4XC8

Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and Mg and without cobalamin (apo-IcmF/GDP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Visualization of a radical B12 enzyme with its G-protein chaperone.

Jost, M.Cracan, V.Hubbard, P.A.Banerjee, R.Drennan, C.L.

(2015) Proc Natl Acad Sci U S A 112: 2419-2424

  • DOI: 10.1073/pnas.1419582112
  • Primary Citation of Related Structures:  
    4XC7, 4XC8, 4XC6

  • PubMed Abstract: 
  • G-protein metallochaperones ensure fidelity during cofactor assembly for a variety of metalloproteins, including adenosylcobalamin (AdoCbl)-dependent methylmalonyl-CoA mutase and hydrogenase, and thus have both medical and biofuel development applications ...

    G-protein metallochaperones ensure fidelity during cofactor assembly for a variety of metalloproteins, including adenosylcobalamin (AdoCbl)-dependent methylmalonyl-CoA mutase and hydrogenase, and thus have both medical and biofuel development applications. Here, we present crystal structures of IcmF, a natural fusion protein of AdoCbl-dependent isobutyryl-CoA mutase and its corresponding G-protein chaperone, which reveal the molecular architecture of a G-protein metallochaperone in complex with its target protein. These structures show that conserved G-protein elements become ordered upon target protein association, creating the molecular pathways that both sense and report on the cofactor loading state. Structures determined of both apo- and holo-forms of IcmF depict both open and closed enzyme states, in which the cofactor-binding domain is alternatively positioned for cofactor loading and for catalysis. Notably, the G protein moves as a unit with the cofactor-binding domain, providing a visualization of how a chaperone assists in the sequestering of a precious cofactor inside an enzyme active site.


    Organizational Affiliation

    Department of Chemistry and Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and cdrennan@mit.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isobutyryl-CoA mutase fusedA, B1113Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: icmFRmet_0210sbm
EC: 5.4.99.13 (PDB Primary Data), 3.6.5 (UniProt)
Find proteins for Q1LRY0 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LRY0 
Go to UniProtKB:  Q1LRY0
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 316.51α = 90
b = 316.51β = 90
c = 342.27γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069857
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Non-polymer description
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence