8PME

Structure of Nal1 indica cultivar IR64, construct 88-458

PDB DOI: https://doi.org/10.2210/pdb8PME/pdb

Classification: PLANT PROTEIN
Organism(s): Oryza sativa Indica Group
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2023-06-28 Released: 2024-04-17
Deposition Author(s): Huang, L.Y., Rety, S., Xi, X.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.235
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The catalytic triad of rice NARROW LEAF1 involves H234.

Huang, L.Y., Liu, N.N., Chen, W.F., Ai, X., Li, H.H., Zhang, Z.L., Hou, X.M., Fosse, P., Mauffret, O., Lei, D.S., Rety, S., Xi, X.G.

(2024) Nat Plants

PubMed: 38600265 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41477-024-01668-1
Primary Citation of Related Structures:
8PME, 8PMG, 8PMI, 8PML, 8PMM, 8PN1, 8PN2

PubMed Abstract:
NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.

Organizational Affiliation

College of Life Sciences, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, People's Republic of China.

Macromolecule Content

Total Structure Weight: 124.27 kDa
Atom Count: 8,163
Modelled Residue Count: 1,033
Deposited Residue Count: 1,113
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Narrow leaf 1	A, B, C	371	Oryza sativa Indica Group	Mutation(s): 0 Gene Names: Nal1
UniProt
Find proteins for A0A8K1DE77 (Oryza sativa) Explore A0A8K1DE77 Go to UniProtKB: A0A8K1DE77
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8K1DE77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B]	D [auth A], H [auth B], K [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B]	F [auth A], G [auth A], J [auth B], M [auth C]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain E [auth A]	E [auth A], I [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.235
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.279	α = 90
b = 103.735	β = 90
c = 143.471	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Huang, L.Y.

Rety, S.

Xi, X.G.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071291
National Natural Science Foundation of China (NSFC)	China	32201042
National Natural Science Foundation of China (NSFC)	China	32071225
National Natural Science Foundation of China (NSFC)	China	31870788