7BQO

The structure of HpiI in complex with its substrate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Literature

An enzymatic Alder-ene reaction.

Ohashi, M.Jamieson, C.S.Cai, Y.Tan, D.Kanayama, D.Tang, M.C.Anthony, S.M.Chari, J.V.Barber, J.S.Picazo, E.Kakule, T.B.Cao, S.Garg, N.K.Zhou, J.Houk, K.N.Tang, Y.

(2020) Nature 586: 64-69

  • DOI: 10.1038/s41586-020-2743-5
  • Primary Citation of Related Structures:  
    7BQJ, 7BQK, 7BQL, 7BQO, 7BQP

  • PubMed Abstract: 
  • An ongoing challenge in chemical research is to design catalysts that select the outcomes of the reactions of complex molecules. Chemists rely on organocatalysts or transition metal catalysts to control stereoselectivity, regioselectivity and periselectivity (selectivity among possible pericyclic reactions) ...

    An ongoing challenge in chemical research is to design catalysts that select the outcomes of the reactions of complex molecules. Chemists rely on organocatalysts or transition metal catalysts to control stereoselectivity, regioselectivity and periselectivity (selectivity among possible pericyclic reactions). Nature achieves these types of selectivity with a variety of enzymes such as the recently discovered pericyclases-a family of enzymes that catalyse pericyclic reactions 1 . Most characterized enzymatic pericyclic reactions have been cycloadditions, and it has been difficult to rationalize how the observed selectivities are achieved 2-13 . Here we report the discovery of two homologous groups of pericyclases that catalyse distinct reactions: one group catalyses an Alder-ene reaction that was, to our knowledge, previously unknown in biology; the second catalyses a stereoselective hetero-Diels-Alder reaction. Guided by computational studies, we have rationalized the observed differences in reactivities and designed mutant enzymes that reverse periselectivities from Alder-ene to hetero-Diels-Alder and vice versa. A combination of in vitro biochemical characterizations, computational studies, enzyme co-crystal structures, and mutational studies illustrate how high regioselectivity and periselectivity are achieved in nearly identical active sites.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. yitang@ucla.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HpiIA463Hymenoscyphus scutulaMutation(s): 0 
UniProt
Find proteins for A0A1F8A906 (Aspergillus bombycis)
Explore A0A1F8A906 
Go to UniProtKB:  A0A1F8A906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1F8A906
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download Ideal Coordinates CCD File 
E [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
F56 (Subject of Investigation/LOI)
Query on F56

Download Ideal Coordinates CCD File 
B [auth A]3-[(E,2S,4S)-2,4-dimethyloct-6-enoyl]-4-oxidanyl-1H-pyridin-2-one
C15 H21 N O3
XOAZFUVQLCZQIQ-NNOMMRTBSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.113α = 90
b = 145.917β = 90
c = 90.061γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China91856202
Ministry of Science and Technology (MoST, China)China2018YFA0901900

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release