3KOY

Crystal Structure of ornithine 4,5 aminomutase in complex with ornithine (Aerobic)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.

Wolthers, K.R., Levy, C., Scrutton, N.S., Leys, D.

(2010) J.Biol.Chem. 285: 13942-13950

  • DOI: 10.1074/jbc.M109.068908
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • D-ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin (AdoCbl) to a pyridoxal 5'-phosphate (PLP) cofactor. We have solved OAM crystal s ...

    D-ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin (AdoCbl) to a pyridoxal 5'-phosphate (PLP) cofactor. We have solved OAM crystal structures in different catalytic states that together demonstrate unusual stability of the AdoCbl Co-C bond and that radical catalysis is coupled to large-scale domain motion. The 2.0-A substrate-free enzyme crystal structure reveals the Rossmann domain, harboring the intact AdoCbl cofactor, is tilted toward the edge of the PLP binding triose-phosphate isomerase barrel domain. The PLP forms an internal aldimine link to the Rossmann domain through Lys(629), effectively locking the enzyme in this "open" pre-catalytic conformation. The distance between PLP and 5'-deoxyadenosyl group is 23 A, and large-scale domain movement is thus required prior to radical catalysis. The OAM crystals contain two Rossmann domains within the asymmetric unit that are unconstrained by the crystal lattice. Surprisingly, the binding of various ligands to OAM crystals (in an oxygen-free environment) leads to transimination in the absence of significant reorientation of the Rossmann domains. In contrast, when performed under aerobic conditions, this leads to extreme disorder in the latter domains correlated with the loss of the 5'-deoxyadenosyl group. Our data indicate turnover and hence formation of the "closed" conformation is occurring within OAM crystals, but that the equilibrium is poised toward the open conformation. We propose that substrate binding induces large-scale domain motion concomitant with a reconfiguration of the 5'-deoxyadenosyl group, triggering radical catalysis in OAM.

    Organizational Affiliation: 

    Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom. kirsten.wolthers@manchester.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-ornithine aminomutase E component
A, B, C, D
763Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654)Mutation(s): 0 
Gene Names: oraE
EC: 5.4.3.5
Find proteins for E3PY95 (Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654))
Go to UniProtKB:  E3PY95
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-ornithine aminomutase S component
E, F, G, H
121Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654)Mutation(s): 0 
Gene Names: oraS
EC: 5.4.3.5
Find proteins for E3PY96 (Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654))
Go to UniProtKB:  E3PY96
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5AD
Query on 5AD
Download SDF File 
Download CCD File 
A, B, C, D
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
 Ligand Interaction
B12
Query on B12
Download SDF File 
Download CCD File 
A, B, C, D
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
Z97
Query on Z97
Download SDF File 
Download CCD File 
A, B, C, D
(E)-N~5~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-ornithine
C13 H20 N3 O7 P
RMKYDMCVWSLEGI-DMSFABOWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.520α = 90.00
b = 233.220β = 103.43
c = 124.140γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
DNAdata collection
PHENIXrefinement
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-10-24
    Type: Non-polymer description