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PDBsum entry 1moq

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Glutamine amidotransferase PDB id
1moq
Jmol
Contents
Protein chain
366 a.a. *
Ligands
GLP
SO4 ×5
MES
MRD
Metals
_NA
Waters ×416
* Residue conservation analysis
PDB id:
1moq
Name: Glutamine amidotransferase
Title: Isomerase domain of glucosamine 6-phosphate synthase complex glucosamine 6-phosphate
Structure: Glucosamine 6-phosphate synthase. Chain: a. Synonym: l-glutamine\:d-fructose-6p amidotransferase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: hfr 3000. Atcc: 25257. Collection: 25257. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.57Å     R-factor:   0.185    
Authors: A.Teplyakov
Key ref:
A.Teplyakov et al. (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. PubMed id: 9739095 DOI: 10.1016/S0969-2126(98)00105-1
Date:
11-Apr-97     Release date:   07-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17169  (GLMS_ECOLI) -  Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Seq:
Struc:
 
Seq:
Struc:
609 a.a.
366 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
+
D-glucosamine 6-phosphate
Bound ligand (Het Group name = GLP)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     carbohydrate binding     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(98)00105-1 Structure 6:1047-1055 (1998)
PubMed id: 9739095  
 
 
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.
A.Teplyakov, G.Obmolova, M.A.Badet-Denisot, B.Badet, I.Polikarpov.
 
