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PDBsum entry 2nm3

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protein ligands links
Lyase PDB id
2nm3
Jmol
Contents
Protein chain
121 a.a. *
Ligands
ACT
MPU
Waters ×172
* Residue conservation analysis
PDB id:
2nm3
Name: Lyase
Title: Crystal structure of dihydroneopterin aldolase from s. Aureu complex with (1s,2s)-monapterin at 1.68 angstrom resolution
Structure: Dihydroneopterin aldolase. Chain: a. Synonym: dhna. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Gene: folb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.68Å     R-factor:   0.227     R-free:   0.262
Authors: J.Blaszczyk,X.Ji,H.Yan
Key ref:
J.Blaszczyk et al. (2007). Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase. J Mol Biol, 368, 161-169. PubMed id: 17331536 DOI: 10.1016/j.jmb.2007.02.009
Date:
20-Oct-06     Release date:   04-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56740  (FOLB_STAAU) -  Dihydroneopterin aldolase
Seq:
Struc:
121 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.2.25  - Dihydroneopterin aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Biosynthesis (late stages)
      Reaction: 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8- dihydropteridine = 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde
2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8- dihydropteridine
=
2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine
Bound ligand (Het Group name = MPU)
matches with 77.78% similarity
+
glycolaldehyde
Bound ligand (Het Group name = ACT)
matches with 60.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     folic acid-containing compound metabolic process   3 terms 
  Biochemical function     lyase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2007.02.009 J Mol Biol 368:161-169 (2007)
PubMed id: 17331536  
 
 
Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase.
J.Blaszczyk, Y.Li, J.Gan, H.Yan, X.Ji.
 
  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 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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereoviews showing the catalytic center of SaDHNA radical dot NP. (a) Representative 2F[o] – F[c] electron density (green net) contoured at 1.2 σ for the NP molecule. The electron density map is shown as green nets. (b) The catalytic center assembly of SaDHNA radical dot NP. Amino acid residues and the ligand are illustrated as ball-and-stick models with the same atomic color scheme as that used in Figure 1. The primary and symmetry-related DHNA molecules are shown in cyan and orange, respectively. NP is highlighted with thicker bonds and larger atoms. The electrostatic interactions between the protein and the ligand are indicated with broken lines.
Figure 3.
Figure 3. Stereoviews showing the catalytic center of SaDHNA radical dot MP. (a) The 2F[o] – F[c] map (green net) contoured at 1.2 σ for the bound MP molecule. (b) The catalytic center assembly of SaDHNA radical dot MP. Amino acid residues and the ligand are illustrated as ball-and-stick models in the same atomic color scheme as that used in Figure 1. The primary and symmetry-related DHNA molecules are shown in cyan and orange, respectively. MP is highlighted with thicker bonds and larger atoms. The electrostatic interactions between the protein and the MP molecule are indicated with broken lines.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 368, 161-169) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19897652 A.Pribat, I.K.Blaby, A.Lara-Núñez, J.F.Gregory, V.de Crécy-Lagard, and A.D.Hanson (2010).
FolX and FolM are essential for tetrahydromonapterin synthesis in Escherichia coli and Pseudomonas aeruginosa.
  J Bacteriol, 192, 475-482.  
19558703 R.Alterovitz, A.Arvey, S.Sankararaman, C.Dallett, Y.Freund, and K.Sjölander (2009).
ResBoost: characterizing and predicting catalytic residues in enzymes.
  BMC Bioinformatics, 10, 197.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.