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

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.

Jost, M.Born, D.A.Cracan, V.Banerjee, R.Drennan, C.L.

(2015) J Biol Chem 290: 26882-26898

  • DOI: https://doi.org/10.1074/jbc.M115.676890
  • Primary Citation of Related Structures:  
    5CJT, 5CJU, 5CJV, 5CJW

  • PubMed Abstract: 

    Acyl-CoA mutases are a growing class of adenosylcobalamin-dependent radical enzymes that perform challenging carbon skeleton rearrangements in primary and secondary metabolism. Members of this class of enzymes must precisely control substrate positioning to prevent oxidative interception of radical intermediates during catalysis. Our understanding of substrate specificity and catalysis in acyl-CoA mutases, however, is incomplete. Here, we present crystal structures of IcmF, a natural fusion protein variant of isobutyryl-CoA mutase, in complex with the adenosylcobalamin cofactor and four different acyl-CoA substrates. These structures demonstrate how the active site is designed to accommodate the aliphatic acyl chains of each substrate. The structures suggest that a conformational change of the 5'-deoxyadenosyl group from C2'-endo to C3'-endo could contribute to initiation of catalysis. Furthermore, detailed bioinformatic analyses guided by our structural findings identify critical determinants of acyl-CoA mutase substrate specificity and predict new acyl-CoA mutase-catalyzed reactions. These results expand our understanding of the substrate specificity and the catalytic scope of acyl-CoA mutases and could benefit engineering efforts for biotechnological applications ranging from production of biofuels and commercial products to hydrocarbon remediation.

  • Organizational Affiliation

    Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isobutyryl-CoA mutase fused
A, B
1,113Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: sbmRmet_0210
Find proteins for Q1LRY0 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LRY0 
Go to UniProtKB:  Q1LRY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LRY0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B12

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
C62 H89 Co N13 O14 P
Query on 52O

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
pivalyl-coenzyme A
C26 H44 N7 O17 P3 S
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
C10 H15 N5 O11 P2
Query on 5AD

Download Ideal Coordinates CCD File 
C10 H13 N5 O3
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 317.52α = 90
b = 317.52β = 90
c = 343.04γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

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: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2015-11-18
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description