4QDI

Crystal structure II of MurF from Acinetobacter baumannii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


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Literature

ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF

Cha, S.S.An, Y.J.Jeong, C.S.Yu, J.H.Chung, K.M.

(2014) Biochem.Biophys.Res.Commun. 450: 1045-1050

  • DOI: 10.1016/j.bbrc.2014.06.108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MurF adds d-Ala-d-Ala dipeptide to UDP-N-acetylmuramyl-l-Ala-γ-d-Glu-m-DAP (or l-Lys) in an ATP-dependent manner, which is the last step in the biosynthesis of monomeric precursor of peptidoglycan. Here we report crystal structures of two MurF-ATP co ...

    MurF adds d-Ala-d-Ala dipeptide to UDP-N-acetylmuramyl-l-Ala-γ-d-Glu-m-DAP (or l-Lys) in an ATP-dependent manner, which is the last step in the biosynthesis of monomeric precursor of peptidoglycan. Here we report crystal structures of two MurF-ATP complexes: the MurF-ATP complex and the MurF-ATP-UDP complex. The ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms the previous biochemical demonstration that a carbamoylated lysine and two Mg(2+) ions are required for enzyme activity of MurF. The UDP-MurF interactions observed in the crystal structure of the MurF-ATP-UDP complex depict the characteristic substrate-binding mode of MurF. The emergence and dissemination of multidrug-resistant Acinetobacter baumannii strains are great threats to public health. Therefore, the structural information on A. baumannii MurF as a validated target for drug discovery will provide a framework to develop antibacterial agents against multidrug-resistant A. baumannii infections as well as to understand the reaction mechanism of MurF.


    Organizational Affiliation

    Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea.,Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju 561-756, Republic of Korea.,Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea; Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Pusan 606-791, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea. Electronic address: chajung@kiost.ac.,Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju 561-756, Republic of Korea; Institute for Medical Science, Chonbuk National University Medical School, Jeonju 561-756, Republic of Korea. Electronic address: kmin@jbnu.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
A
472Acinetobacter baumannii (strain AB307-0294)Mutation(s): 0 
Gene Names: murF
EC: 6.3.2.10
Find proteins for A0A0J9X1Z8 (Acinetobacter baumannii (strain AB307-0294))
Go to UniProtKB:  A0A0J9X1Z8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.783α = 90.00
b = 85.783β = 90.00
c = 130.203γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4phasing
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release