8Y4U | pdb_00008y4u

Crystal structure of a His1 from oryza sativa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.249 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Y4U

This is version 1.1 of the entry. See complete history

Literature

Crystal structure of HPPD inhibitor sensitive protein from Oryza sativa.

Wang, N.He, S.Yang, B.Zhang, H.Liu, D.Song, P.Chen, T.Wang, W.Ge, H.Ma, J.

(2024) Biochem Biophys Res Commun 704: 149672-149672

  • DOI: https://doi.org/10.1016/j.bbrc.2024.149672
  • Primary Citation Related Structures: 
    8Y4U

  • PubMed Abstract: 

    4-hydroxyphenylpyruvate dioxygenase (HPPD) Inhibitor Sensitive 1 (HIS1) is an endogenous gene of rice, conferring broad-spectrum resistance to β-triketone herbicides. Similar genes, known as HIS1-like genes (HSLs), exhibit analogous functions and can complement the herbicide-resistant characteristics endowed by HIS1. The identification of HIS1 and HSLs represents a valuable asset, as the intentional pairing of herbicides with resistance genes emerges as an effective strategy for crop breeding. Encoded by HIS1 is a Fe(II)/2-oxoglutarate-dependent oxygenase responsible for detoxifying β-triketone herbicides through hydroxylation. However, the precise structure supporting this function remains unclear. This work, which determined the crystal structure of HIS1, reveals a conserved core motif of Fe(II)/2-oxoglutarate-dependent oxygenase and pinpoints the crucial residue dictating substrate preference between HIS1 and HSL.


  • Organizational Affiliation
    • Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China. Electronic address: wangn6@ahu.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 40.22 kDa 
  • Atom Count: 2,446 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 351 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe(II)/2-oxoglutarate-dependent oxygenase351Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: HIS1LOC_Os02g17940Os02g0280700OSNPB_020280700
UniProt
Find proteins for Q6ES21 (Oryza sativa subsp. japonica)
Explore Q6ES21 
Go to UniProtKB:  Q6ES21
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ES21
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.249 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.431α = 90
b = 101.028β = 90
c = 130.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references