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Isomerase PDB id
1hot
Jmol
Contents
Protein chains
266 a.a. *
Ligands
16G ×2
PO4 ×2
Waters ×189
* Residue conservation analysis
PDB id:
1hot
Name: Isomerase
Title: Glucosamine 6-phosphate deaminase complexed with the allosteric activator n-acetyl-glucosamine-6-phosphate
Structure: Glucosamine 6-phosphate deaminase. Chain: a, b. Ec: 5.3.1.10
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
2.40Å     R-factor:   0.165    
Authors: G.Oliva,M.L.Fontes,R.Garratt,M.M.Altamirano,M.L.Calcagno, E.Horjales
Key ref:
G.Oliva et al. (1995). Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution. Structure, 3, 1323-1332. PubMed id: 8747459 DOI: 10.1016/S0969-2126(01)00270-2
Date:
17-Nov-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
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: D-glucosamine 6-phosphate + H2O = D-fructose 6-phosphate + NH3
D-glucosamine 6-phosphate
Bound ligand (Het Group name = 16G)
matches with 84.00% similarity 		+ 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     carbohydrate metabolic process   4 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(01)00270-2 Structure 3:1323-1332 (1995)
PubMed id: 8747459  
 
 
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution.
G.Oliva, M.R.Fontes, R.C.Garratt, M.M.Altamirano, M.L.Calcagno, E.Horjales.
 
  ABSTRACT  
 
BACKGROUND: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldoseketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. RESULTS: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 A resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. CONCLUSIONS: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. . Two views of the hexamer. The chain segments are colour coded as in Figure 1. (a) View along the threefold axis, with the three twofold axes in the plane of the figure. (b) The threefold axis is parallel to the plane of the figure. Figure 2. . Two views of the hexamer. The chain segments are colour coded as in [4]Figure 1. (a) View along the threefold axis, with the three twofold axes in the plane of the figure. (b) The threefold axis is parallel to the plane of the figure.
Figure 6.
Figure 6. . Main-chain averaged B-factors. The values for the two independent monomers in the asymmetric unit are shown by full and dashed lines. Figure 6. . Main-chain averaged B-factors. The values for the two independent monomers in the asymmetric unit are shown by full and dashed lines.
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1323-1332) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21203480 T.Naderer, J.Heng, and M.J.McConville (2010).
Evidence that intracellular stages of Leishmania major utilize amino sugars as a major carbon source.
  PLoS Pathog, 6, e1001245.  
18156259 A.Mukherjee, M.K.Mammel, J.E.LeClerc, and T.A.Cebula (2008).
Altered utilization of N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak.
  J Bacteriol, 190, 1710-1717.  
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.  
18554327 P.Rezácová, M.Kozísek, S.F.Moy, I.Sieglová, A.Joachimiak, M.Machius, and Z.Otwinowski (2008).
Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.
  Mol Microbiol, 69, 895-910.
PDB codes: 2okg 3bxe 3bxf 3bxg 3bxh
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.  
17277311 E.E.Kooijman, D.P.Tieleman, C.Testerink, T.Munnik, D.T.Rijkers, K.N.Burger, and B.de Kruijff (2007).
An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins.
  J Biol Chem, 282, 11356-11364.  
  17768362 G.J.Hu, L.F.Li, D.Li, C.Liu, S.C.Wei, Y.H.Liang, and X.D.Su (2007).
Protein preparation and preliminary X-ray crystallographic analysis of a putative glucosamine 6-phosphate deaminase from Streptococcus mutants.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 809-811.  
17387737 K.J.Kim, M.H.Kim, G.H.Kim, and B.S.Kang (2007).
The crystal structure of a novel glucosamine-6-phosphate deaminase from the hyperthermophilic archaeon Pyrococcus furiosus.
  Proteins, 68, 413-417.
PDB code: 2cb0
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.  
16199574 T.Tanaka, F.Takahashi, T.Fukui, S.Fujiwara, H.Atomi, and T.Imanaka (2005).
Characterization of a novel glucosamine-6-phosphate deaminase from a hyperthermophilic archaeon.
  J Bacteriol, 187, 7038-7044.  
14557261 F.Vincent, D.Yates, E.Garman, G.J.Davies, and J.A.Brannigan (2004).
The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.
  J Biol Chem, 279, 2809-2816.
PDB codes: 1un7 2vhl
11249189 E.L.Jarroll, P.T.Macechko, P.A.Steimle, D.Bulik, C.D.Karr, H.van Keulen, T.A.Paget, G.Gerwig, J.Kamerling, J.Vliegenthart, and S.Erlandsen (2001).
Regulation of carbohydrate metabolism during Giardia encystment.
  J Eukaryot Microbiol, 48, 22-26.  
11717264 V.Chazalet, K.Uehara, R.A.Geremia, and C.Breton (2001).
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ.
  J Bacteriol, 183, 7067-7075.  
10617596 S.L.Bearne, and C.Blouin (2000).
Inhibition of Escherichia coli glucosamine-6-phosphate synthase by reactive intermediate analogues. The role of the 2-amino function in catalysis.
  J Biol Chem, 275, 135-140.  
  10091662 A.Teplyakov, G.Obmolova, M.A.Badet-Denisot, and B.Badet (1999).
The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase.
  Protein Sci, 8, 596-602.
PDB codes: 1mor 1mos
10564476 L.A.Knodler, S.G.Svärd, J.D.Silberman, B.J.Davids, and F.D.Gillin (1999).
Developmental gene regulation in Giardia lamblia: first evidence for an encystation-specific promoter and differential 5' mRNA processing.
  Mol Microbiol, 34, 327-340.  
9601045 G.M.Montero-Morán, E.Horjales, M.L.Calcagno, and M.M.Altamirano (1998).
Tyr254 hydroxyl group acts as a two-way switch mechanism in the coupling of heterotropic and homotropic effects in Escherichia coli glucosamine-6-phosphate deaminase.
  Biochemistry, 37, 7844-7849.  
9864853 H.Van Keulen, P.A.Steimle, D.A.Bulik, R.K.Borowiak, and E.L.Jarroll (1998).
Cloning of two putative Giardia lamblia glucosamine 6-phosphate isomerase genes only one of which is transcriptionally activated during encystment.
  J Eukaryot Microbiol, 45, 637-642.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9108018 M.M.Altamirano, R.Golbik, R.Zahn, A.M.Buckle, and A.R.Fersht (1997).
Refolding chromatography with immobilized mini-chaperones.
  Proc Natl Acad Sci U S A, 94, 3576-3578.  
8994883 A.Mattevi, M.Rizzi, and M.Bolognesi (1996).
New structures of allosteric proteins revealing remarkable conformational changes.
  Curr Opin Struct Biol, 6, 824-829.  
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.