3CI3

Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with partial adenosylcobalamin and PPPi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

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 3POClick on this verticalbar to view detailsBest fitted 5ADClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate.

St Maurice, M.Mera, P.Park, K.Brunold, T.C.Escalante-Semerena, J.C.Rayment, I.

(2008) Biochemistry 47: 5755-5766

  • DOI: https://doi.org/10.1021/bi800132d
  • Primary Citation of Related Structures:  
    3CI1, 3CI3, 3CI4

  • PubMed Abstract: 

    ATP:cob(I)alamin adenosyltransferases (ACAs) catalyze the transfer of the 5'-deoxyadenosyl moiety from ATP to the upper axial ligand position of cobalamin in the synthesis of coenzyme B 12. For the ACA-catalyzed reaction to proceed, cob(II)alamin must be reduced to cob(I)alamin in the enzyme active site. This reduction is facilitated through the generation of a four-coordinate cob(II)alamin intermediate on the enzyme. We have determined the high-resolution crystal structure of a human-type ACA from Lactobacillus reuteri with a four-coordinate cob(II)alamin bound in the enzyme active site and with the product, adenosylcobalamin, partially occupied in the active site. The assembled structures represent snapshots of the steps in the ACA-catalyzed formation of the cobalt-carbon bond of coenzyme B 12. The structures define the corrinoid binding site and provide visual evidence for a base-off, four-coordinate cob(II)alamin intermediate. The complete structural description of ACA-mediated catalysis reveals the molecular features of four-coordinate cob(II)alamin stabilization and provides additional insights into the molecular basis for dysfunction in human patients suffering from methylmalonic aciduria.


  • Organizational Affiliation

    Departments of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cobalamin adenosyltransferase PduO-like protein194Limosilactobacillus reuteriMutation(s): 0 
Gene Names: cobA
EC: 2.5.1.17
UniProt
Find proteins for Q50EJ2 (Limosilactobacillus reuteri)
Explore Q50EJ2 
Go to UniProtKB:  Q50EJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50EJ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download Ideal Coordinates CCD File 
F [auth A]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
3PO
Query on 3PO

Download Ideal Coordinates CCD File 
D [auth A]TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
5AD
Query on 5AD

Download Ideal Coordinates CCD File 
E [auth A]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.965α = 90
b = 67.965β = 90
c = 110.941γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

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 3POClick on this verticalbar to view detailsBest fitted 5ADClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-24
    Changes: Non-polymer description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations