9ICZ | pdb_00009icz

C-Methyltransferase SeMT from Saccharopolyspora erythraea

PDB DOI: https://doi.org/10.2210/pdb9ICZ/pdb

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

Deposited: 2025-02-14 Released: 2025-12-10
Deposition Author(s): Weiergraeber, O.H., Haase, M., Pietruszka, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.193 (Depositor), 0.195 (DCC)
R-Value Work:
0.173 (Depositor), 0.175 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Re-engineering a transferase scaffold for indole C3 methylation in diketopiperazines.

Haase, M., Weiergraber, O.H., Pietruszka, J.

(2025) Protein Sci 34: e70254-e70254

PubMed: 40878043 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70254
Primary Citation Related Structures:
9ICZ

PubMed Abstract:
The pyrroloindole (hexahydropyrrolo[2,3-b]indole, HPI) structural motif is present in a wide range of natural products with various biological activities, yet its chemical synthesis poses a challenge, particularly regarding methylation at the indole C3 position. In nature, S-adenosyl methionine (SAM)-dependent methyltransferases efficiently catalyze this reaction with high stereoselectivity. This study presents the investigation and rational re-design of a potential methyltransferase, termed SeMT, from the actinomycete Saccharopolyspora erythraea. While its three-dimensional structure elucidated via X-ray crystallography confirmed extensive structural similarity to cyclic dipeptide-processing methyltransferases such as SgMT, its putative catalytic center is clearly divergent. Accordingly, wild-type SeMT displayed minimal activity with diketopiperazine (DKP) substrates, triggering an extensive mutagenesis effort aimed at iteratively enhancing this methyltransferase function. This work yielded a variant with appreciable activity, which was comprehensively characterized. Notably, a specific mutation within the catalytic triad of SeMT proved critical not only for its own function but also for the temperature-activity profile of its homolog protein SgMT. Beyond the specific properties of SeMT, these findings hence provide important insights into the active center architecture of indole C3-methyltransferases, supporting further development of these enzymes into refined biocatalysts for synthetic applications.

Organizational Affiliation

Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich, Germany.

Macromolecule Content

Total Structure Weight: 64.69 kDa
Atom Count: 5,753
Modeled Residue Count: 535
Deposited Residue Count: 554
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine (SAM)-dependent methyltransferase	A, B	277	Saccharopolyspora erythraea	Mutation(s): 0 Gene Names: SACE_3471
UniProt
Find proteins for A4FFC0 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)) Explore A4FFC0 Go to UniProtKB: A4FFC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4FFC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A]	H [auth A], Q [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] 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] G [auth A] J [auth B] D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [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 J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	C [auth A], I [auth B]	Unknown ligand QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]