Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to ATP

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

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Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions.

Gouda, H.Mascarenhas, R.Pillay, S.Ruetz, M.Koutmos, M.Banerjee, R.

(2021) J Biol Chem 297: 101373-101373

  • DOI: https://doi.org/10.1016/j.jbc.2021.101373
  • Primary Citation of Related Structures:  
    7RUT, 7RUU, 7RUV

  • PubMed Abstract: 

    Human ATP:cob(I)alamin adenosyltransferase (ATR) is a mitochondrial enzyme that catalyzes an adenosyl transfer to cob(I)alamin, synthesizing 5'-deoxyadenosylcobalamin (AdoCbl) or coenzyme B 12 . ATR is also a chaperone that escorts AdoCbl, transferring it to methylmalonyl-CoA mutase, which is important in propionate metabolism. Mutations in ATR lead to methylmalonic aciduria type B, an inborn error of B 12 metabolism. Our previous studies have furnished insights into how ATR protein dynamics influence redox-linked cobalt coordination chemistry, controlling its catalytic versus chaperone functions. In this study, we have characterized three patient mutations at two conserved active site residues in human ATR, R190C/H, and E193K and obtained crystal structures of R190C and E193K variants, which display only subtle structural changes. All three mutations were found to weaken affinities for the cob(II)alamin substrate and the AdoCbl product and increase K M(ATP) . 31 P NMR studies show that binding of the triphosphate product, formed during the adenosylation reaction, is also weakened. However, although the k cat of this reaction is significantly diminished for the R190C/H mutants, it is comparable with the WT enzyme for the E193K variant, revealing the catalytic importance of Arg-190. Furthermore, although the E193K mutation selectively impairs the chaperone function by promoting product release into solution, its catalytic function might be unaffected at physiological ATP concentrations. In contrast, the R190C/H mutations affect both the catalytic and chaperoning activities of ATR. Because the E193K mutation spares the catalytic activity of ATR, our data suggest that the patients carrying this mutation are more likely to be responsive to cobalamin therapy.

  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Corrinoid adenosyltransferase196Homo sapiensMutation(s): 1 
Gene Names: MMAB
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY8 (Homo sapiens)
Explore Q96EY8 
Go to UniProtKB:  Q96EY8
GTEx:  ENSG00000139428 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EY8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth A]
GA [auth D]
I [auth E]
N [auth C]
R [auth F]
AA [auth A],
GA [auth D],
I [auth E],
N [auth C],
R [auth F],
V [auth B]
C10 H16 N5 O13 P3
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Query on K

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
H [auth E]
L [auth C]
DA [auth D],
EA [auth D],
FA [auth D],
H [auth E],
L [auth C],
M [auth C],
Q [auth F],
T [auth B],
U [auth B],
Y [auth A],
Z [auth A]
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
G [auth E]
J [auth C]
K [auth C]
BA [auth D],
CA [auth D],
G [auth E],
J [auth C],
K [auth C],
O [auth F],
P [auth F],
S [auth B],
X [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.151α = 90
b = 75.769β = 91.3
c = 95.844γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

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 Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK45776

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description