PDBsum entry: 2qgq

Structural genomics, unknown function

PDB-id: 2qgq

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Protein chains

272 a.a. *

Ligands

CXS ×4

Waters ×1443

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2qgq

Name:

Structural genomics, unknown function

Title:

Crystal structure of tm_1862 from thermotoga maritima. Northeast structural genomics consortium target vr77

Structure:

Protein tm_1862. Chain: a, b, c, d, e, f, g, h. Fragment: residues 135-430, see remark 999. Engineered: yes

Source:

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8, dsm 3109, jcm 10099. Atcc: 43589. Gene: tm_1862. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B, C, D, E, F, G, H: Q9X2H6 (RIMO_THEMA)

Seq:

Struc:

Seq:

430 a.a.

Struc:

272 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.00Å

R-factor:

0.212

R-free:

0.251

Authors:

F.Forouhar,H.Neely,M.Hussain,J.Seetharaman,Y.Fang,C.X.Chen, K.Cunningham,K.Conover,L-C.Ma,R.Xiao,T.B.Acton, G.T.Montelione,L.Tong,J.F.Hunt,Northeast Structural Genomics Consortium (Nesg)

Key ref:

S.Arragain et al. (2009). Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical-SAM methylthiotransferase.. J Biol Chem, 285, 5792-5801. [PubMed id: 20007320] [DOI: 10.1074/jbc.M109.065516]

Date:

29-Jun-07

Release date:

17-Jul-07

Related entries:

Vr77 related db: targetdb

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Key reference

DOI no: 10.1074/jbc.M109.065516

J Biol Chem 285:5792-5801 (2009)

PubMed id: 20007320

Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical-SAM methylthiotransferase.

S.Arragain, R.Garcia-Serres, G.Blondin, T.Douki, M.Clemancey, J.M.Latour, F.Forouhar, H.Neely, G.T.Montelione, J.F.Hunt, E.Mulliez, M.Fontecave, M.Atta.

ABSTRACT

Post translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene was involved in generation of the 3-methylthio derivative of residue asp-89 in ribosomal protein S12 (Anton, B. P., et al. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine-37 near the anticodon of several tRNAs. We herein present spectroscopic evidence that T. maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical-SAM domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bis-methylthio derivatives. Finally, we present the 2.0 angstrom crystal structure of the central radical-SAM and the C-terminal TRAM domains in apo RimO. While the core of the open TIM-barrel of the radical-SAM domain is conserved, RimO shows differences in domain organization compared to other radical-SAM enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical-SAM domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM-barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical-SAM enzymes in the MiaB/RimO family.