4XC6

Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, and Mg (holo-IcmF/GDP)

• PDB DOI:  https://doi.org/10.2210/pdb4XC6/pdb

• Classification: ISOMERASE
• Organism(s): Cupriavidus metallidurans CH34
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-17 Released: 2015-02-11 
• Deposition Author(s): Jost, M., Drennan, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.198 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

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

• PubMed: 25675500 
• DOI: https://doi.org/10.1073/pnas.1419582112
• Primary Citation of Related Structures:  
  4XC6, 4XC7, 4XC8


• 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. 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.

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Organizational Affiliation: 

Department of Chemistry and Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 249.81 kDa 
• Atom Count: 16,546 
• Modelled Residue Count: 2,128 
• Deposited Residue Count: 2,226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isobutyryl-CoA mutase fused	A, B	1,113	Cupriavidus metallidurans CH34	Mutation(s): 0  Gene Names: icmF, Rmet_0210, sbm EC: 5.4.99.13 (PDB Primary Data), 3.6.5 (UniProt)
UniProt
Find proteins for Q1LRY0 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)) Explore Q1LRY0  Go to UniProtKB:  Q1LRY0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12	C [auth A], I [auth B]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
GDP	E [auth A], J [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
5AD	D [auth A]	5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N
ACT	H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	F [auth A], G [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.198 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: H 3 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/83

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 318.76	α = 90
b = 318.76	β = 90
c = 343.52	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing
SHARP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Jost, M., Drennan, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM069857
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence