6G56

Apo-structure of the alanine racemase from Staphylococcus aureus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics.

Hoegl, A., Nodwell, M.B., Kirsch, V.C., Bach, N.C., Pfanzelt, M., Stahl, M., Schneider, S., Sieber, S.A.

(2018) Nat Chem 10: 1234-1245

  • DOI: https://doi.org/10.1038/s41557-018-0144-2
  • Primary Citation of Related Structures:  
    6G56, 6G58, 6G59

  • PubMed Abstract: 

    • Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging ...

    Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. Here we present a chemical proteomic method for reporting on PLP-DEs using functionalized cofactor probes. We synthesized pyridoxal analogues modified at the 2'-position, which are taken up by cells and metabolized in situ. These pyridoxal analogues are phosphorylated to functional cofactor surrogates by cellular pyridoxal kinases and bind to PLP-DEs via an aldimine bond which can be rendered irreversible by NaBH 4 reduction. Conjugation to a reporter tag enables the subsequent identification of PLP-DEs using quantitative, label-free mass spectrometry. Using these probes we accessed a significant portion of the Staphylococcus aureus PLP-DE proteome (73%) and annotate uncharacterized proteins as novel PLP-DEs. We also show that this approach can be used to study structural tolerance within PLP-DE active sites and to screen for off-targets of the PLP-DE inhibitor D-cycloserine.

    Organizational Affiliation: 

    Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany. stephan.sieber@tum.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alanine racemase 1
A, B
404Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: alr1, alr, SAV2070
EC: 5.1.1.1
UniProt
Find proteins for P63479 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P63479 
Go to UniProtKB:  P63479
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63479
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
BA [auth B],
CA [auth B],
K [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.701α = 90
b = 114.521β = 90
c = 126.093γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilGermany725085
German Research FoundationGermanyEXC 114

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-05
    Changes: Data collection, Database references