6SLF

Nalpha-acylglutamine aminoacylase from Corynebacterium sp.releasing human axilla odorants co-crystallised with high affinity inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The specific biochemistry of human axilla odour formation viewed in an evolutionary context.

Natsch, A.Emter, R.

(2020) Philos Trans R Soc Lond B Biol Sci 375: 20190269-20190269

  • DOI: https://doi.org/10.1098/rstb.2019.0269
  • Primary Citation of Related Structures:  
    6SLF

  • PubMed Abstract: 

    Human body odour is dominated by the scent of specific odourants emanating from specialized glands in the axillary region. These specific odourants are produced by an intricate interplay between biochemical pathways in the host and odour-releasing enzymes present in commensal microorganisms of the axillary microbiome. Key biochemical steps for the release of highly odouriferous carboxylic acids and sulfur compounds have been elucidated over the past 15 years. Based on the profound molecular understanding and specific analytical methods developed, evolutionary questions could be asked for the first time with small population studies: (i) a genetic basis for body odour could be shown with a twin study, (ii) no effect of genes in the human leukocyte antigen complex on the pattern of odourant carboxylic acid was found, and (iii) loss of odour precursor secretion by a mutation in the ABCC11 gene could explain why a large fraction of the population in the Far East lack body odour formation. This review summarizes what is currently known at the molecular level on the biochemistry of the formation of key odourants in the human axilla. At the same time, we present for the first time the crystal structure of the N α -acyl-aminoacylase, a key human odour-releasing enzyme, thus describing at the molecular level how bacteria on the skin surface have adapted their enzyme to the specific substrates secreted by the human host. This article is part of the Theo Murphy meeting issue 'Olfactory communication in humans'.


  • Organizational Affiliation

    Givaudan Schweiz AG, Kemptpark 50, CH-8310 Kemptthal, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acyl-glutamine aminoacylase
A, B, C, D
400Corynebacterium striatumMutation(s): 0 
Gene Names: agaA
UniProt
Find proteins for Q8GGD4 (Corynebacterium striatum)
Explore Q8GGD4 
Go to UniProtKB:  Q8GGD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GGD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LJ8 (Subject of Investigation/LOI)
Query on LJ8

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
R [auth C],
V [auth D]
(2~{S})-5-azanyl-2-[[[(3~{S})-3-methyl-5-phenyl-pentyl]-oxidanyl-phosphoryl]methyl]-5-oxidanylidene-pentanoic acid
C18 H28 N O5 P
QVWDMOWNQBVUFQ-GOEBONIOSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
X [auth D]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
P [auth C]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
S [auth C],
W [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.688α = 90
b = 181.919β = 104.14
c = 93.122γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description