30XM | pdb_000030xm

Engineered pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina barkeri (Mb) in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb30XM/pdb

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

Deposited: 2026-05-15 Released: 2026-08-26
Deposition Author(s): Wanka, V., Kvasha, D., Cigler, M., Heymes-Krauskopf, K., Ruckgaber, P., Heider, A., Fottner, M., Groll, M., Lang, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Genetically Encoded Electrophilic Lysine Derivative Enables Sortase-Mediated Assembly of SUMO Activity-Based Probes.

Wanka, V., Kvasha, D., Cigler, M., Heymes-Krauskopf, K., Ruckgaber, P., Heider, A., Fottner, M., Groll, M., Lang, K.

(2026) J Am Chem Soc

PubMed: 42682006 Search on PubMed
DOI: https://doi.org/10.1021/jacs.6c10081
Primary Citation Related Structures:
30XL, 30XM

PubMed Abstract:
Activity-based probes (ABPs) have become powerful tools for profiling enzymes that write and erase ubiquitin (Ub) and ubiquitin-like modifier (Ubl) signals. Extending this strategy to small ubiquitin-like modifier (SUMO)-specific proteases in defined substrate contexts remains challenging, because site-specific SUMO attachment must be combined with precise electrophile placement near the scissile isopeptide linkage. Here, we introduce a sortase-enabled chemoenzymatic platform for generating SUMO ABPs ranging from monoSUMO probes to native-like SUMO-substrate conjugates. The engineered sortase Srt2A ligates SUMO variants to glycine-bearing electrophiles, providing facile access to monoSUMO probes that trap deSUMOylases in vitro, in cellular lysates, and in living cells. To generate SUMO-substrate probes, we develop AzGVAisoK, a genetically encodable bifunctional lysine derivative containing both an azide-protected sortase handle and a vinyl amide electrophile. An engineered pyrrolysyl-tRNA synthetase/tRNA pair enables its site-specific incorporation into target proteins. Subsequent on-protein Staudinger reduction and sortase-mediated SUMOylation furnish defined SUMO-substrate ABPs under mild aqueous conditions. Applying this platform to PCNA and K11-linked diSUMO conjugates revealed distinct deSUMOylase trapping profiles governed by SUMO paralog and acceptor-substrate contexts. This work establishes a modular route to native-like SUMO probes and provides a general strategy for interrogating context-dependent enzyme recognition in Ubl signaling.

Organizational Affiliation

Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, 8093Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 62.79 kDa
Atom Count: 4,526
Modeled Residue Count: 511
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrrolysine--tRNA ligase	A, B	267	Methanosarcina barkeri	Mutation(s): 0 Gene Names: pylS EC: 6.1.1.26
UniProt
Find proteins for Q6WRH6 (Methanosarcina barkeri) Explore Q6WRH6 Go to UniProtKB: Q6WRH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6WRH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [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 I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]