6H9E | pdb_00006h9e

Structure of glutamate mutase reconstituted with homo-coenzyme B12

PDB DOI: https://doi.org/10.2210/pdb6H9E/pdb

Classification: ISOMERASE
Organism(s): Clostridium cochlearium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-08-03 Released: 2019-08-14
Deposition Author(s): Gruber, K., Csitkovits, V., Kratky, C.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.168 (Depositor), 0.168 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues.

Gruber, K., Csitkovits, V., Lyskowski, A., Kratky, C., Krautler, B.

(2022) Angew Chem Int Ed Engl 61: e202208295-e202208295

PubMed: 35793207 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202208295
Primary Citation Related Structures:
6H9E, 6H9F

PubMed Abstract:
Catalysis by radical enzymes dependent on coenzyme B ₁₂ (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 10 ¹² -fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.

Organizational Affiliation

Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, 8010, Graz, Austria.

Macromolecule Content

Total Structure Weight: 140.84 kDa
Atom Count: 11,482
Modeled Residue Count: 1,240
Deposited Residue Count: 1,240
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate mutase sigma subunit	A, C	137	Clostridium cochlearium	Mutation(s): 0 Gene Names: glmS EC: 5.4.99.1
UniProt
Find proteins for P80078 (Clostridium cochlearium) Explore P80078 Go to UniProtKB: P80078
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80078
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate mutase epsilon subunit	B, D	483	Clostridium cochlearium	Mutation(s): 0 Gene Names: glmE EC: 5.4.99.1
UniProt
Find proteins for P80077 (Clostridium cochlearium) Explore P80077 Go to UniProtKB: P80077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80077
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C]	E [auth A], J [auth C]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
FWK (Subject of Investigation/LOI) Query on FWK Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain L [auth D] MOL2 format, chain F [auth B] MOL2 format, chain L [auth D] mmCIF format, chain F [auth B] mmCIF format, chain L [auth D]	F [auth B], L [auth D]	(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol C₁₁ H₁₅ N₅ O₃ RLOSCLOIJYLPHI-IOSLPCCCSA-N		Interactions Focus chain F [auth B] Focus chain L [auth D] Interactions & Density Focus chain F [auth B] Focus chain L [auth D]
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain M [auth D] MOL2 format, chain G [auth B] MOL2 format, chain M [auth D] mmCIF format, chain G [auth B] mmCIF format, chain M [auth D]	G [auth B], M [auth D]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain G [auth B] Focus chain M [auth D] Interactions & Density Focus chain G [auth B] Focus chain M [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	H [auth B], I [auth B], K [auth C], N [auth D], O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D]