6ZAH

Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 800ms.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.

Rabe, P.Kamps, J.J.A.G.Sutherlin, K.D.Linyard, J.D.S.Aller, P.Pham, C.C.Makita, H.Clifton, I.McDonough, M.A.Leissing, T.M.Shutin, D.Lang, P.A.Butryn, A.Brem, J.Gul, S.Fuller, F.D.Kim, I.S.Cheah, M.H.Fransson, T.Bhowmick, A.Young, I.D.O'Riordan, L.Brewster, A.S.Pettinati, I.Doyle, M.Joti, Y.Owada, S.Tono, K.Batyuk, A.Hunter, M.S.Alonso-Mori, R.Bergmann, U.Owen, R.L.Sauter, N.K.Claridge, T.D.W.Robinson, C.V.Yachandra, V.K.Yano, J.Kern, J.F.Orville, A.M.Schofield, C.J.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abh0250
  • Primary Citation of Related Structures:  
    6Y0P, 6ZAE, 6ZAF, 6ZAG, 6ZAH, 6ZAI, 6ZAJ, 6ZAL, 6ZAM, 6ZAN, 6ZAO, 6ZAP, 6ZAQ, 6ZW8

  • PubMed Abstract: 

    Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isopenicillin N synthase331Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: ipnAipsAN2622
EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P05326 
Go to UniProtKB:  P05326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05326
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.918α = 90
b = 75.895β = 90
c = 101.923γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106244/Z/14/Z
Medical Research Council (MRC, United Kingdom)United Kingdom106244/Z/14/Z
Wellcome TrustUnited Kingdom210734/Z/18/Z
Royal SocietyUnited KingdomRSWF/R2/182017
Wellcome TrustUnited Kingdom102593
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S50676X/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133081
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM126289
Department of Energy (DOE, United States)United StatesDOE BES DE-AC02-05CH11231
Department of Energy (DOE, United States)United StatesDOE BES DE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description