1YUB | pdb_00001yub

SOLUTION STRUCTURE OF AN RRNA METHYLTRANSFERASE (ERMAM) THAT CONFERS MACROLIDE-LINCOSAMIDE-STREPTOGRAMIN ANTIBIOTIC RESISTANCE, NMR, MINIMIZED AVERAGE STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1YUB/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-03-04 Released: 1998-03-04 
• Deposition Author(s): Yu, L., Petros, A.M., Schnuchel, A., Zhong, P., Severin, J.M., Walter, K., Holzman, T.F., Fesik, S.W.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 17 
• Conformers Submitted: 1 
• Selection Criteria: LOWEST ENERGY AND LEAST RESTRAINT VIOLATION 

Literature

Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance.

Yu, L., Petros, A.M., Schnuchel, A., Zhong, P., Severin, J.M., Walter, K., Holzman, T.F., Fesik, S.W.

(1997) Nat Struct Biol 4: 483-489

• PubMed: 9187657 
• DOI: https://doi.org/10.1038/nsb0697-483
• Primary Citation Related Structures: 
  1YUB


• PubMed Abstract: 
  

  The Erm family of methyltransferases is responsible for the development of resistance to the macrolide-lincosamide-streptogramin type B (MLS) antibiotics. These enzymes methylate an adenine of 23S ribosomal RNA that prevents the MLS antibiotics from binding to the ribosome and exhibiting their antibacterial activity. Here we describe the three-dimensional structure of an Erm family member, ErmAM, as determined by NMR spectroscopy. The catalytic domain of ErmAM is structurally similar to that found in other methyltransferases and consists of a seven-stranded beta-sheet flanked by alpha-helices and a small two-stranded beta-sheet. In contrast to the catalytic domain, the substrate binding domain is different from other methyltransferases and adopts a novel fold that consists of four alpha-helices.

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Organizational Affiliation: 
• Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.86 kDa 
• Atom Count: 2,039 
• Modeled Residue Count: 245 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RRNA METHYLTRANSFERASE	A	245	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ERM EC: 2.1.1.48 (PDB Primary Data), 2.1.1.184 (UniProt)
UniProt
Find proteins for P21236 (Streptococcus pneumoniae) Explore P21236  Go to UniProtKB:  P21236

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 17 
• Conformers Submitted: 1 
• Selection Criteria: LOWEST ENERGY AND LEAST RESTRAINT VIOLATION 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-04 
Deposition Author(s): Yu, L., Petros, A.M., Schnuchel, A., Zhong, P., Severin, J.M., Walter, K., Holzman, T.F., Fesik, S.W.

Revision History  

• Version 1.0: 1998-03-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection