9RUI | pdb_00009rui

Apo state of the CdmB methyltransferase involved in the anaerobic dehalogenation of haloalkanes

PDB DOI: https://doi.org/10.2210/pdb9RUI/pdb

Classification: TRANSFERASE
Organism(s): Acetobacterium malicum subsp. dehalogenans DSM 11527
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-04 Released: 2026-06-03
Deposition Author(s): Wagner, T., Lemaire, O.N.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Identification and characterisation of an elusive bacterial enzyme system for chloromethane dehalogenation.

Bernhardt, J., Hofmann, L.K.R., Klemm, P., Paczia, N., Lemaire, O.N., Vuilleumier, S., Wagner, T., Kurth, J.M.

(2026) Nat Commun 17

PubMed: 42218128 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-73764-z
Primary Citation Related Structures:
9RUI, 9RUL, 9RUO

PubMed Abstract:
Chloromethane, a toxic gas primarily produced naturally, contributes to stratospheric ozone destruction. The anaerobic acetogen Acetobacterium dehalogenans can utilise chloromethane as a carbon and energy source, but the associated dehalogenase/methyltransferase has remained elusive. Through comparative transcriptomics we identify a gene cluster, cdmBCA, which encodes a corrinoid-dependent methyltransferase system distinct from the characterised Cmu system used for chloromethane degradation in aerobic methylotrophs. Biochemical characterisation reveals that the Cdm system reacts with other haloalkanes, but not with methoxylated aromatics, unlike closely related O-demethylases. X-ray structural analysis of the protein CdmB shows a hydrophobic channelling system directing haloalkanes towards cobalamin-dependent activation. Homologous proteins are found in anaerobic prokaryotes, particularly within the phyla Bacillota and Asgardarchaeota, suggesting previously unidentified microbial transformation of chloromethane in the environment. Discovery of the Cdm dehalogenation/methyltransferase system sheds light on the microbial contribution to the global chloromethane cycle.

Organizational Affiliation

Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.

Macromolecule Content

Total Structure Weight: 100.21 kDa
Atom Count: 7,447
Modeled Residue Count: 838
Deposited Residue Count: 858
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdmB from Acetobacterium malicum subsp. dehalogenans	A, B	429	Acetobacterium malicum subsp. dehalogenans DSM 11527	Mutation(s): 0 Gene Names: ACIUZZ_RS16855

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ETE Query on ETE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain H [auth A] SDF format, chain BA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth A]	BA [auth A] H [auth A] I [auth A] L [auth A] Q [auth A] BA [auth A], H [auth A], I [auth A], L [auth A], Q [auth A], QA [auth B], R [auth A], S [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain BA [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain GA [auth A]	GA [auth A], HA [auth A], IA [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain W [auth A] SDF format, chain NA [auth B] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain E [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain E [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain E [auth A]	E [auth A] K [auth A] KA [auth B] MA [auth B] NA [auth B] E [auth A], K [auth A], KA [auth B], MA [auth B], NA [auth B], W [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain W [auth A] Interactions & Density Focus chain E [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain W [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain J [auth A] SDF format, chain O [auth A] SDF format, chain PA [auth B] SDF format, chain RA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain WA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain YA [auth B] SDF format, chain XA [auth B] SDF format, chain X [auth A] SDF format, chain VA [auth B] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain N [auth A] SDF format, chain LA [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain DA [auth A] SDF format, chain AA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] CA [auth A] D [auth A] DA [auth A] F [auth A] AA [auth A], CA [auth A], D [auth A], DA [auth A], F [auth A], G [auth A], J [auth A], LA [auth B], N [auth A], O [auth A], OA [auth B], P [auth A], PA [auth B], RA [auth B], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain LA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain LA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain ZA [auth B] SDF format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain FA [auth A]	EA [auth A], FA [auth A], ZA [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A] Focus chain ZA [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain JA [auth A] MOL2 format, chain JA [auth A] mmCIF format, chain JA [auth A]	JA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain JA [auth A] Interactions & Density Focus chain JA [auth A]