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 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cobalamin adenosyltransferase PduO-like proteinA194Limosilactobacillus reuteriMutation(s): 0 
Gene Names: cobAEW144_04760GIX72_03265
EC: 2.5.1.17
UniProt
Find proteins for Q50EJ2 (Lactobacillus reuteri)
Explore Q50EJ2 
Go to UniProtKB:  Q50EJ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
F [auth A]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
3PO (Subject of Investigation/LOI)
Query on 3PO

Download Ideal Coordinates CCD File 
D [auth A]TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
 Ligand Interaction
5AD (Subject of Investigation/LOI)
Query on 5AD

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • 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

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Ligand Structure Quality Assessment  



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