3POT | pdb_00003pot

Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis

• PDB DOI: https://doi.org/10.2210/pdb3POT/pdb

• Classification: TRANSFERASE
• Organism(s): Methanothermobacter marburgensis
• Mutation(s): No 


• Deposited: 2010-11-23 Released: 2011-04-13 
• Deposition Author(s): Cedervall, P.E., Wilmot, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis.

Cedervall, P.E., Dey, M., Li, X., Sarangi, R., Hedman, B., Ragsdale, S.W., Wilmot, C.M.

(2011) J Am Chem Soc 133: 5626-5628

• PubMed: 21438550 
• DOI: https://doi.org/10.1021/ja110492p
• Primary Citation of Related Structures:  
  3POT


• PubMed Abstract: 
  

  We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.

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: 277.55 kDa 
• Atom Count: 22,289 
• Modelled Residue Count: 2,472 
• Deposited Residue Count: 2,484 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit alpha	A, D	550	Methanothermobacter marburgensis	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11558  Go to UniProtKB:  P11558

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit beta	B, E	443	Methanothermobacter marburgensis	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11560  Go to UniProtKB:  P11560

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase I subunit gamma	C, F	249	Methanothermobacter marburgensis	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11562  Go to UniProtKB:  P11562

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F43	K [auth A], V [auth D]	FACTOR 430 C42 H51 N6 Ni O13 XLFIRMYGVLUNOY-SXMZNAGASA-M
TP7	N [auth A], W [auth D]	Coenzyme B C11 H22 N O7 P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N
TXZ	M [auth A], X [auth D]	O-phosphono-N-(6-sulfanylhexanoyl)-L-threonine C10 H20 N O7 P S PRNNQVAYHYUTOD-APPZFPTMSA-N
COM	L [auth A], Y [auth D]	1-THIOETHANESULFONIC ACID C2 H6 O3 S2 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
06C	O [auth A], Z [auth D]	Iodomethane C H3 I INQOMBQAUSQDDS-UHFFFAOYSA-N
EDO	AA [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	P [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	BA [auth E], CA [auth E], DA [auth F], G [auth A], H [auth A], I [auth A], J [auth A], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM	A, D	L-PEPTIDE LINKING	C7 H17 N4 O2		ARG
GL3	A, D	L-PEPTIDE LINKING	C2 H5 N O S		GLY
MGN	A, D	L-PEPTIDE LINKING	C6 H12 N2 O3		GLN
MHS	A, D	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS
SMC	A, D	L-PEPTIDE LINKING	C4 H9 N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.886	α = 90
b = 118.165	β = 91.94
c = 122.388	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Cedervall, P.E., Wilmot, C.M.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-05-20
  Changes: Non-polymer description
• Version 1.3: 2017-03-29
  Changes: Non-polymer description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description