6ZK3

Plant nucleoside hydrolase - ZmNRh2b in complex with ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Plant nucleoside N-ribohydrolases: riboside binding and role in nitrogen storage mobilization.

Luptakova, E.Vigouroux, A.Koncitikova, R.Kopecna, M.Zalabak, D.Novak, O.Salcedo Sarmiento, S.Cavar Zeljkovic, S.Kopecny, D.J.von Schwartzenberg, K.Strnad, M.Spichal, L.De Diego, N.Kopecny, D.Morera, S.

(2023) Plant J 

  • DOI: https://doi.org/10.1111/tpj.16572
  • Primary Citation of Related Structures:  
    6ZK1, 6ZK2, 6ZK3, 6ZK4, 6ZK5

  • PubMed Abstract: 

    Cells save their energy during nitrogen starvation by selective autophagy of ribosomes and degradation of RNA to ribonucleotides and nucleosides. Nucleosides are hydrolyzed by nucleoside N-ribohydrolases (nucleosidases, NRHs). Subclass I of NRHs preferentially hydrolyzes the purine ribosides while subclass II is more active towards uridine and xanthosine. Here, we performed a crystallographic and kinetic study to shed light on nucleoside preferences among plant NRHs followed by in vivo metabolomic and phenotyping analyses to reveal the consequences of enhanced nucleoside breakdown. We report the crystal structure of Zea mays NRH2b (subclass II) and NRH3 (subclass I) in complexes with the substrate analog forodesine. Purine and pyrimidine catabolism are inseparable because nucleobase binding in the active site of ZmNRH is mediated via a water network and is thus unspecific. Dexamethasone-inducible ZmNRH overexpressor lines of Arabidopsis thaliana, as well as double nrh knockout lines of moss Physcomitrium patents, reveal a fine control of adenosine in contrast to other ribosides. ZmNRH overexpressor lines display an accelerated early vegetative phase including faster root and rosette growth upon nitrogen starvation or osmotic stress. Moreover, the lines enter the bolting and flowering phase much earlier. We observe changes in the pathways related to nitrogen-containing compounds such as β-alanine and several polyamines, which allow plants to reprogram their metabolism to escape stress. Taken together, crop plant breeding targeting enhanced NRH-mediated nitrogen recycling could therefore be a strategy to enhance plant growth tolerance and productivity under adverse growth conditions.


  • Organizational Affiliation

    Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrimidine-specific ribonucleoside hydrolase rihA
A, B, C, D, E
A, B, C, D, E, F
343Zea maysMutation(s): 0 
Gene Names: 542168ZEAMMB73_Zm00001d031958
UniProt
Find proteins for B6THD4 (Zea mays)
Explore B6THD4 
Go to UniProtKB:  B6THD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6THD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
HB [auth F]
IB [auth F]
JB [auth F]
BA [auth C],
CA [auth C],
HB [auth F],
IB [auth F],
JB [auth F],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
XA [auth E]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
RIB (Subject of Investigation/LOI)
Query on RIB

Download Ideal Coordinates CCD File 
DB [auth F]
GA [auth D]
H [auth A]
P [auth B]
RA [auth E]
DB [auth F],
GA [auth D],
H [auth A],
P [auth B],
RA [auth E],
X [auth C]
alpha-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth E]
BB [auth E]
DA [auth C]
EA [auth C]
KB [auth F]
AB [auth E],
BB [auth E],
DA [auth C],
EA [auth C],
KB [auth F],
LB [auth F],
MA [auth D],
N [auth A],
NA [auth D],
OA [auth D],
PA [auth D],
V [auth B],
YA [auth E],
ZA [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
EB [auth F]
FB [auth F]
GB [auth F]
HA [auth D]
AA [auth C],
EB [auth F],
FB [auth F],
GB [auth F],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
LA [auth D],
Q [auth B],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CB [auth F]
FA [auth D]
G [auth A]
O [auth B]
QA [auth E]
CB [auth F],
FA [auth D],
G [auth A],
O [auth B],
QA [auth E],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.81α = 90
b = 86.71β = 99.44
c = 131.91γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Refinement description