PDBsum entry 2nxn

Transferase

PDB id: 2nxn

Contents

Protein chains

250 a.a. *

139 a.a. *

Waters ×95

* Residue conservation analysis

PDB id:

2nxn

Name:

Transferase

Title:

T. Thermophilus ribosomal protein l11 methyltransferase (prma) in complex with ribosomal protein l11

Structure:

Ribosomal protein l11 methyltransferase. Chain: a. Synonym: l11 mtase. Engineered: yes. 50s ribosomal protein l11. Chain: b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: prma. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rplk, rpl11.

Resolution:

2.40Å R-factor: 0.223 R-free: 0.273

Authors:

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

Key ref:

H.Demirci et al. (2007). Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA. EMBO J, 26, 567-577. PubMed id: 17215866 DOI: 10.1038/sj.emboj.7601508

Date:

17-Nov-06 Release date: 26-Dec-06

Protein chain

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

Seq: 254 a.a.

Struc: 250 a.a.

Protein chain

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

Seq: 147 a.a.

Struc: 139 a.a.

Enzyme reactions

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

DOI no: 10.1038/sj.emboj.7601508

EMBO J 26:567-577 (2007)

PubMed id: 17215866

Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.

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

ABSTRACT

Bacterial ribosomal protein L11 is post-translationally trimethylated at multiple residues by a single methyltransferase, PrmA. Here, we describe four structures of PrmA from the extreme thermophile Thermus thermophilus. Two apo-PrmA structures at 1.59 and 2.3 A resolution and a third with bound cofactor S-adenosyl-L-methionine at 1.75 A each exhibit distinct relative positions of the substrate recognition and catalytic domains, revealing how PrmA can position the L11 substrate for multiple, consecutive side-chain methylation reactions. The fourth structure, the PrmA-L11 enzyme-substrate complex at 2.4 A resolution, illustrates the highly specific interaction of the N-terminal domain with its substrate and places Lys39 in the PrmA active site. The presence of a unique flexible loop in the cofactor-binding site suggests how exchange of AdoMet with the reaction product S-adenosyl-L-homocysteine can occur without necessitating the dissociation of PrmA from L11. Finally, the mode of interaction of PrmA with L11 explains its observed preference for L11 as substrate before its assembly into the 50S ribosomal subunit.

Selected figure(s)

Figure 4.
Figure 4 The PrmA–L11 complex structure. (A) Cartoon representation of the overall structure. PrmA and L11 are colored in salmon and cyan. The Lys39 side chain is shown in a stick representation. (B) Final 2F[o]-F[c] density for the active site region contoured at the 1 level. (C) Ribbon diagram of binding interactions between the PrmA N-terminal domain and L11. (D) Ribbon diagram of binding interactions between the PrmA catalytic domain and L11. (E) Stereo representation comparing the PrmA–L11 complex with the L11–RNA complex (PDB code 1MMS) after least-squares alignment of L11. PrmA is colored in salmon and L11 is colored in cyan in the PrmA complex and in blue in the RNA complex. RNA is shown in yellow.

Figure 5.
Figure 5 The active site of PrmA. (A) Stereo representation of the active site. The position of AdoMet and Phe99 is modeled by least-squares alignment from the position observed in PrmA3. (B, C) Comparison of the PrmA surface in the complex structure (B, flexible loop absent) with the cofactor-bound structure PrmA3 (C, flexible loop present, L11 surface is shown for reference).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 567-577) copyright 2007.

Figures were selected by an automated process.