6H9E

Structure of glutamate mutase reconstituted with homo-coenzyme B12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

Starting Model: experimental
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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

  • DOI: https://doi.org/10.1002/anie.202208295
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate mutase sigma subunit
A, C
137Clostridium cochleariumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80078
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate mutase epsilon subunit
B, D
483Clostridium cochleariumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80077
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
FWK (Subject of Investigation/LOI)
Query on FWK

Download Ideal Coordinates CCD File 
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
TAR
Query on TAR

Download Ideal Coordinates CCD File 
G [auth B],
M [auth D]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
K [auth C],
N [auth D],
O [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.89α = 90
b = 112.62β = 95.69
c = 108.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description