9IWF | pdb_00009iwf

crystal structure of P. beijingensis xanthine-II riboswitch in complex with xanthine

PDB DOI: https://doi.org/10.2210/pdb9IWF/pdb
NAKB: 9IWF

Classification: RNA
Organism(s): Paenibacillus beijingensis
Mutation(s): Yes

Deposited: 2024-07-25 Released: 2025-06-04
Deposition Author(s): Xu, X.C., Ren, A.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.219 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-based principles underlying ligand recognition of xanthine-II riboswitch.

Xu, X., He, M., Tai, X., Ren, Q., Shen, X., Li, C., Ren, A.

(2025) Sci China Life Sci 68: 2073-2084

PubMed: 40304919 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s11427-024-2800-0
Primary Citation Related Structures:
9IWF, 9IWG

PubMed Abstract:
Riboswitches are conserved RNA elements that specifically recognize the cognate metabolites and regulate downstream gene expression involved in the metabolic pathways. To date, two classes of xanthine-responsive riboswitches involved in xanthine homeostasis have been identified. The recently reported xanthine-II riboswitch originates from guanine riboswitch family, featuring a single U-to-G mutation and several nucleotide insertions. Here, we report the complex structure of xanthine-II riboswitch bound to xanthine. The tertiary structure of xanthine-II riboswitch adopts a three-way junction scaffold similar to that of guanine riboswitch. However, the distinctive mutation and insertions in xanthine-II riboswitch facilitate the formation of a highly specific binding pocket for xanthine, distinguishing it from guanine riboswitches. Xanthine is bound in the junction region, forming a base triple with C64 and the mutant nucleotide G37, and is sandwiched by one base pair U8-A38 and one base triple A7-C36-U65. Structural alignment and ligand recognition specificity of the xanthine-II riboswitch are further verified by ligand-binding assays of structure-based mutation using isothermal titration calorimetry. Furthermore, leveraging the ligand specificity of the xanthine-II riboswitch, we develop a highly specific and sensitive biosensor for xanthine detection by fusing xanthine-II riboswitch with Pepper fluorogenic aptamer, highlighting the potential applications of xanthine-II riboswitch in diagnosing diseases related to xanthine metabolism disorders.

Organizational Affiliation

Department of Cardiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.

Macromolecule Content

Total Structure Weight: 45.84 kDa
Atom Count: 3,133
Modeled Residue Count: 138
Deposited Residue Count: 138
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
P. beijingensis xanthine-II riboswitch (70-MER)	A, B	69	Paenibacillus beijingensis
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], M [auth B]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
XAN (Subject of Investigation/LOI) Query on XAN Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain L [auth A] mmCIF format, chain U [auth B] mmCIF format, chain L [auth A]	L [auth A], U [auth B]	XANTHINE C₅ H₄ N₄ O₂ LRFVTYWOQMYALW-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain U [auth B] Interactions & Density Focus chain L [auth A] Focus chain U [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]