Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

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Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus .

Johnson, B.P.Kumar, V.Scull, E.M.Thomas, L.M.Bourne, C.R.Singh, S.

(2022) ACS Chem Biol 17: 85-102

  • DOI: https://doi.org/10.1021/acschembio.1c00655
  • Primary Citation of Related Structures:  
    7LNT, 7LNU, 7LNV, 7LNW, 7LNX, 7N9D

  • PubMed Abstract: 

    Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the alternate mevalonate pathways of the archaea and plant cytoplasm. In recent years, IPKs have also been employed in artificial biosynthetic pathways called "(iso) prenol pathways" that utilize promiscuous kinases to sequentially phosphorylate (iso) prenol and generate the isoprenoid precursors IPP and dimethylallyl diphosphate (DMAPP). Furthermore, IPKs have garnered attention for their impressive substrate promiscuity toward non-natural alkyl-monophosphates (alkyl-Ps), which has prompted their utilization as biocatalysts for the generation of novel isoprenoids. However, none of the IPK crystal structures currently available contain non-natural substrates, leaving the roles of active-site residues in substrate promiscuity ambiguous. To address this, we present herein the high-resolution crystal structures of an IPK from Candidatus methanomethylophilus alvus (CMA) in the apo form and bound to natural and non-natural substrates. Additionally, we describe active-site engineering studies leading to enzyme variants with broadened substrate scope, as well as structure determination of two such variants (Ile74Ala and Ile146Ala) bound to non-natural alkyl-Ps. Collectively, our crystallographic studies compare six structures of CMA variants in different ligand-bound forms and highlight contrasting structural dynamics of the two substrate-binding sites. Furthermore, the structural and mutational studies confirm a novel role of the highly conserved DVTGG motif in catalysis, both in CMA and in IPKs at large. As such, the current study provides a molecular basis for the substrate-binding modes and catalytic performance of CMA toward the goal of developing IPKs into useful biocatalysts.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, 101 Stephenson Pkwy, Norman, Oklahoma 73019, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isopentenyl phosphate kinase
A, B
279Methanomethylophilus alviMutation(s): 0 
Gene Names: BKD89_07040
Find proteins for M9SEQ1 (Methanomethylophilus alvi (strain Mx1201))
Explore M9SEQ1 
Go to UniProtKB:  M9SEQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM9SEQ1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
C10 H16 N5 O13 P3
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C10 H15 N5 O10 P2
IPE (Subject of Investigation/LOI)
Query on IPE

Download Ideal Coordinates CCD File 
C5 H12 O7 P2
IP8 (Subject of Investigation/LOI)
Query on IP8

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
Isopentenyl phosphate
C5 H11 O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.892α = 90
b = 74.503β = 90
c = 171.691γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references
  • Version 1.2: 2022-02-02
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description