Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 66.28 kDa 
• Atom Count: 4519 
• Modelled Residue Count: 524 
• Deposited Residue Count: 562 
• Unique protein chains: 2

5W78

Human acyloxyacyl hydrolase (AOAH), proteolytically processed

• DOI: 10.2210/pdb5W78/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2017-06-19 Released: 2018-01-03 
• Deposition Author(s): Gorelik, A., Illes, K., Nagar, B.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Crystal structure of the mammalian lipopolysaccharide detoxifier.

Gorelik, A., Illes, K., Nagar, B.

(2018) Proc Natl Acad Sci U S A 115: E896-E905

• PubMed: 29343645 
• DOI: 10.1073/pnas.1719834115
• Primary Citation of Related Structures:  
  5W78, 5W7A, 5W7B, 5W7C, 5W7D, 5W7E, 5W7F


• PubMed Abstract: 
  

LPS is a potent bacterial endotoxin that triggers the innate immune system. Proper recognition of LPS by pattern-recognition receptors requires a full complement of typically six acyl chains in the lipid portion. Acyloxyacyl hydrolase (AOAH) is a host enzyme that removes secondary (acyloxyacyl-linked) fatty acids from LPS, rendering it immunologically inert. This activity is critical for recovery from immune tolerance that follows Gram-negative infection. To understand the molecular mechanism of AOAH function, we determined its crystal structure and its complex with LPS. The substrate's lipid moiety is accommodated in a large hydrophobic pocket formed by the saposin and catalytic domains with a secondary acyl chain inserted into a narrow lateral hydrophobic tunnel at the active site. The enzyme establishes dispensable contacts with the phosphate groups of LPS but does not interact with its oligosaccharide portion. Proteolytic processing allows movement of an amphipathic helix possibly involved in substrate access at membranes.

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Organizational Affiliation: 

Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, H3G0B1, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyloxyacyl hydrolase	A	139	Homo sapiens	Mutation(s): 0  Gene Names: AOAH EC: 3.1.1.77 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28039 (Homo sapiens) Explore P28039  Go to UniProtKB:  P28039
PHAROS:  P28039 GTEx:  ENSG00000136250

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyloxyacyl hydrolase	B	423	Homo sapiens	Mutation(s): 0  Gene Names: AOAH EC: 3.1.1.77 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28039 (Homo sapiens) Explore P28039  Go to UniProtKB:  P28039
PHAROS:  P28039 GTEx:  ENSG00000136250

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM (Subject of Investigation/LOI)	J [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
MYR (Subject of Investigation/LOI)	F [auth A], G [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO (Subject of Investigation/LOI)	K [auth B]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.402	α = 90
b = 87.356	β = 90
c = 146.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-19 
• Released Date: 2018-01-03 
Deposition Author(s): Gorelik, A., Illes, K., Nagar, B.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-133535

Revision History  

• Version 1.0: 2018-01-03
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2018-01-31
  Changes: Database references
• Version 1.3: 2018-02-14
  Changes: Database references
• Version 1.4: 2020-01-08
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary