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PDBsum entry 1gdo

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protein ligands metals Protein-protein interface(s) links
Complex (transferase/inhibitor) PDB id
1gdo
Jmol
Contents
Protein chains
238 a.a.
Ligands
ACT ×2
GLU ×4
Metals
_NA ×4
Waters ×758
Superseded by: 1xff
PDB id:
1gdo
Name: Complex (transferase/inhibitor)
Title: Glutaminase domain of glucosamine 6-phosphate synthase complexed with glutamate
Structure: Glucosamine 6-phosphate synthase. Chain: a, b, c, d. Fragment: glutaminase domain. Synonym: l-glutamine\:d-fructose-6p amidotransferase. Engineered: yes. L-glutamate. Chain: e, f, g, h. Engineered: yes. Other_details: l-glutamate is an inhibitor
Source: Escherichia coli. Strain: 3000hfr. Atcc: 25257. Expressed in: escherichia coli. Synthetic: yes
Resolution:
1.80Å     R-factor:   0.179     R-free:   0.254
Authors: M.N.Isupov,A.Teplyakov
Key ref:
M.N.Isupov et al. (1996). Substrate binding is required for assembly of the active conformation of the catalytic site in Ntn amidotransferases: evidence from the 1.8 A crystal structure of the glutaminase domain of glucosamine 6-phosphate synthase. Structure, 4, 801-810. PubMed id: 8805567 DOI: 10.1016/S0969-2126(96)00087-1
Date:
05-Apr-96     Release date:   14-Oct-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P17169  (GLMS_ECOLI) -  Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Seq:
Struc:
 
Seq:
Struc:
609 a.a.
238 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.16  - Glutamine--fructose-6-phosphate transaminase (isomerizing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
UDP-N-acetylglucosamine Biosynthesis
      Reaction: L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate
L-glutamine
+ D-fructose 6-phosphate
=
L-glutamate
Bound ligand (Het Group name = GLU)
corresponds exactly
+ D-glucosamine 6-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(96)00087-1 Structure 4:801-810 (1996)
PubMed id: 8805567  
 
 
Substrate binding is required for assembly of the active conformation of the catalytic site in Ntn amidotransferases: evidence from the 1.8 A crystal structure of the glutaminase domain of glucosamine 6-phosphate synthase.
M.N.Isupov, G.Obmolova, S.Butterworth, M.A.Badet-Denisot, B.Badet, I.Polikarpov, J.A.Littlechild, A.Teplyakov.
 
  ABSTRACT  
 
BACKGROUND: Amidotransferases use the amide nitrogen of glutamine in a number of important biosynthetic reactions. They are composed of a glutaminase domain, which catalyzes the hydrolysis of glutamine to glutamate and ammonia, and a synthetase domain, catalyzing amination of the substrate. To gain insight into the mechanism of nitrogen transfer, we examined the structure of the glutaminase domain of glucosamine 6-phosphate synthase (GLMS). RESULTS: The crystal structures of the enzyme complexed with glutamate and with a competitive inhibitor, Glu-hydroxamate, have been determined to 1.8 A resolution. The protein fold has structural homology to other members of the superfamily of N-terminal nucleophile (Ntn) hydrolases, being a sandwich of antiparallel beta sheets surrounded by two layers of alpha helices. CONCLUSIONS: The structural homology between the glutaminase domain of GLMS and that of PRPP amidotransferase (the only other Ntn amidotransferase whose structure is known) indicates that they may have diverged from a common ancestor. Cys1 is the catalytic nucleophile in GLMS, and the nucleophilic character of its thiol group appears to be increased through general base activation by its own alpha-amino group. Cys1 can adopt two conformations, one active and one inactive; glutamine binding locks the residue in a predetermined conformation. We propose that when a nitrogen acceptor is present Cys1 is kept in the active conformation, explaining the phenomenon of substrate-induced activation of the enzyme, and that Arg26 is central in this coupling.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Active site of the glutaminase domain of GLMS with the bound product, glutamate, shown in outline. Hydrogen bonds are indicated by dashed lines. The loop 73-78 is in the closed conformation. Cys1 and Asn98 are in the inactive conformation.
Figure 6.
Figure 6. Proposed catalytic mechanism of glutamine hydrolysis by amidotransferases. Residue numbers are those of GLMS. The nucleophilicity of Cys1 is enhanced by its own free a-amino group. This interaction is mediated by a bridging water molecule which serves as a virtual base. Deacylation involves another water molecule which is activated through the same mechanism. Residues Asn98 and Gly99 form the oxyanion hole for the tetrahedral intermediates.
 
  The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 801-810) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19706171 K.Lakomek, A.Dickmanns, M.Kettwig, H.Urlaub, R.Ficner, and T.Lübke (2009).
Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography.
  BMC Struct Biol, 9, 56.
PDB codes: 3fgr 3fgt 3fgw
18448325 E.D.Levy, and J.B.Pereira-Leal (2008).
Evolution and dynamics of protein interactions and networks.
  Curr Opin Struct Biol, 18, 349-357.  
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
17157318 Y.Wang, and H.C.Guo (2007).
Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.
  J Mol Biol, 366, 82-92.
PDB code: 2gl9
16477602 J.Seetharaman, K.R.Rajashankar, V.Solorzano, R.Kniewel, C.D.Lima, J.B.Bonanno, S.K.Burley, and S.Swaminathan (2006).
Crystal structures of two putative phosphoheptose isomerases.
  Proteins, 63, 1092-1096.
PDB codes: 1tk9 1x94
16408321 S.Milewski, I.Gabriel, and J.Olchowy (2006).
Enzymes of UDP-GlcNAc biosynthesis in yeast.
  Yeast, 23, 1.  
16339762 S.Mouilleron, M.A.Badet-Denisot, and B.Golinelli-Pimpaneau (2006).
Glutamine binding opens the ammonia channel and activates glucosamine-6P synthase.
  J Biol Chem, 281, 4404-4412.
PDB codes: 2bpj 2bpl 2j6h 4amv
15987679 F.Levitin, O.Stern, M.Weiss, C.Gil-Henn, R.Ziv, Z.Prokocimer, N.I.Smorodinsky, D.B.Rubinstein, and D.H.Wreschner (2005).
The MUC1 SEA module is a self-cleaving domain.
  J Biol Chem, 280, 33374-33386.  
16216576 J.A.Khan, B.M.Dunn, and L.Tong (2005).
Crystal structure of human Taspase1, a crucial protease regulating the function of MLL.
  Structure, 13, 1443-1452.
PDB codes: 2a8i 2a8j 2a8l 2a8m
15150276 H.H.Lin, G.W.Chang, J.Q.Davies, M.Stacey, J.Harris, and S.Gordon (2004).
Autocatalytic cleavage of the EMR2 receptor occurs at a conserved G protein-coupled receptor proteolytic site motif.
  J Biol Chem, 279, 31823-31832.  
15498940 V.M.Coiro, A.Di Nola, M.A.Vanoni, M.Aschi, A.Coda, B.Curti, and D.Roccatano (2004).
Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates.
  Protein Sci, 13, 2979-2991.  
14633979 F.Schmitzberger, M.L.Kilkenny, C.M.Lobley, M.E.Webb, M.Vinkovic, D.Matak-Vinkovic, M.Witty, D.Y.Chirgadze, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.
  EMBO J, 22, 6193-6204.
PDB codes: 1ppy 1pqe 1pqf 1pqh 1pt0 1pt1 1pyq 1pyu
12147680 E.Wiame, G.Delpierre, F.Collard, and E.Van Schaftingen (2002).
Identification of a pathway for the utilization of the Amadori product fructoselysine in Escherichia coli.
  J Biol Chem, 277, 42523-42529.  
11188694 C.Binda, R.T.Bossi, S.Wakatsuki, S.Arzt, A.Coda, B.Curti, M.A.Vanoni, and A.Mattevi (2000).
Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase.
  Structure, 8, 1299-1308.
PDB code: 1ea0
10673442 C.Bompard-Gilles, V.Villeret, G.J.Davies, L.Fanuel, B.Joris, J.M.Frère, and J.Van Beeumen (2000).
A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
  Structure, 8, 153-162.
PDB code: 1b65
  11206054 C.Oinonen, and J.Rouvinen (2000).
