3KP1

Crystal structure of ornithine 4,5 aminomutase (Resting State)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    3KP0, 3KP1, 3KOW, 3KOX, 3KOY, 3KOZ

  • 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 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 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-ornithine aminomutase E componentA, C [auth B], G [auth C], E [auth D]763Acetoanaerobium sticklandiiMutation(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))
Explore E3PY95 
Go to UniProtKB:  E3PY95
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
D-ornithine aminomutase S componentB [auth E], D [auth F], H [auth G], F [auth H]121Acetoanaerobium sticklandiiMutation(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))
Explore E3PY96 
Go to UniProtKB:  E3PY96
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.43α = 90
b = 234.51β = 103.51
c = 124.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
DNAdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    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: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2019-10-30
    Changes: Advisory, Data collection, Database references, Derived calculations