5W7C

Human acyloxyacyl hydrolase (AOAH), proteolytically processed, S263A mutant, with LPS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, H3G0B1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyloxyacyl hydrolaseA,
C [auth B]
139Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28039
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P28039-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyloxyacyl hydrolaseB [auth C],
D
423Homo sapiensMutation(s): 1 
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28039
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P28039-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTT
Query on FTT

Download Ideal Coordinates CCD File 
J [auth A]
P [auth C]
Q [auth C]
S [auth B]
Y [auth D]
J [auth A],
P [auth C],
Q [auth C],
S [auth B],
Y [auth D],
Z [auth D]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C],
R [auth B],
W [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
DAO
Query on DAO

Download Ideal Coordinates CCD File 
O [auth C],
X [auth D]
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth C]
L [auth C]
M [auth C]
T [auth D]
U [auth D]
K [auth C],
L [auth C],
M [auth C],
T [auth D],
U [auth D],
V [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.17α = 90
b = 104.08β = 90
c = 145.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-133535

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary