5A0Y | pdb_00005a0y

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb5A0Y/pdb

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

Deposited: 2015-04-24 Released: 2016-05-11
Deposition Author(s): Wagner, T., Ermler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.129 (Depositor), 0.140 (DCC)
R-Value Work:
0.111 (Depositor), 0.120 (DCC)
R-Value Observed:
0.112 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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 of 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: 276.76 kDa
Atom Count: 22,747
Modelled Residue Count: 2,477
Deposited Residue Count: 2,484
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11558
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11560
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11562
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 Query on F43 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain V [auth D] mmCIF format, chain I [auth A] mmCIF format, chain V [auth D]	I [auth A], V [auth D]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain I [auth A] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain V [auth D]
TP7 Query on TP7 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain X [auth D] MOL2 format, chain K [auth A] MOL2 format, chain X [auth D] mmCIF format, chain K [auth A] mmCIF format, chain X [auth D]	K [auth A], X [auth D]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain K [auth A] Focus chain X [auth D] Interactions & Density Focus chain K [auth A] Focus chain X [auth D]
COM Query on COM Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain W [auth D] MOL2 format, chain J [auth A] MOL2 format, chain W [auth D] mmCIF format, chain J [auth A] mmCIF format, chain W [auth D]	J [auth A], W [auth D]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain W [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain P [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain P [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain P [auth A]	AA [auth D], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain P [auth A] Interactions & Density Focus chain AA [auth D] Focus chain P [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth D]	BA [auth D] CA [auth E] DA [auth E] EA [auth E] FA [auth F] BA [auth D], CA [auth E], DA [auth E], EA [auth E], FA [auth F], G [auth A], GA [auth F], H [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain Y [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Z [auth D] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth D]	O [auth A], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Z [auth D] Interactions & Density Focus chain O [auth A] Focus chain Z [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.129 (Depositor), 0.140 (DCC)
R-Value Work: 0.111 (Depositor), 0.120 (DCC)
R-Value Observed: 0.112 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.227	α = 90
b = 118.3	β = 91.9
c = 122.56	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-11

Deposition Author(s):

Wagner, T.

Ermler, U.

Revision History (Full details and data files)

Version 1.0: 2016-05-11
Type: Initial release
Version 1.1: 2016-08-10
Changes: Database references
Version 1.2: 2016-09-28
Changes: Database references
Version 1.3: 2017-03-29
Changes: Non-polymer description
Version 2.0: 2019-04-24
Changes: Data collection, Derived calculations, Polymer sequence
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 5A0Y | pdb_00005a0y

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

5A0Y | pdb_00005a0y