2R6T

Structure of a R132K variant PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history


Literature

Structural and functional analyses of the human-type corrinoid adenosyltransferase (PduO) from Lactobacillus reuteri.

Mera, P.E.St Maurice, M.Rayment, I.Escalante-Semerena, J.C.

(2007) Biochemistry 46: 13829-13836

  • DOI: 10.1021/bi701622j
  • Primary Citation of Related Structures:  
    2R6T, 2R6X

  • PubMed Abstract: 
  • ATP:Co(I)rrinoid adenosyltransferase (ACA) catalyzes the conversion of cobalamin to coenzyme B12, an essential cofactor in animal metabolism. Several mutations of conserved residues in the active site of human ACA have been identified in humans with methylmalonic aciduria ...

    ATP:Co(I)rrinoid adenosyltransferase (ACA) catalyzes the conversion of cobalamin to coenzyme B12, an essential cofactor in animal metabolism. Several mutations of conserved residues in the active site of human ACA have been identified in humans with methylmalonic aciduria. However, the catalytic role of these residues remains unclear. To better understand the function of these residues and to determine how the enzyme promotes catalysis, several variants of a human-type ACA from the lactic acid bacterium Lactobacillus reuteri (LrPduO) were kinetically and structurally characterized. Kinetic analyses of a series of alternate nucleotides were also performed. Substrate inhibition was observed at subsaturating concentrations of ATP, consistent with an ordered binding scheme where ATP is bound first by the enzyme. Modification or elimination of an active site, inter-subunit salt bridge resulted in a reduced "on" rate for ATP binding, with a less significant disruption in the rate of subsequent catalytic steps. Kinetic and structural data demonstrate that residue Arg132 is not involved in orienting ATP in the active site but, rather, it stabilizes the altered substrate in the transition state. Two functional groups of ATP explain the reduced ability of the enzyme to use alternate nucleotides: the amino group at the C-6 position of ATP contributes approximately 6 kcal/mol of free energy to ground state binding, and the nitrogen at the N-7 position assists in coordinating the magnesium ion in the active site. This study provides new insight into the role of substrate binding determinants and active site residues in the reaction catalyzed by a human-type ACA.


    Organizational Affiliation

    Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cobalamin adenosyltransferase PduO-like proteinA, B194Limosilactobacillus reuteriMutation(s): 1 
Gene Names: cobAGIX77_03270
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.678α = 90
b = 64.678β = 90
c = 169.197γ = 120
Software Package:
Software NamePurpose
SAINTdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations