6D5K

Structure of Human ATP:Cobalamin Adenosyltransferase bound to ATP, and Adenosylcobalamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B12as a Cofactor Conservation Strategy.

Campanello, G.C.Ruetz, M.Dodge, G.J.Gouda, H.Gupta, A.Twahir, U.T.Killian, M.M.Watkins, D.Rosenblatt, D.S.Brunold, T.C.Warncke, K.Smith, J.L.Banerjee, R.

(2018) J. Am. Chem. Soc. 140: 13205-13208

  • DOI: 10.1021/jacs.8b08659
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A sophisticated intracellular trafficking pathway in humans is used to tailor vitamin B <sub>12 </sub> into its active cofactor forms, and to deliver it to two known B <sub>12 </sub>-dependent enzymes. Herein, we report an unexpected strategy for cel ...

    A sophisticated intracellular trafficking pathway in humans is used to tailor vitamin B 12 into its active cofactor forms, and to deliver it to two known B 12 -dependent enzymes. Herein, we report an unexpected strategy for cellular retention of B 12 , an essential and reactive cofactor. If methylmalonyl-CoA mutase is unavailable to accept the coenzyme B 12 product of adenosyltransferase, the latter catalyzes homolytic scission of the cobalt-carbon bond in an unconventional reversal of the nucleophilic displacement reaction that was used to make it. The resulting homolysis product binds more tightly to adenosyltransferase than does coenzyme B 12 , facilitating cofactor retention. We have trapped, and characterized spectroscopically, an intermediate in which the cobalt-carbon bond is weakened prior to being broken. The physiological relevance of this sacrificial catalytic activity for cofactor retention is supported by the significantly lower coenzyme B 12 concentration in patients with dysfunctional methylmalonyl-CoA mutase but normal adenosyltransferase activity.


    Organizational Affiliation

    Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States.,Life Sciences Institute, University of Michigan , Ann Arbor , Michigan 48109-0600 , United States.,Department of Physics , Emory University , Atlanta , Georgia 30322-2430 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Indian Institute of Science Education and Research , Pune 411008 , India.,Department of Human Genetics , McGill University , Montreal , Quebec H3A 1B1 , Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
A, B, C
196Homo sapiensMutation(s): 0 
Gene Names: MMAB
EC: 2.5.1.17
Find proteins for Q96EY8 (Homo sapiens)
Go to Gene View: MMAB
Go to UniProtKB:  Q96EY8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
EPE
Query on EPE

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Download CCD File 
C
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
5AD
Query on 5AD

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Download CCD File 
A, B
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
 Ligand Interaction
B12
Query on B12

Download SDF File 
Download CCD File 
A
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.252α = 90.00
b = 112.252β = 90.00
c = 117.993γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK45776

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-31
    Type: Data collection, Database references