5HR7

X-ray crystal structure of C118A RlmN from Escherichia coli with cross-linked in vitro transcribed tRNA

PDB DOI: https://doi.org/10.2210/pdb5HR7/pdb
NAKB: 5HR7

Classification: OXIDOREDUCTASE/RNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-22 Released: 2016-04-13
Deposition Author(s): Schwalm, E.L., Grove, T.L., Booker, S.J., Boal, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247
R-Value Work: 0.216
R-Value Observed: 0.217

Starting Models: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA.

Schwalm, E.L., Grove, T.L., Booker, S.J., Boal, A.K.

(2016) Science 352: 309-312

PubMed: 27081063 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.aad5367
Primary Citation of Related Structures:
5HR6, 5HR7

PubMed Abstract:
RlmN is a dual-specificity RNA methylase that modifies C2 of adenosine 2503 (A2503) in 23S rRNA and C2 of adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNAs). A related methylase, Cfr, modifies C8 of A2503 via a similar mechanism, conferring resistance to multiple classes of antibiotics. Here, we report the x-ray structure of a key intermediate in the RlmN reaction, in which a Cys(118)→Ala variant of the protein is cross-linked to a tRNA(Glu)substrate through the terminal methylene carbon of a formerly methylcysteinyl residue and C2 of A37. RlmN contacts the entire length of tRNA(Glu), accessing A37 by using an induced-fit strategy that completely unfolds the tRNA anticodon stem-loop, which is likely critical for recognition of both tRNA and ribosomal RNA substrates.

Organizational Affiliation

Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.

Macromolecule Content

Total Structure Weight: 141.23 kDa
Atom Count: 8,837
Modelled Residue Count: 860
Deposited Residue Count: 960
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual-specificity RNA methyltransferase RlmN	C [auth B], D [auth A]	404	Escherichia coli	Mutation(s): 0 Gene Names: rlmN, EcE24377A_2801 EC: 2.1.1.192
UniProt
Find proteins for P36979 (Escherichia coli (strain K12)) Explore P36979 Go to UniProtKB: P36979
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36979
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA Glu	A [auth D], B [auth C]	76	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain O [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth A]	L [auth B], O [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain O [auth A] Interactions & Density Focus chain L [auth B] Focus chain O [auth A]
5AD Query on 5AD Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain P [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth A]	M [auth B], P [auth A]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain M [auth B] Focus chain P [auth A] Interactions & Density Focus chain M [auth B] Focus chain P [auth A]
MET Query on MET Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Q [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth A]	N [auth B], Q [auth A]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain N [auth B] Focus chain Q [auth A] Interactions & Density Focus chain N [auth B] Focus chain Q [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain F [auth D] SDF format, chain G [auth D] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain E [auth D] MOL2 format, chain F [auth D] MOL2 format, chain G [auth D] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain E [auth D] mmCIF format, chain F [auth D] mmCIF format, chain G [auth D] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	E [auth D] F [auth D] G [auth D] H [auth C] I [auth C] E [auth D], F [auth D], G [auth D], H [auth C], I [auth C], J [auth C], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS Query on CAS	C [auth B], D [auth A]	L-PEPTIDE LINKING	C₅ H₁₂ As N O₂ S		CYS
SMC Query on SMC	C [auth B], D [auth A]	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247
R-Value Work: 0.216
R-Value Observed: 0.217
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.717	α = 90
b = 70.383	β = 90.11
c = 151.81	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2016-04-27
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary