9UAY | pdb_00009uay

Crystal structure of CmnI

PDB DOI: https://doi.org/10.2210/pdb9UAY/pdb

Classification: TRANSFERASE
Organism(s): Saccharothrix mutabilis subsp. capreolus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-01 Released: 2026-03-11
Deposition Author(s): Hsiao, P.Y., Chang, C.Y., Peng, C.Y.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.246 (Depositor), 0.252 (DCC)
R-Value Work:
0.215 (Depositor), 0.221 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: in silico
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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

Biosynthesis of Antituberculosis Antibiotic Capreomycin Involves a trans -Iterative Adenylation Domain within the Nonribosomal Peptide Synthetase Machinery.

Lai, Y.T., Peng, C.Y., Liao, H.T., Hsiao, P.Y., Hsieh, C.K., Luo, Y.R., Huang, S.C., Wang, Y.L., Ma, T., Chen, Y.R., Kuo, Y.M., Lin, Y.C., Chu, J., Chang, C.Y.

(2025) Org Lett 27: 9553-9558

PubMed: 40815678 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.orglett.5c03112
Primary Citation of Related Structures:
9UAY

PubMed Abstract:
Capreomycin (CMN) is a nonribosomal peptide (NRP) antituberculosis antibiotic. CMN biosynthesis involves a non-canonical trans -iterative adenylation (A) domain. Here, we report that the A domain-less nonribosomal peptide synthetase (NRPS) module CmnI utilizes another module's A domain CmnA-A ₁ to load the required amino acid onto its thiolation (T) domain. This study provides evidence of an unusual mode of NRP biosynthesis in bacteria, involving a trans -iterative A domain in the NRPS machinery.

Organizational Affiliation

Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan.

Macromolecule Content

Total Structure Weight: 124.53 kDa
Atom Count: 6,862
Modeled Residue Count: 849
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CmnI	A, B	568	Saccharothrix mutabilis subsp. capreolus	Mutation(s): 0 Gene Names: cmnI
UniProt
Find proteins for A6YEI0 (Saccharothrix mutabilis subsp. capreolus) Explore A6YEI0 Go to UniProtKB: A6YEI0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6YEI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AE4 (Subject of Investigation/LOI) Query on AE4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL C₁₂ H₂₆ O₆ NJRFAMBTWHGSDE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
AE3 (Subject of Investigation/LOI) Query on AE3 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-(2-ETHOXYETHOXY)ETHANOL C₆ H₁₄ O₃ XXJWXESWEXIICW-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PEG (Subject of Investigation/LOI) Query on PEG 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 H [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B]	D [auth A], E [auth A], F [auth A], H [auth B], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B]