7Q6Z | pdb_00007q6z

Structure of Hedgehog acyltransferase (HHAT) in complex with megabody 177 bound to IMP-1575

• PDB DOI: https://doi.org/10.2210/pdb7Q6Z/pdb
• EM Map EMD-13860: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli K-12
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-11-09 Released: 2022-01-26 
• Deposition Author(s): Coupland, C., Carrique, L., Siebold, C.
• Funding Organization(s): Cancer Research UK, Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure, mechanism, and inhibition of Hedgehog acyltransferase.

Coupland, C.E., Andrei, S.A., Ansell, T.B., Carrique, L., Kumar, P., Sefer, L., Schwab, R.A., Byrne, E.F.X., Pardon, E., Steyaert, J., Magee, A.I., Lanyon-Hogg, T., Sansom, M.S.P., Tate, E.W., Siebold, C.

(2021) Mol Cell 81: 5025-5038.e10

• PubMed: 34890564 
• DOI: https://doi.org/10.1016/j.molcel.2021.11.018
• Primary Citation Related Structures: 
  7Q1U, 7Q6Z


• PubMed Abstract: 
  

  The Sonic Hedgehog (SHH) morphogen pathway is fundamental for embryonic development and stem cell maintenance and is implicated in various cancers. A key step in signaling is transfer of a palmitate group to the SHH N terminus, catalyzed by the multi-pass transmembrane enzyme Hedgehog acyltransferase (HHAT). We present the high-resolution cryo-EM structure of HHAT bound to substrate analog palmityl-coenzyme A and a SHH-mimetic megabody, revealing a heme group bound to HHAT that is essential for HHAT function. A structure of HHAT bound to potent small-molecule inhibitor IMP-1575 revealed conformational changes in the active site that occlude substrate binding. Our multidisciplinary analysis provides a detailed view of the mechanism by which HHAT adapts the membrane environment to transfer an acyl chain across the endoplasmic reticulum membrane. This structure of a membrane-bound O-acyltransferase (MBOAT) superfamily member provides a blueprint for other protein-substrate MBOATs and a template for future drug discovery.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
Department of Chemistry, Imperial College London, 82 Wood Lane, London W12 0BZ, UK.
Department of Biochemistry, University of Oxford, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Pleinlaan 2, 1050 Brussels, Belgium.
National Heart and Lung Institute, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
Department of Chemistry, Imperial College London, 82 Wood Lane, London W12 0BZ, UK. Electronic address: [e-mail].
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 162.53 kDa 
• Atom Count: 4,970 
• Modeled Residue Count: 597 
• Deposited Residue Count: 1,422 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-cysteine N-palmitoyltransferase HHAT	A	503	Homo sapiens	Mutation(s): 0  Gene Names: HHAT, MART2, SKI1 EC: 2.3.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VTY9 (Homo sapiens) Explore Q5VTY9  Go to UniProtKB:  Q5VTY9
PHAROS:  Q5VTY9 GTEx:  ENSG00000054392

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody 177	B	919	Escherichia coli K-12	Mutation(s): 0  EC: 3.2.1 Membrane Entity: Yes
UniProt
Find proteins for P42592 (Escherichia coli (strain K12)) Explore P42592  Go to UniProtKB:  P42592

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CLR	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
9V3 (Subject of Investigation/LOI)	E [auth A]	2-(2-methylpropylamino)-1-[(4R)-4-(6-methylpyridin-2-yl)-6,7-dihydro-4H-thieno[3,2-c]pyridin-5-yl]ethanone C19 H25 N3 O S OVUGAMKQXDOHDJ-LJQANCHMSA-N
PLM	F [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9V3	BindingDB:  7Q6Z	Ki: 38 (nM) from 1 assay(s)
		IC50: min: 76, max: 750 (nM) from 2 assay(s)
		EC50: 99 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
MODEL REFINEMENT	Coot	0.9.2
RECONSTRUCTION	cryoSPARC	V3.1.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Coupland, C., Carrique, L., Siebold, C.

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Funding Organization	Location	Grant Number
Cancer Research UK	European Union	C20724/A26752
Cancer Research UK	European Union	C20724/A14414
Biotechnology and Biological Sciences Research Council (BBSRC)	European Union	BB/T01508X/1
European Research Council (ERC)	European Union	647278

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary