8CPB

1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with AMPPNP, and AnhMurNAc at 1.7 Angstroms resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa.

El-Araby, A.M.Jimenez-Faraco, E.Feltzer, R.Martin-Garcia, J.M.Karri, B.R.Ramachandran, B.Kim, C.Fisher, J.F.Hermoso, J.A.Mobashery, S.

(2023) J Biol Chem 299: 105198-105198

  • DOI: https://doi.org/10.1016/j.jbc.2023.105198
  • Primary Citation of Related Structures:  
    8BRE, 8C0U, 8CP9, 8CPB

  • PubMed Abstract: 

    The bacterial cell envelope is the structure with which the bacterium engages with, and is protected from, its environment. Within this envelop is a conserved peptidoglycan polymer which confers shape and strength to the cell envelop. The enzymatic processes that build, remodel, and recycle the chemical components of this cross-linked polymer are preeminent targets of antibiotics and exploratory targets for emerging antibiotic structures. We report a comprehensive kinetic and structural analysis for one such enzyme, the Pseudomonas aeruginosa anhydro-N-acetylmuramic acid (anhNAM) kinase (AnmK). AnmK is an enzyme in the peptidoglycan-recycling pathway of this pathogen. It catalyzes the pairing of hydrolytic ring opening of anhNAM with concomitant ATP-dependent phosphoryl transfer. AnmK follows a random-sequential kinetic mechanism with respect to its anhNAM and ATP substrates. Crystallographic analyses of four distinct structures (apo AnmK, AnmK:AMPPNP, AnmK:AMPPNP:anhNAM, and AnmK:ATP:anhNAM) demonstrate that both substrates enter the active site independently in an ungated conformation of the substrate subsites, with protein loops acting as gates for anhNAM binding. Catalysis occurs within a closed conformational state for the enzyme. We observe this state crystallographically using ATP-mimetic molecules. A remarkable X-ray structure for dimeric AnmK sheds light on the precatalytic and postcatalytic ternary complexes. Computational simulations in conjunction with the high-resolution X-ray structures reveal the full catalytic cycle. We further report that a P. aeruginosa strain with disrupted anmK gene is more susceptible to the β-lactam imipenem compared to the WT strain. These observations position AnmK for understanding the nexus among peptidoglycan recycling, susceptibility to antibiotics, and bacterial virulence.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anhydro-N-acetylmuramic acid kinase
A, B
368Pseudomonas aeruginosaMutation(s): 0 
Gene Names: anmKPA0666
EC: 2.7.1.170
UniProt
Find proteins for Q9I5Q5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I5Q5 
Go to UniProtKB:  Q9I5Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I5Q5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
AH0 (Subject of Investigation/LOI)
Query on AH0

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID
C11 H17 N O7
ZFEGYUMHFZOYIY-YVNCZSHWSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.67α = 90
b = 90.67β = 90
c = 171.686γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Estatal de Investigacion (AEI)SpainPID2020-115331GB_I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references