PDBsum entry 3cjs

Transferase/ribosomal protein

PDB id: 3cjs

Contents

Protein chains

58 a.a.

72 a.a. *

68 a.a. *

Ligands

EDO ×3

Waters ×255

* Residue conservation analysis

PDB id:

3cjs

Name:

Transferase/ribosomal protein

Title:

Minimal recognition complex between prma and ribosomal protein l11

Structure:

Ribosomal protein l11 methyltransferase. Chain: a. Fragment: n-terminal domain. Synonym: l11 mtase. Engineered: yes. 50s ribosomal protein l11. Chain: b, c. Fragment: n-terminal domain. Engineered: yes

Source:

Thermus thermophilus. Strain: hb8. Gene: prma. Expressed in: escherichia coli. Gene: rplk, rpl11.

Resolution:

1.37Å R-factor: 0.182 R-free: 0.206

Authors:

H.Demirci,S.T.Gregory,A.E.Dahlberg,G.Jogl

Key ref:

H.Demirci et al. (2008). Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure, 16, 1059-1066. PubMed id: 18611379 DOI: 10.1016/j.str.2008.03.016

Date:

13-Mar-08 Release date: 20-May-08

Protein chain

Q84BQ9  (PRMA_THET8) -  Ribosomal protein L11 methyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 254 a.a.

Struc: 58 a.a.

Protein chain

P36238  (RL11_THETH) -  Large ribosomal subunit protein uL11 from Thermus thermophilus

Seq: 147 a.a.

Struc: 72 a.a.

Protein chain

P36238  (RL11_THETH) -  Large ribosomal subunit protein uL11 from Thermus thermophilus

Seq: 147 a.a.

Struc: 68 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.2.1.1.- - ?????

DOI no: 10.1016/j.str.2008.03.016

Structure 16:1059-1066 (2008)

PubMed id: 18611379

Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.

H.Demirci, S.T.Gregory, A.E.Dahlberg, G.Jogl.

ABSTRACT

Ribosomal protein L11 is a universally conserved component of the large subunit, and plays a significant role during initiation, elongation, and termination of protein synthesis. In Escherichia coli, the lysine methyltransferase PrmA trimethylates the N-terminal alpha-amino group and the epsilon-amino groups of Lys3 and Lys39. Here, we report four PrmA-L11 complex structures in different orientations with respect to the PrmA active site. Two structures capture the L11 N-terminal alpha-amino group in the active site in a trimethylated post-catalytic state and in a dimethylated state with bound S-adenosyl-L-homocysteine. Two other structures show L11 in a catalytic orientation to modify Lys39 and in a noncatalytic orientation. The comparison of complex structures in different orientations with a minimal substrate recognition complex shows that the binding mode remains conserved in all L11 orientations, and that substrate orientation is brought about by the unusual interdomain flexibility of PrmA.

Selected figure(s)

Figure 1.
Figure 1. Substrate Binding in the Full-Length and Minimal PrmA-L11 Complex Structures
(A) Structure of the full-length complex 2 with the L11 N-terminal α-amino group placed in the active site.
(B) Structure of the minimal substrate recognition complex formed between the PrmA and L11 N-terminal domains. Interacting residues in the complex interface are shown as sticks.
(C) Least-squares alignment of both structures shows that substrate binding and orientation are conserved in both complexes.

Figure 4.
Figure 4. Comparison of Three Different L11 Orientations in Complex with PrmA
PrmA and L11 are colored cyan and yellow in the N-terminal position and blue and orange in the Lys39 position. The Met1 and Lys39 residues and the AdoHcy or AdoMet cofactors are shown as sticks.
(A) Structure of the L11 N terminus placed in the active site (complex 2).
(B) Structure of the noncatalytic L11 orientation (complex 4).
(C) Structure of L11 Lys39 placed in the active site (complex 1).
(D) Comparison of the L11 orientation in the two catalytic orientations.
(E) Close-up view of the position of the modified nitrogen atoms of the N-terminal amino group and Lys39.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1059-1066) copyright 2008.

Figures were selected by the author.