Structural comparison of Ntn-hydrolases.
  Protein Sci, 9, 2329-2337.  
11027147 F.Krekel, A.K.Samland, P.Macheroux, N.Amrhein, and J.N.Evans (2000).
Determination of the pKa value of C115 in MurA (UDP-N-acetylglucosamine enolpyruvyltransferase) from Enterobacter cloacae.
  Biochemistry, 39, 12671-12677.  
10903946 T.Nakai, T.Hasegawa, E.Yamashita, M.Yamamoto, T.Kumasaka, T.Ueki, H.Nanba, Y.Ikenaka, S.Takahashi, M.Sato, and T.Tsukihara (2000).
Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
  Structure, 8, 729-737.
PDB code: 1erz
  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
10090755 H.G.Schnizer, S.K.Boehlein, J.D.Stewart, N.G.Richards, and S.M.Schuster (1999).
Formation and isolation of a covalent intermediate during the glutaminase reaction of a class II amidotransferase.
  Biochemistry, 38, 3677-3682.  
10571008 N.N.Aronson (1999).
Aspartylglycosaminuria: biochemistry and molecular biology.
  Biochim Biophys Acta, 1455, 139-154.  
10490104 Q.Xu, D.Buckley, C.Guan, and H.C.Guo (1999).
Structural insights into the mechanism of intramolecular proteolysis.
  Cell, 98, 651-661.
PDB codes: 9gaa 9gac 9gaf
  10024571 S.J.Billington, A.S.Huggins, P.A.Johanesen, P.K.Crellin, J.K.Cheung, M.E.Katz, C.L.Wright, V.Haring, and J.I.Rood (1999).
Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin.
  Infect Immun, 67, 1277-1286.  
10587437 T.M.Larsen, S.K.Boehlein, S.M.Schuster, N.G.Richards, J.B.Thoden, H.M.Holden, and I.Rayment (1999).
Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
  Biochemistry, 38, 16146-16157.
PDB code: 1ct9
9739095 A.Teplyakov, G.Obmolova, M.A.Badet-Denisot, B.Badet, and I.Polikarpov (1998).
Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain.
  Structure, 6, 1047-1055.
PDB code: 1moq
  9514258 C.R.Muchmore, J.M.Krahn, J.H.Kim, H.Zalkin, and J.L.Smith (1998).
Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli.
  Protein Sci, 7, 39-51.
PDB codes: 1ecf 1ecj
9914248 J.L.Smith (1998).
Glutamine PRPP amidotransferase: snapshots of an enzyme in action.
  Curr Opin Struct Biol, 8, 686-694.  
9753692 M.Rizzi, M.Bolognesi, and A.Coda (1998).
A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure.
  Structure, 6, 1129-1140.
PDB code: 2nsy
9333323 J.M.Krahn, J.H.Kim, M.R.Burns, R.J.Parry, H.Zalkin, and J.L.Smith (1997).
Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site.
  Biochemistry, 36, 11061-11068.
PDB codes: 1ecb 1ecc
9254614 S.K.Boehlein, E.S.Walworth, and S.M.Schuster (1997).
Identification of cysteine-523 in the aspartate binding site of Escherichia coli asparagine synthetase B.
  Biochemistry, 36, 10168-10177.  
  9003765 G.Schmidtke, R.Kraft, S.Kostka, P.Henklein, C.Frömmel, J.Löwe, R.Huber, P.M.Kloetzel, and M.Schmidt (1996).
Analysis of mammalian 20S proteasome biogenesis: the maturation of beta-subunits is an ordered two-step mechanism involving autocatalysis.
  EMBO J, 15, 6887-6898.  
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.