5C3Q

Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and thymine (T)

  • Classification: OXIDOREDUCTASE
  • Organism(s): Neurospora crassa
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-06-17 Released: 2015-10-21 
  • Deposition Author(s): Li, W., Zhang, T., Ding, J.
  • Funding Organization(s): Ministry of Science and Technology of China, National Natural Science Foundation of China, Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi

Li, W.Zhang, T.Ding, J.

(2015) Nucleic Acids Res 43: 10026-10038

  • DOI: https://doi.org/10.1093/nar/gkv979
  • Primary Citation of Related Structures:  
    5C3O, 5C3P, 5C3Q, 5C3R, 5C3S

  • PubMed Abstract: 

    TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.


  • Organizational Affiliation

    National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymine dioxygenase
A, B, C, D
343Neurospora crassaMutation(s): 0 
Gene Names: NCU06416
UniProt
Find proteins for Q7RYZ9 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7RYZ9 
Go to UniProtKB:  Q7RYZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7RYZ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
BA [auth D],
F [auth A],
N [auth B],
W [auth C]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
TDR
Query on TDR

Download Ideal Coordinates CCD File 
CA [auth D],
G [auth A],
O [auth B],
X [auth C]
THYMINE
C5 H6 N2 O2
RWQNBRDOKXIBIV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
H [auth A]
I [auth A]
DA [auth D],
EA [auth D],
FA [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
M [auth B],
V [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.9α = 90
b = 156.318β = 91.77
c = 76.028γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2011CB966301
Ministry of Science and Technology of ChinaChina2013CB910404
National Natural Science Foundation of ChinaChina31221001
Chinese Academy of SciencesChinaXDB08010302

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description