3PS9

Crystal structure of MnmC from E. coli

• PDB DOI: https://doi.org/10.2210/pdb3PS9/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli BL21
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-01 Released: 2010-12-22 
• Deposition Author(s): Kim, J., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.247 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.

Kim, J., Almo, S.C.

(2013) BMC Struct Biol 13: 5-5

• PubMed: 23617613 
• DOI: https://doi.org/10.1186/1472-6807-13-5
• Primary Citation of Related Structures:  
  3PS9, 3PVC, 3SGL


• PubMed Abstract: 
  

  Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34).

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Organizational Affiliation: 

Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.56 kDa 
• Atom Count: 5,523 
• Modelled Residue Count: 668 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC	A	676	Escherichia coli BL21	Mutation(s): 0  Gene Names: B21_02209, mnmC, yfcK EC: 2.1.1.61

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.247 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.063	α = 90
b = 100.063	β = 90
c = 159.19	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Kim, J., Almo, S.C.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2013-08-21
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations