3AWI | pdb_00003awi

Bifunctional tRNA modification enzyme MnmC from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3AWI/pdb

Classification: TRANSFERASE, OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-23 Released: 2011-06-01
Deposition Author(s): Kitamura, A., Sengoku, T., Nishimoto, M., Yokoyama, S., Bessho, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.251 (Depositor), 0.236 (DCC)
R-Value Work:
0.204 (Depositor), 0.196 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli

Kitamura, A., Sengoku, T., Nishimoto, M., Yokoyama, S., Bessho, Y.

(2011) Protein Sci

PubMed: 21574198 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.659
Primary Citation Related Structures:
3AWI

PubMed Abstract:
Post-transcriptional modifications of bases within the transfer RNAs (tRNA) anticodon significantly affect the decoding system. In bacteria and eukaryotes, uridines at the wobble position (U34) of some tRNAs are modified to 5-methyluridine derivatives (xm⁵U). These xm⁵U34-containing tRNAs read codons ending with A or G, whereas tRNAs with the unmodified U34 are able to read all four synonymous codons of a family box. In Escherichia coli (E.coli), the bifunctional enzyme MnmC catalyzes the two consecutive reactions that convert 5-carboxymethylaminomethyl uridine (cmnm⁵U) to 5-methylaminomethyl uridine (mnm⁵U). The C-terminal domain of MnmC (MnmC1) is responsible for the flavin adenine dinucleotide (FAD)-dependent deacetylation of cmnm⁵U to 5-aminomethyl uridine (nm⁵U), whereas the N-terminal domain (MnmC2) catalyzes the subsequent S-adenosyl-L-methionine-dependent methylation of nm⁵U, leading to the final product, mnm⁵U34. Here, we determined the crystal structure of E.coli MnmC containing FAD, at 3.0 Å resolution. The structure of the MnmC1 domain can be classified in the FAD-dependent glutathione reductase 2 structural family, including the glycine oxidase ThiO, whereas the MnmC2 domain adopts the canonical class I methyltransferase fold. A structural comparison with ThiO revealed the residues that may be involved in cmnm⁵U recognition, supporting previous mutational analyses. The catalytic sites of the two reactions are both surrounded by conserved basic residues for possible anticodon binding, and are located far away from each other, on opposite sides of the protein. These results suggest that, although the MnmC1 and MnmC2 domains are physically linked, they could catalyze the two consecutive reactions in a rather independent manner.

Organizational Affiliation

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Macromolecule Content

Total Structure Weight: 465.85 kDa
Atom Count: 30,287
Modeled Residue Count: 3,799
Deposited Residue Count: 4,128
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC	A, B, C, D, E A, B, C, D, E, F	688	Escherichia coli K-12	Mutation(s): 0 Gene Names: mnmC, yfcK, b2324, JW5380 EC: 2.1.1.61 (PDB Primary Data), 1.5 (PDB Primary Data)
UniProt
Find proteins for P77182 (Escherichia coli (strain K12)) Explore P77182 Go to UniProtKB: P77182
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77182
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain V [auth F] SDF format, chain T [auth E] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E]	G [auth A] J [auth B] M [auth C] Q [auth D] T [auth E] G [auth A], J [auth B], M [auth C], Q [auth D], T [auth E], V [auth F]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D], U [auth E], W [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.251 (Depositor), 0.236 (DCC)
R-Value Work: 0.204 (Depositor), 0.196 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.138	α = 90
b = 243.022	β = 90.42
c = 175.527	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations