9ECN

M. acetivorans MCR containing a 2-methylglutamine modification

• PDB DOI: https://doi.org/10.2210/pdb9ECN/pdb

• Classification: TRANSFERASE
• Organism(s): Methanosarcina acetivorans C2A
• Expression System: Methanosarcina acetivorans C2A
• Mutation(s): No 


• Deposited: 2024-11-14 Released: 2024-12-25 
• Deposition Author(s): Nair, S.K., Borkar, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.193 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

Genetic and biochemical characterization of a radical SAM enzyme required for posttranslational glutamine methylation of methyl-coenzyme M reductase

Rodriguez Carrero, R.J., Lloyd, C.T., Borkar, J., Nath, S., Mirica, L.M., Nair, S.K., Booker, S.J., Metcalf, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 287.66 kDa 
• Atom Count: 20,407 
• Modelled Residue Count: 2,494 
• Deposited Residue Count: 2,650 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit alpha	A, B	570	Methanosarcina acetivorans C2A	Mutation(s): 0  Gene Names: mcrA, MA_4546 EC: 2.8.4.1
UniProt
Find proteins for Q8THH1 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8THH1  Go to UniProtKB:  Q8THH1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit beta	C, D	434	Methanosarcina acetivorans C2A	Mutation(s): 0  Gene Names: MA_4550 EC: 2.8.4.1
UniProt
Find proteins for Q8THG7 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8THG7  Go to UniProtKB:  Q8THG7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit gamma	E, F	321	Methanosarcina acetivorans C2A	Mutation(s): 0  Gene Names: MA_4547 EC: 2.8.4.1
UniProt
Find proteins for Q8THH0 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8THH0  Go to UniProtKB:  Q8THH0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F43 (Subject of Investigation/LOI)	G [auth A], H [auth A]	FACTOR 430 C42 H51 N6 Ni O13 XLFIRMYGVLUNOY-SXMZNAGASA-M
SHT (Subject of Investigation/LOI)	K [auth B]	O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE C13 H24 N O10 P S3 CVQZOMWKHKTFCZ-UIALCFJWSA-N
TP7 (Subject of Investigation/LOI)	J [auth B]	Coenzyme B C11 H22 N O7 P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N
PEG	I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM	A, B	L-PEPTIDE LINKING	C7 H17 N4 O2		ARG
DYA	A, B	L-PEPTIDE LINKING	C4 H5 N O4		ASP
GL3	A, B	L-PEPTIDE LINKING	C2 H5 N O S		GLY
MGN	A, B	L-PEPTIDE LINKING	C6 H12 N2 O3		GLN
MHS	A, B	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS
SMC	A, B	L-PEPTIDE LINKING	C4 H9 N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.193 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.47	α = 90
b = 82.94	β = 93.78
c = 122.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Nair, S.K., Borkar, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release