8PMM

Deposited: 2023-06-29 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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

(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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NARROW LEAF 1	A, B, C	433	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147
UniProt
Find proteins for B4XT64 (Oryza sativa subsp. japonica) Explore B4XT64 Go to UniProtKB: B4XT64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4XT64
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 G [auth B] SDF format, chain I [auth C] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain D [auth A]	D [auth A], G [auth B], I [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C]	E [auth A], H [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C]

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History & Funding Information

Deposition Author(s):

Huang, L.Y.

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