5W7B

Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S262A mutant, with LPS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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 hydrolase small subunitA,
C [auth B]
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: AOAH
EC: 3.1.1.77
Membrane Entity: Yes 
UniProt
Find proteins for O18823 (Oryctolagus cuniculus)
Explore O18823 
Go to UniProtKB:  O18823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18823
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyloxyacyl hydrolase large subunitB [auth C],
D
422Oryctolagus cuniculusMutation(s): 1 
Gene Names: AOAH
EC: 3.1.1.77
Membrane Entity: Yes 
UniProt
Find proteins for O18823 (Oryctolagus cuniculus)
Explore O18823 
Go to UniProtKB:  O18823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18823
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose
F, J
3N/A
Glycosylation Resources
GlyTouCan:  G74817EY
GlyCosmos:  G74817EY
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G, K
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTT (Subject of Investigation/LOI)
Query on FTT

Download Ideal Coordinates CCD File 
JB [auth D]
KB [auth D]
NA [auth C]
OA [auth C]
P [auth A]
JB [auth D],
KB [auth D],
NA [auth C],
OA [auth C],
P [auth A],
RA [auth B]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
1PE (Subject of Investigation/LOI)
Query on 1PE

Download Ideal Coordinates CCD File 
FB [auth D],
GB [auth D],
JA [auth C],
KA [auth C]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MYR (Subject of Investigation/LOI)
Query on MYR

Download Ideal Coordinates CCD File 
LB [auth D],
PA [auth C],
Q [auth A],
SA [auth B]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
MES (Subject of Investigation/LOI)
Query on MES

Download Ideal Coordinates CCD File 
QA [auth B],
V [auth C],
XA [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
CB [auth D]
DB [auth D]
EB [auth D]
GA [auth C]
HA [auth C]
CB [auth D],
DB [auth D],
EB [auth D],
GA [auth C],
HA [auth C],
IA [auth C],
O [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth D]
BA [auth C]
BB [auth D]
CA [auth C]
AA [auth C],
AB [auth D],
BA [auth C],
BB [auth D],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
M [auth A],
N [auth A],
W [auth C],
X [auth C],
Y [auth C],
YA [auth D],
Z [auth C],
ZA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
U [auth C],
WA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
HB [auth D],
IB [auth D],
LA [auth C],
MA [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
R [auth C]
S [auth C]
T [auth C]
TA [auth D]
UA [auth D]
R [auth C],
S [auth C],
T [auth C],
TA [auth D],
UA [auth D],
VA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.522α = 90
b = 138.806β = 90
c = 89.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary