PDBsum entry 2put

Transferase

PDB id: 2put

Contents

Protein chains

339 a.a. *

Ligands

ACT ×2

UD1 ×4

F6R ×4

Metals

_NA ×4

Waters ×748

* Residue conservation analysis

PDB id:

2put

Name:

Transferase

Title:

The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from candida albicans

Structure:

Isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing). Chain: a, b, c, d. Fragment: isomerase domain. Synonym: hexosephosphate aminotransferase. D-fructose-6- phosphate amidotransferase. Gfat. Engineered: yes

Source:

Candida albicans. Organism_taxid: 237561. Strain: sc5314. Gene: gfa1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.172 R-free: 0.215

Authors:

J.Raczynska,J.Olchowy,S.Milewski,W.Rypniewski

Key ref:

J.Raczynska et al. (2007). The Crystal and Solution Studies of Glucosamine-6-phosphate Synthase from Candida albicans. J Mol Biol, 372, 672-688. PubMed id: 17681543 DOI: 10.1016/j.jmb.2007.07.002

Date:

09-May-07 Release date: 11-Sep-07

Protein chains

P53704  (GFA1_CANAL) -  Glutamine--fructose-6-phosphate aminotransferase [isomerizing] from Candida albicans (strain SC5314 / ATCC MYA-2876)

Seq: 713 a.a.

Struc: 339 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.16 - glutamine--fructose-6-phosphate transaminase (isomerizing).
• Pathway: UDP-N-acetylglucosamine Biosynthesis
• Reaction: D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate

D-fructose 6-phosphate (Bound ligand (Het Group name = F6R) corresponds exactly) + L-glutamine (Bound ligand (Het Group name = ACT) matches with 40.00% similarity) = D-glucosamine 6-phosphate + L-glutamate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2007.07.002

J Mol Biol 372:672-688 (2007)

PubMed id: 17681543

The Crystal and Solution Studies of Glucosamine-6-phosphate Synthase from Candida albicans.

J.Raczynska, J.Olchowy, P.V.Konariev, D.I.Svergun, S.Milewski, W.Rypniewski.

ABSTRACT

Glucosamine 6-phosphate (GlcN-6-P) synthase is an ubiquitous enzyme that catalyses the first committed step in the reaction pathway that leads to formation of uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc), a precursor of macromolecules that contain amino sugars. Despite sequence similarities, the enzyme in eukaryotes is tetrameric, whereas in prokaryotes it is a dimer. The activity of eukaryotic GlcN-6-P synthase (known as Gfa1p) is regulated by feedback inhibition by UDP-GlcNAc, the end product of the reaction pathway, whereas in prokaryotes the GlcN-6-P synthase (known as GlmS) is not regulated at the post-translational level. In bacteria and fungi the enzyme is essential for cell wall synthesis. In human the enzyme is a mediator of insulin resistance. For these reasons, Gfa1p is a target in anti-fungal chemotherapy and in therapeutics for type-2 diabetes. The crystal structure of the Gfa1p isomerase domain from Candida albicans has been analysed in complex with the allosteric inhibitor UDP-GlcNAc and in the presence of glucose 6-phosphate, fructose 6-phosphate and an analogue of the reaction intermediate, 2-amino-2-deoxy-d-mannitol 6-phosphate (ADMP). A solution structure of the native Gfa1p has been deduced using small-angle X-ray scattering (SAXS). The tetrameric Gfa1p can be described as a dimer of dimers, with each half similar to the related enzyme from Escherichia coli. The core of the protein consists of the isomerase domains. UDP-GlcNAc binds, together with a metal cation, in a well-defined pocket on the surface of the isomerase domain. The residues responsible for tetramerisation and for binding UDP-GlcNAc are conserved only among eukaryotic sequences. Comparison with the previously studied GlmS from E. coli reveals differences as well as similarities in the isomerase active site. This study of Gfa1p focuses on the features that distinguish it from the prokaryotic homologue in terms of quaternary structure, control of the enzymatic activity and details of the isomerase active site.

Selected figure(s)

Figure 8.
Figure 8. Schematic representation of ligands interactions with: (a) Glc-6-P closed form, (b) Glc-6-P/Fru-6-P open form, (c) ADMP. Contacts present in all chains are depicted as black broken lines and those present only in some of the chains are shown as light grey lines. For comparison with the protein–ligand interactions in E.

Figure 9.
Figure 9. (a) The UDP-GlcNAc and the metal cation (blue) bound to ISOM. A pocket in the protein surface is visible and it accommodates the uracil ring. The ribose moiety and the phosphate groups also interact with the protein whereas the glucosamine moiety extends to the solvent. The 2F[o]-F[c] electron density map is contoured at 1σ level. (b) Details of the UDP-GlcNAc binding to ISOM. Hydrogen bonds between UDP-GlcNAc and the protein are shown as black broken lines and the interactions of the metal ion (blue sphere) are shown in grey. (c) Superposition of ISOM with bound UDP-GlcNAc (protein in red, ligand in green), ISOM without the inhibitor (yellow) and GlmS ISOM (blue). The largest conformational change associated with UDP-GlcNAc binding is in the position of the Trp388 residue.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 372, 672-688) copyright 2007.

Figures were selected by an automated process.