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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B12Click on this verticalbar to view detailsBest fitted ATPClick on this verticalbar to view detailsBest fitted 5ADClick on this verticalbar to view details

This is version 1.4 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: https://doi.org/10.1021/jacs.8b08659
  • Primary Citation of Related Structures:  
    6D5K, 6D5X

  • PubMed Abstract: 

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial
A, B, C
196Homo sapiensMutation(s): 0 
Gene Names: MMAB
EC: 2.5.1.17 (PDB Primary Data), 2.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY8 (Homo sapiens)
Explore Q96EY8 
Go to UniProtKB:  Q96EY8
PHAROS:  Q96EY8
GTEx:  ENSG00000139428 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
L [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
5AD (Subject of Investigation/LOI)
Query on 5AD

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
N [auth C]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth B]
O [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
M [auth C],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.252α = 90
b = 112.252β = 90
c = 117.993γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B12Click on this verticalbar to view detailsBest fitted ATPClick on this verticalbar to view detailsBest fitted 5ADClick on this verticalbar to view details

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: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description