  ABSTRACT  
 
BACKGROUND: Glucosamine 6-phosphate synthase (GlmS) catalyses the first step in hexosamine metabolism, converting fructose-6P (6 phosphate) into glucosamine-6P using glutamine as a nitrogen source. GlmS is a bienzyme complex consisting of two domains that catalyse glutamine hydrolysis and sugar-phosphate isomerisation, respectively. Knowledge of the three-dimensional structure of GlmS is essential for understanding the general principles of catalysis by ketol isomerases and the mechanism of nitrogen transfer in glutamine amidotransferases. RESULTS: The crystal structure of the isomerase domain of the Escherichia coli GlmS with the reaction product, glucosamine-6P, has been determined at 1.57 A resolution. It is comprised of two topologically identical subdomains, each of which is dominated by a nucleotide-binding motif of a flavodoxin type. The catalytic site is assembled by dimerisation of the protein. CONCLUSIONS: The isomerase active site of GlmS seems to be the result of evolution through gene duplication and subsequent dimerisation. Isomerisation of fructose-6P is likely to involve the formation of a Schiff base with Lys603 of the enzyme, the ring-opening step catalysed by His504, and the proton transfer from C1 to C2 of the substrate effected by Glu488. The highly conserved C-terminal fragment of the chain may play a key role in substrate binding, catalysis and communication with the glutaminase domain. The corresponding sequence pattern DXPXXLAK[SC]VT (in single-letter amino-acid code, where X is any amino acid and letters in brackets indicate that either serine or cysteine may take this position) may be considered as a fingerprint of GlmS.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Residues 418 and 419 are modelled as lysine and leucine, respectively, and not as asparagine and valine, as the DNA sequence suggests. The figure shows the (3F[o]-2F[c]) electron density at residues Lys418 and Leu419 contoured at 1.5s.
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1047-1055) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21337483 C.Airoldi, S.Sommaruga, S.Merlo, P.Sperandeo, L.Cipolla, A.Polissi, and F.Nicotra (2011).
Targeting bacterial membranes: identification of Pseudomonas aeruginosa D-arabinose-5P isomerase and NMR characterisation of its substrate recognition and binding properties.
  Chembiochem, 12, 719-727.  
20954237 L.J.Gourlay, S.Sommaruga, M.Nardini, P.Sperandeo, G.Dehò, A.Polissi, and M.Bolognesi (2010).
Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography.
  Protein Sci, 19, 2430-2439.
PDB code: 2xhz
19400948 H.R.Kushwaha, A.K.Singh, S.K.Sopory, S.L.Singla-Pareek, and A.Pareek (2009).
Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa L. reveals their developmental and stress regulation.
  BMC Genomics, 10, 200.  
19643913 N.L.Beer, N.D.Tribble, L.J.McCulloch, C.Roos, P.R.Johnson, M.Orho-Melander, and A.L.Gloyn (2009).
The P446L variant in GCKR associated with fasting plasma glucose and triglyceride levels exerts its effect through increased glucokinase activity in liver.
  Hum Mol Genet, 18, 4081-4088.  
18477634 A.Nigham, L.Tucker-Kellogg, I.Mihalek, C.Verma, and D.Hsu (2008).
pFlexAna: detecting conformational changes in remotely related proteins.
  Nucleic Acids Res, 36, W246-W251.  
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.  
18056714 P.L.Taylor, K.M.Blakely, G.P.de Leon, J.R.Walker, F.McArthur, E.Evdokimova, K.Zhang, M.A.Valvano, G.D.Wright, and M.S.Junop (2008).
Structure and Function of Sedoheptulose-7-phosphate Isomerase, a Critical Enzyme for Lipopolysaccharide Biosynthesis and a Target for Antibiotic Adjuvants.
  J Biol Chem, 283, 2835-2845.
PDB codes: 1x92 2i22 2i2w 3bjz
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
16508760 H.Scheib, I.McLay, N.Guex, J.J.Clare, F.E.Blaney, T.J.Dale, S.N.Tate, and G.M.Robertson (2006).
Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding.
  J Mol Model, 12, 813-822.  
16986193 J.Lim, B.C.Grove, A.Roth, and R.R.Breaker (2006).
Characteristics of ligand recognition by a glmS self-cleaving ribozyme.
  Angew Chem Int Ed Engl, 45, 6689-6693.  
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
16214343 A.Gutteridge, and J.M.Thornton (2005).
Understanding nature's catalytic toolkit.
  Trends Biochem Sci, 30, 622-629.  
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.  
15511226 F.A.Lunn, and S.L.Bearne (2004).
Alternative substrates for wild-type and L109A E. coli CTP synthases: kinetic evidence for a constricted ammonia tunnel.
  Eur J Biochem, 271, 4204-4212.  
15363790 R.Sanishvili, R.Wu, D.E.Kim, J.D.Watson, F.Collart, and A.Joachimiak (2004).
Crystal structure of Bacillus subtilis YckF: structural and functional evolution.
  J Struct Biol, 148, 98.
PDB code: 1m3s
12842041 W.K.Wang, V.Tereshko, P.Boccuni, D.MacGrogan, S.D.Nimer, and D.J.Patel (2003).
Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets.
  Structure, 11, 775-789.
PDB codes: 1oyx 1oz2 1oz3
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.  
11842094 K.O.Broschat, C.Gorka, J.D.Page, C.L.Martin-Berger, M.S.Davies, H.C.Huang Hc, E.A.Gulve, W.J.Salsgiver, and T.P.Kasten (2002).
Kinetic characterization of human glutamine-fructose-6-phosphate amidotransferase I: potent feedback inhibition by glucosamine 6-phosphate.
  J Biol Chem, 277, 14764-14770.  
11839305 L.A.Martinez-Cruz, M.K.Dreyer, D.C.Boisvert, H.Yokota, M.L.Martinez-Chantar, R.Kim, and S.H.Kim (2002).
Crystal structure of MJ1247 protein from M. jannaschii at 2.0 A resolution infers a molecular function of 3-hexulose-6-phosphate isomerase.
  Structure, 10, 195-204.
PDB code: 1jeo
11756407 M.Veiga-da-Cunha, and E.Van Schaftingen (2002).
Identification of fructose 6-phosphate- and fructose 1-phosphate-binding residues in the regulatory protein of glucokinase.
  J Biol Chem, 277, 8466-8473.  
11178340 N.H.Georgopapadakou (2001).
Update on antifungals targeted to the cell wall: focus on beta-1,3-glucan synthase inhibitors.
  Expert Opin Investig Drugs, 10, 269-280.  
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.  
10203754 A.Bateman (1999).
The SIS domain: a phosphosugar-binding domain.
  Trends Biochem Sci, 24, 94-95.  
  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
9914248 J.L.Smith (1998).
Glutamine PRPP amidotransferase: snapshots of an enzyme in action.
  Curr Opin Struct Biol, 8, 686-694.  
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 code is shown on the right.