5A8R | pdb_00005a8r

METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER MARBURGENSIS AT 2.15 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb5A8R/pdb

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

Deposited: 2015-07-16 Released: 2016-08-10
Deposition Author(s): Wagner, T., Ermler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.196 (Depositor), 0.195 (DCC)
R-Value Work:
0.156 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation.

Wagner, T., Kahnt, J., Ermler, U., Shima, S.

(2016) Angew Chem Int Ed Engl 55: 10630

PubMed: 27467699 Search on PubMed
DOI: https://doi.org/10.1002/anie.201603882
Primary Citation Related Structures:
5A0Y, 5A8K, 5A8R, 5A8W

PubMed Abstract:
All methanogenic and methanotrophic archaea known to date contain methyl-coenzyme M reductase (MCR) that catalyzes the reversible reduction of methyl-coenzyme M to methane. This enzyme contains the nickel porphinoid F430 as a prosthetic group and, highly conserved, a thioglycine and four methylated amino acid residues near the active site. We describe herein the presence of a novel post-translationally modified amino acid, didehydroaspartate, adjacent to the thioglycine as revealed by mass spectrometry and high-resolution X-ray crystallography. Upon chemical reduction, the didehydroaspartate residue was converted into aspartate. Didehydroaspartate was found in MCR I and II from Methanothermobacter marburgensis and in MCR of phylogenetically distantly related Methanosarcina barkeri but not in MCR I and II of Methanothermobacter wolfeii, which indicates that didehydroaspartate is dispensable but might have a role in fine-tuning the active site to increase the catalytic efficiency.

Organizational Affiliation

Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany.

Macromolecule Content

Total Structure Weight: 559.56 kDa
Atom Count: 40,798
Modeled Residue Count: 5,008
Deposited Residue Count: 5,044
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA	A, D, G, J	553	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P58815 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P58815 Go to UniProtKB: P58815
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58815
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA	B, E, H, K	443	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for D9PXZ6 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PXZ6 Go to UniProtKB: D9PXZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9PXZ6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA	C, F, I, L	265	Methanothermobacter marburgensis	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for P58816 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P58816 Go to UniProtKB: P58816
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58816
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 Query on F43 Download:Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain X [auth G] SDF format, chain S [auth D] SDF format, chain O [auth A] MOL2 format, chain BA [auth J] MOL2 format, chain X [auth G] MOL2 format, chain S [auth D] MOL2 format, chain O [auth A] mmCIF format, chain BA [auth J] mmCIF format, chain X [auth G] mmCIF format, chain S [auth D] mmCIF format, chain O [auth A]	BA [auth J], O [auth A], S [auth D], X [auth G]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain BA [auth J] Focus chain O [auth A] Focus chain S [auth D] Focus chain X [auth G] Interactions & Density Focus chain BA [auth J] Focus chain O [auth A] Focus chain S [auth D] Focus chain X [auth G]
TP7 Query on TP7 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth G] SDF format, chain R [auth D] SDF format, chain AA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain W [auth G] MOL2 format, chain R [auth D] MOL2 format, chain AA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain W [auth G] mmCIF format, chain R [auth D] mmCIF format, chain AA [auth J]	AA [auth J], N [auth A], R [auth D], W [auth G]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain AA [auth J] Focus chain N [auth A] Focus chain R [auth D] Focus chain W [auth G] Interactions & Density Focus chain AA [auth J] Focus chain N [auth A] Focus chain R [auth D] Focus chain W [auth G]
COM Query on COM Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Z [auth J] SDF format, chain V [auth G] SDF format, chain Q [auth D] MOL2 format, chain M [auth A] MOL2 format, chain Z [auth J] MOL2 format, chain V [auth G] MOL2 format, chain Q [auth D] mmCIF format, chain M [auth A] mmCIF format, chain Z [auth J] mmCIF format, chain V [auth G] mmCIF format, chain Q [auth D]	M [auth A], Q [auth D], V [auth G], Z [auth J]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth D] Focus chain V [auth G] Focus chain Z [auth J] Interactions & Density Focus chain M [auth A] Focus chain Q [auth D] Focus chain V [auth G] Focus chain Z [auth J]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain DA [auth J] SDF format, chain T [auth D] SDF format, chain Y [auth G] SDF format, chain U [auth D] SDF format, chain P [auth A] SDF format, chain EA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain DA [auth J] MOL2 format, chain T [auth D] MOL2 format, chain Y [auth G] MOL2 format, chain U [auth D] MOL2 format, chain P [auth A] MOL2 format, chain EA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain DA [auth J] mmCIF format, chain T [auth D] mmCIF format, chain Y [auth G] mmCIF format, chain U [auth D] mmCIF format, chain P [auth A] mmCIF format, chain EA [auth J]	CA [auth J] DA [auth J] EA [auth J] P [auth A] T [auth D] CA [auth J], DA [auth J], EA [auth J], P [auth A], T [auth D], U [auth D], Y [auth G]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain P [auth A] Focus chain T [auth D] Focus chain U [auth D] Focus chain Y [auth G] Interactions & Density Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain P [auth A] Focus chain T [auth D] Focus chain U [auth D] Focus chain Y [auth G]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.196 (Depositor), 0.195 (DCC)
R-Value Work: 0.156 (Depositor), 0.158 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.66	α = 90
b = 246.61	β = 90
c = 103.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Wagner, T.

Ermler, U.

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-09-28
Changes: Database references
Version 1.2: 2017-03-29
Changes: Non-polymer description
Version 2.0: 2019-04-24
Changes: Data collection, Derived calculations, Polymer sequence
Version 2.1: 2019-05-15
Changes: Data collection, Experimental preparation
Version 2.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description