PDBsum entry 2cxn

Isomerase

PDB id: 2cxn

Contents

Protein chains

557 a.a. *

Ligands

PO4

GOL ×4

Waters ×1192

* Residue conservation analysis

PDB id:

2cxn

Name:

Isomerase

Title:

Crystal structure of mouse amf / phosphate complex

Structure:

Glucose-6-phosphate isomerase. Chain: a, b. Synonym: cytokine, gpi, phosphoglucose isomerase, pgi, phosphohexose isomerase, phi, neuroleukin, nlk. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.40Å R-factor: 0.172 R-free: 0.188

Authors:

N.Tanaka,A.Haga,N.Naba,K.Shiraiwa,Y.Kusakabe,K.Hashimoto,T.Funasaka, H.Nagase,A.Raz,K.T.Nakamura

Key ref:

N.Tanaka et al. (2006). Crystal structures of mouse autocrine motility factor in complex with carbohydrate phosphate inhibitors provide insight into structure-activity relationship of the inhibitors. J Mol Biol, 356, 312-324. PubMed id: 16375918 DOI: 10.1016/j.jmb.2005.11.076

Date:

30-Jun-05 Release date: 23-May-06

Protein chains

P06745  (G6PI_MOUSE) -  Glucose-6-phosphate isomerase from Mus musculus

Seq: 558 a.a.

Struc: 557 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.3.1.9 - glucose-6-phosphate isomerase.
• Reaction: alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate

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

Added reference

DOI no: 10.1016/j.jmb.2005.11.076

J Mol Biol 356:312-324 (2006)

PubMed id: 16375918

Crystal structures of mouse autocrine motility factor in complex with carbohydrate phosphate inhibitors provide insight into structure-activity relationship of the inhibitors.

N.Tanaka, A.Haga, N.Naba, K.Shiraiwa, Y.Kusakabe, K.Hashimoto, T.Funasaka, H.Nagase, A.Raz, K.T.Nakamura.

ABSTRACT

Autocrine motility factor (AMF), a tumor-secreted cytokine, stimulates cell migration in vitro and metastasis in vivo. AMF is identical to the extracellular cytokines neuroleukin and maturation factor and, interestingly, to the intracellular enzyme phosphoglucose isomerase. The cytokine activity of AMF is inhibited by carbohydrate phosphate compounds as they compete for AMF binding with the carbohydrate moiety of the AMF receptor (AMFR), which is a glycosylated seven transmembrane helix protein. Here, we report the first comprehensive high-resolution crystal structure analyses of the inhibitor-free form and the eight types of inhibitor (phosphate, erythrose 4-phosphate (E4P), arabinose 5-phosphate (A5P), sorbitol 6-phosphate (S6P), 6-phosphogluconic acid (6PGA), fructose 6-phosphate (F6P), glucose 6-phosphate (G6P), or mannose 6-phosphate (M6P)) complexes of mouse AMF (mAMF). We assayed the inhibitory activities of these inhibitors against the cytokine activity of mAMF. The inhibitory activities of the six-carbon sugars (G6P, F6P, M6P, and 6PGA) were found to be significantly higher than those of the four or five-carbon sugars (E4P or A5P). The inhibitory activities clearly depend on the length of the inhibitor molecules. A structural comparison revealed that a water-mediated hydrogen bond between one end of the inhibitor and a rigid portion of the protein surface in the shorter-chain inhibitor (E4P) complex is replaced by a direct hydrogen bond in the longer-chain inhibitor (6PGA) complex. Thus, to obtain a new compound with higher inhibitory activities against AMF, water molecules at the inhibitor binding site of AMF should be replaced by a functional group of inhibitors in order to introduce direct interactions with the protein surface. The present structure-activity relationship studies will be valuable not only for designing more effective AMF inhibitors but also for studying general protein-inhibitor interactions.

Selected figure(s)

Figure 2.
Figure 2. The inhibitor-binding site in subunit A of mouse AMF. The carbon and phosphorus atoms of the bound inhibitor molecule are shown in cyan and green, respectively. The bound inhibitor molecule is superimposed on the F[o] -F[c] omit electron density map (contoured at 15.0s (red) and 3.0s (violet) for (a), (b), (g), and (h), and at 15.0s (red) and 4.0s (violet) for (c), (d), (e), and (f)). Possible hydrogen bonds are indicated by broken lines (green). The bound water molecules are shown as ball models (pink). (a) Acetate (in inhibitor-free mAMF); (b) phosphate; (c) E4P; (d) A5P; (e) S6P; (f) 6PGA; (g) F6P; (h) G6P (the bound ligand is modeled as the reaction product F6P).

Figure 3.
Figure 3. Inhibitory activities of carbohydrate phosphate compounds against the cytokine activity of mAMF. (a) The cell motility-stimulating activity of mAMF toward mouse melanoma B16-BL6 cells analyzed by phagokinetic track assay in the presence of various inhibitors at three concentrations ([inhibitor]/[mAMF]=1/5, 1, and 5). (b) Statistical analysis for the difference of the inhibitory activities of AMF inhibitors examined by Student's t-test (n>30).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 312-324) copyright 2006.

Figures were selected by the author.