9L8V | pdb_00009l8v

PyrN C-terminl domain in complex with L-glutamyl-sulfamoyl-adenosine (GSA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and Mechanistic Insights into Bacterial Hydrazine Biosynthesis.

Zhao, G.Huang, H.Li, Y.Yang, J.Guo, Y.Y.Xu, L.Wang, L.Shi, J.Wu, M.Feng, Y.Wang, B.Zhang, Z.M.Du, Y.L.

(2025) J Am Chem Soc 147: 42984-42993

  • DOI: https://doi.org/10.1021/jacs.5c15949
  • Primary Citation Related Structures: 
    9L8V

  • PubMed Abstract: 

    Nitrogen-nitrogen (N-N) bond-containing motifs are prevalent in both clinical drugs and natural products. Bacterial hydrazine synthetases catalyze N-N bond formation by coupling an amino acid and a hydroxylamine via a distinctive O -aminoacyl-hydroxylamine intermediate. Despite its wide occurrence, the structural and mechanistic basis of this process has remained elusive. Here, we report the first crystal structures of the O -aminoacyl-hydroxylamine synthetase (aaHS) component of a bacterial hydrazine synthetase, captured in binary and ternary complexes with substrates and catalytic intermediates. These structures reveal the molecular determinants of substrate recognition and, together with biochemical and computational analyses, establish a detailed mechanistic framework for the hydrazine synthetase family. Leveraging these insights, we expanded hydrazine biosynthesis through the targeted discovery of novel hydrazine synthetases and implemented a chemoenzymatic synthesis strategy. This work provides fundamental insights into hydrazine synthetases and lays the groundwork for their rational engineering as versatile biocatalysts.


  • Organizational Affiliation
    • The Fourth Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China.

Macromolecule Content 

  • Total Structure Weight: 242.61 kDa 
  • Atom Count: 17,498 
  • Modeled Residue Count: 2,129 
  • Deposited Residue Count: 2,184 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionine-tRNA ligaseA,
B,
C [auth D],
D [auth B00Z]
546Streptomyces candidusMutation(s): 0 
Gene Names: pyrNprfJ
EC: 5.4.3 (UniProt), 6.1.2 (UniProt)
UniProt
Find proteins for A0A516ELE7 (Streptomyces candidus)
Explore A0A516ELE7 
Go to UniProtKB:  A0A516ELE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A516ELE7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSU
(Subject of Investigation/LOI)

Query on GSU



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B],
S [auth D],
X [auth B00Z]
O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
C15 H21 N7 O9 S
YBRKRYFZKHICLS-WERHYGNASA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
E [auth A]
I [auth B]
J [auth B]
K [auth B]
O [auth D]
E [auth A],
I [auth B],
J [auth B],
K [auth B],
O [auth D],
P [auth D],
T [auth B00Z],
U [auth B00Z]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
L [auth B]
M [auth B]
Q [auth D]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
Q [auth D],
R [auth D],
V [auth B00Z],
W [auth B00Z]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.01α = 90
b = 243.81β = 99.04
c = 100.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2025-12-31
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Database references