2ZE6

Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with substrate analog, DMASPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report



Literature

Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis.

Sugawara, H.Ueda, N.Kojima, M.Makita, N.Yamaya, T.Sakakibara, H.

(2008) Proc Natl Acad Sci U S A 105: 2734-2739

  • DOI: 10.1073/pnas.0707374105
  • Primary Citation of Related Structures:  
    2ZE5, 2ZE6, 2ZE7, 2ZE8

  • PubMed Abstract: 
  • The phytohormone cytokinin regulates plant growth and development. This hormone is also synthesized by some phytopathogenic bacteria, such as Agrobacterium tumefaciens, and is as a key factor in the formation of plant tumors. The rate-limiting step o ...

    The phytohormone cytokinin regulates plant growth and development. This hormone is also synthesized by some phytopathogenic bacteria, such as Agrobacterium tumefaciens, and is as a key factor in the formation of plant tumors. The rate-limiting step of cytokinin biosynthesis is catalyzed by adenosine phosphate-isopentenyltransferase (IPT). Agrobacterium IPT has a unique substrate specificity that enables it to increase trans-zeatin production by recruiting a metabolic intermediate of the host plant's biosynthetic pathway. Here, we show the crystal structures of Tzs, an IPT from A. tumefaciens, complexed with AMP and a prenyl-donor analogue, dimethylallyl S-thiodiphosphate. The structures reveal that the carbon-nitrogen-based prenylation proceeds by the SN2-reaction mechanism. Site-directed mutagenesis was used to determine the amino acid residues, Asp-173 and His-214, which are responsible for differences in prenyl-donor substrate specificity between plant and bacterial IPTs. IPT and the p loop-containing nucleoside triphosphate hydrolases likely evolved from a common ancestral protein. Despite structural similarities, IPT has evolved a distinct role in which the p loop transfers a prenyl moiety in cytokinin biosynthesis.


    Organizational Affiliation

    RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isopentenyl transferaseA253Agrobacterium tumefaciensMutation(s): 0 
Gene Names: tzs
EC: 2.5.1.27
Find proteins for P58758 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore P58758 
Go to UniProtKB:  P58758
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
DST
Query on DST

Download CCD File 
A
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.417α = 90
b = 96.417β = 90
c = 65.068γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-12-06 
  • Released Date: 2008-02-05 
  • Deposition Author(s): Sakakibara, H.

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2019-10-16
    Changes: Data collection, Non-polymer description, Structure summary