9CHY | pdb_00009chy

Crystal structure of the human MESH1 (D66K)-PAPS complex

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2024-07-02 Released: 2025-12-10 
  • Deposition Author(s): Rose, J., Zhou, P.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

MESH1 functions as a metazoan PAPS phosphatase to regulate sulfation.

Lin, C.C.Rose, J.Zhang, A.Mirando, A.J.Mestre, A.A.Ding, C.C.Liao, Y.Chen, S.Y.Setayeshpour, Y.Wu, J.Li, Z.Yan, D.Hilton, M.J.Zhou, P.Chi, J.T.

(2026) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-026-02190-5
  • Primary Citation Related Structures: 
    9CHY

  • PubMed Abstract: 

    Biological sulfation reactions require 3'-phosphoadenosine-5'-phosphosulfate (PAPS) as the universal sulfate donor. While the biosynthetic pathway of PAPS has been well characterized, the phosphatase degrading PAPS remains unidentified. Here, we discover MESH1 as a PAPS phosphatase that hydrolyzes PAPS into adenosine-5'-phosphosulfate and phosphate. Our crystallographic analysis of the MESH1-PAPS complex confirms PAPS as a bona fide substrate of MESH1. We further show that MESH1 localizes to Golgi, where sulfotransferases consume PAPS to produce sulfated glycosaminoglycan (sGAG). We show that MESH1 (also known as HDDC3) knockdown enhances sGAG production in a chondrogenic cell line. Furthermore, in brachymorphic mice, Mesh1 knockout significantly elevates sGAG levels in joint cartilage and improves bone density. In Caenorhabditis elegans lacking bpnt-1, neurotoxic PAP accumulation is alleviated by MESH1 overexpression, reducing upstream PAPS levels. Our biochemical, structural and functional findings establish MESH1 as a key PAPS phosphatase and highlights its potential as a therapeutic target in disorders characterized by sulfation deficiency.


  • Organizational Affiliation
    • Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 42.3 kDa 
  • Atom Count: 3,223 
  • Modeled Residue Count: 359 
  • Deposited Residue Count: 360 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
A, B
180Homo sapiensMutation(s): 1 
Gene Names: HDDC3MESH1
EC: 3.1.7.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4P3 (Homo sapiens)
Explore Q8N4P3 
Go to UniProtKB:  Q8N4P3
PHAROS:  Q8N4P3
GTEx:  ENSG00000184508 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N4P3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PPS
(Subject of Investigation/LOI)

Query on PPS



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE
C10 H15 N5 O13 P2 S
GACDQMDRPRGCTN-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY

Query on ACY



Download:Ideal Coordinates CCD File
H [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.95α = 90
b = 71.7β = 90
c = 75.92γ = 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 Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references