165

K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.

Proteins, 68, 109-122.

16604424

B.Bardiaux, T.E.Malliavin, M.Nilges, and A.K.Mazur (2006).
Comparison of different torsion angle approaches for NMR structure determination.

J Biomol NMR, 34, 153-166.

17021109

M.Mueller, S.Bunk, I.Diterich, M.Weichel, C.Rauter, D.Hassler, C.Hermann, R.Crameri, and T.Hartung (2006).
Identification of Borrelia burgdorferi ribosomal protein L25 by the phage surface display method and evaluation of the protein's value for serodiagnosis.

J Clin Microbiol, 44, 3778-3780.

15718233

G.M.Gongadze, A.P.Korepanov, E.A.Stolboushkina, N.V.Zelinskaya, A.V.Korobeinikova, M.V.Ruzanov, B.D.Eliseev, O.S.Nikonov, S.V.Nikonov, M.B.Garber, and V.I.Lim (2005).
The crucial role of conserved intermolecular H-bonds inaccessible to the solvent in formation and stabilization of the TL5.5 SrRNA complex.

J Biol Chem, 280, 16151-16156.

15665103

J.Noeske, C.Richter, M.A.Grundl, H.R.Nasiri, H.Schwalbe, and J.Wöhnert (2005).
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs.

Proc Natl Acad Sci U S A, 102, 1372-1377.

14731275

J.Zhong, and A.G.Barbour (2004).
Cross-species hybridization of a Borrelia burgdorferi DNA array reveals infection- and culture-associated genes of the unsequenced genome of the relapsing fever agent Borrelia hermsii.

Mol Microbiol, 51, 729-748.

15339800

K.Réblová, N.Spacková, J.Koca, N.B.Leontis, and J.Sponer (2004).
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.

Biophys J, 87, 3397-3412.

14523911

B.Fürtig, C.Richter, J.Wöhnert, and H.Schwalbe (2003).
NMR spectroscopy of RNA.

Chembiochem, 4, 936-962.

12513990

R.Gardan, O.Duché, S.Leroy-Sétrin, and J.Labadie (2003).
Role of ctc from Listeria monocytogenes in osmotolerance.

Appl Environ Microbiol, 69, 154-161.

12399033

O.Duché, F.Trémoulet, A.Namane, and J.Labadie (2002).
A proteomic analysis of the salt stress response of Listeria monocytogenes.

FEMS Microbiol Lett, 215, 183-188.

11911365

R.Zell, K.Sidigi, E.Bucci, A.Stelzner, and M.Görlach (2002).
Determinants of the recognition of enteroviral cloverleaf RNA by coxsackievirus B3 proteinase 3C.

RNA, 8, 188-201.

11418764

R.Fedorov, V.Meshcheryakov, G.Gongadze, N.Fomenkova, N.Nevskaya, M.Selmer, M.Laurberg, O.Kristensen, S.Al-Karadaghi, A.Liljas, M.Garber, and S.Nikonov (2001).
Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.

Acta Crystallogr D Biol Crystallogr, 57, 968-976.

PDB code:

1feu

11350033

T.Nakashima, M.Yao, S.Kawamura, K.Iwasaki, M.Kimura, and I.Tanaka (2001).
Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

RNA, 7, 692-701.

PDB code:

1iq4

10675344

B.L.Staker, P.Korber, J.C.Bardwell, and M.A.Saper (2000).
Structure of Hsp15 reveals a novel RNA-binding motif.

EMBO J, 19, 749-757.

PDB code:

1dm9

10799526

D.I.Svergun, and K.H.Nierhaus (2000).
A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.

J Biol Chem, 275, 14432-14439.

10696113

M.Lu, and T.A.Steitz (2000).
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.

Proc Natl Acad Sci U S A, 97, 2023-2028.

PDB code:

1dfu

10592262

M.Szymanski, and J.Barciszewski (2000).
Aminoacyl-tRNA synthetases database Y2K.

Nucleic Acids Res, 28, 326-328.

10592212

M.Szymanski, M.Z.Barciszewska, J.Barciszewski, and V.A.Erdmann (2000).
5S ribosomal RNA database Y2K.

Nucleic Acids Res, 28, 166-167.

10408894

A.Danchin (1999).
From protein sequence to function.

Curr Opin Struct Biol, 9, 363-367.

10454606

J.Wöhnert, A.J.Dingley, M.Stoldt, M.Görlach, S.Grzesiek, and L.R.Brown (1999).
Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy.

Nucleic Acids Res, 27, 3104-3110.

10430882

M.Sissler, C.Delorme, J.Bond, S.D.Ehrlich, P.Renault, and C.Francklyn (1999).
An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis.

Proc Natl Acad Sci U S A, 96, 8985-8990.

10562563

M.Stoldt, J.Wöhnert, O.Ohlenschläger, M.Görlach, and L.R.Brown (1999).
The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.

EMBO J, 18, 6508-6521.

PDB code:

1d6k

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.