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PDBsum entry 1cd5

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protein links
Isomerase PDB id
1cd5
Jmol
Contents
Protein chain
266 a.a. *
Waters ×423
* Residue conservation analysis
PDB id:
1cd5
Name: Isomerase
Title: Glucosamine-6-phosphate deaminase from e.Coli, t conformer
Structure: Protein (glucosamine 6-phosphate deaminase). Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.30Å     R-factor:   0.207     R-free:   0.252
Authors: E.Horjales,M.M.Altamirano,M.L.Calcagno,R.C.Garratt,G.Oliva
Key ref:
E.Horjales et al. (1999). The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution. Structure, 7, 527-537. PubMed id: 10378272 DOI: 10.1016/S0969-2126(99)80069-0
Date:
05-Mar-99     Release date:   06-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A759  (NAGB_ECOLI) -  Glucosamine-6-phosphate deaminase
Seq:
Struc:
266 a.a.
266 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.99.6  - Glucosamine-6-phosphate deaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
UDP-N-acetylglucosamine Biosynthesis
      Reaction: Alpha-D-glucosamine 6-phosphate + H2O = D-fructose 6-phosphate + NH3
Alpha-D-glucosamine 6-phosphate
+ H(2)O
= D-fructose 6-phosphate
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Key reference    
 
 
DOI no: 10.1016/S0969-2126(99)80069-0 Structure 7:527-537 (1999)
PubMed id: 10378272  
 
 
The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution.
E.Horjales, M.M.Altamirano, M.L.Calcagno, R.C.Garratt, G.Oliva.
 
  ABSTRACT  
 
BACKGROUND: The allosteric hexameric enzyme glucosamine-6-phosphate deaminase from Escherichia coli catalyses the regulatory step of N-acetylglucosamine catabolism, which consists of the isomerisation and deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonia. The reversibility of the catalysis and its rapid-equilibrium random kinetic mechanism, among other properties, make this enzyme a good model for studying allosteric processes. RESULTS: Here we present the structure of P6(3)22 crystals, obtained in sodium acetate, of GlcN6P deaminase in its ligand-free T state. These crystals are very sensitive to X-ray radiation and have a high (78%) solvent content. The activesite lid (residues 162-185) is highly disordered in the T conformer; this may contribute significantly to the free-energy change of the whole allosteric transition. Comparison of the structure with the crystallographic coordinates of the R conformer (Brookhaven Protein Data Bank entry 1 dea) allows us to describe the geometrical changes associated with the allosteric transition as the movement of two rigid entities within each monomer. The active site, located in a deep cleft between these two rigid entities, presents a more open geometry in the T conformer than in the R conformer. CONCLUSIONS: The differences in active-site geometry are related to alterations in the substrate-binding properties associated with the allosteric transition. The rigid nature of the two mobile structural units of each monomer seems to be essential in order to explain the observed kinetics of the deaminase hexamer. The triggers for both the homotropic and heterotropic allosteric transitions are discussed and particular residues are assigned to these functions. A structural basis for an entropic term in the allosteric transition is an interesting new feature that emerges from this study.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The allosteric site observed in the same orientation for (a) the T conformer and (b) the R conformer.
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 527-537) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18186466 K.Fukushima, M.Wada, and M.Sakurai (2008).
An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes.
  Proteins, 71, 1940-1954.  
18186488 T.Doan, L.Martin, S.Zorrilla, D.Chaix, S.Aymerich, G.Labesse, and N.Declerck (2008).
A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor.
  Proteins, 71, 2038-2050.  
15755726 F.Vincent, G.J.Davies, and J.A.Brannigan (2005).
Structure and kinetics of a monomeric glucosamine 6-phosphate deaminase: missing link of the NagB superfamily?
  J Biol Chem, 280, 19649-19655.
PDB codes: 2bkv 2bkx
15838023 L.I.Alvarez-Añorve, M.L.Calcagno, and J.Plumbridge (2005).
Why does Escherichia coli grow more slowly on glucosamine than on N-acetylglucosamine? Effects of enzyme levels and allosteric activation of GlcN6P deaminase (NagB) on growth rates.
  J Bacteriol, 187, 2974-2982.  
12426581 I.J.MacRae, I.H.Segel, and A.J.Fisher (2002).
Allosteric inhibition via R-state destabilization in ATP sulfurylase from Penicillium chrysogenum.
  Nat Struct Biol, 9, 945-949.
PDB code: 1m8p
11320322 V.Hlinková, L.Urbániková, D.Krajcíková, and J.Sevcík (2001).
Purification, crystallization and preliminary X-ray analysis of two crystal forms of ribonuclease Sa3.
  Acta Crystallogr D Biol Crystallogr, 57, 737-739.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.