2NM2

Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2R)-neopterin at 1.50 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase.

Blaszczyk, J.Li, Y.Gan, J.Yan, H.Ji, X.

(2007) J.Mol.Biol. 368: 161-169

  • DOI: 10.1016/j.jmb.2007.02.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and the epimerization of DHNP to 7,8-dihydromonopterin (DHMP). Although crystal structures of the enzyme from several m ...

    Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and the epimerization of DHNP to 7,8-dihydromonopterin (DHMP). Although crystal structures of the enzyme from several microorganisms have been reported, no structural information is available about the critical interactions between DHNA and the trihydroxypropyl moiety of the substrate, which undergoes bond cleavage and formation. Here, we present the structures of Staphylococcus aureus DHNA (SaDHNA) in complex with neopterin (NP, an analog of DHNP) and with monapterin (MP, an analog of DHMP), filling the gap in the structural analysis of the enzyme. In combination with previously reported SaDHNA structures in its ligand-free form (PDB entry 1DHN) and in complex with HP (PDB entry 2DHN), four snapshots for the catalytic center assembly along the reaction pathway can be derived, advancing our knowledge about the molecular mechanism of SaDHNA-catalyzed reactions. An additional step appears to be necessary for the epimerization of DHMP to DHNP. Three active site residues (E22, K100, and Y54) function coordinately during catalysis: together, they organize the catalytic center assembly, and individually, each plays a central role at different stages of the catalytic cycle.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroneopterin aldolase
A, B, C, D
121Staphylococcus aureusMutation(s): 0 
Gene Names: folB
EC: 4.1.2.25
Find proteins for P56740 (Staphylococcus aureus)
Go to UniProtKB:  P56740
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEU
Query on NEU

Download SDF File 
Download CCD File 
A, B, C, D
L-NEOPTERIN
2-AMINO-6-((1S,2R)-1,2,3-TRIHYDROXYPROPYL)PTERIDIN-4(3H)-ONE
C9 H11 N5 O4
BMQYVXCPAOLZOK-XINAWCOVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 60.033α = 90.00
b = 60.033β = 90.00
c = 123.057γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2019-07-24
    Type: Data collection, Refinement description