2DHN | pdb_00002dhn

COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 2.2 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2DHN/pdb

• Classification: PRODUCT COMPLEX
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-03-31 Released: 1999-04-20 
• Deposition Author(s): Hennig, M., D'Arcy, A., Hampele, I.C., Page, M.G.P., Oefner, C.H., Dale, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.298 (Depositor) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from Staphylococcus aureus.

Hennig, M., D'Arcy, A., Hampele, I.C., Page, M.G., Oefner, C., Dale, G.E.

(1998) Nat Struct Biol 5: 357-362

• PubMed: 9586996 
• DOI: https://doi.org/10.1038/nsb0598-357
• Primary Citation Related Structures: 
  1DHN, 2DHN


• PubMed Abstract: 
  

  Dihydroneopterin aldolase catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin during the de novo synthesis of folic acid from guanosine triphosphate. The gene encoding the dihydroneopterin aldolase from S. aureus has been cloned, sequenced and expressed in Escherichia coli. The protein has been purified for biochemical characterization and its X-ray structure determined at 1.65 A resolution. The protein forms an octamer of 110,000 Mr molecular weight. Four molecules assemble into a ring, and two rings come together to give a cylinder with a hole of at least 13 A diameter. The structure of the binary complex with the product 6-hydroxymethyl-7,8-dihydropterin has defined the location of the active site. The structural information and results of site directed mutagenesis allow an enzyme reaction mechanism to be proposed.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.96 kDa 
• Atom Count: 1,055 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-DIHYDRONEOPTERIN ALDOLASE	A	121	Staphylococcus aureus	Mutation(s): 0  Gene Names: DHNA EC: 5.1.99.8 (UniProt), 4.1.2.25 (UniProt)
UniProt
Find proteins for P56740 (Staphylococcus aureus) Explore P56740  Go to UniProtKB:  P56740

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PH2	B [auth A]	2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE C7 H9 N5 O2 CQQNNQTXUGLUEV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.298 (Depositor) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.2	α = 90
b = 62.2	β = 90
c = 123.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-20 
Deposition Author(s): Hennig, M., D'Arcy, A., Hampele, I.C., Page, M.G.P., Oefner, C.H., Dale, G.

Revision History  

• Version 1.0: 1999-04-20
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-04-03
  Changes: Refinement description