PDBsum entry 1fp3

Isomerase

PDB id: 1fp3

Contents

Protein chains

402 a.a. *

Waters ×145

* Residue conservation analysis

PDB id:

1fp3

Name:

Isomerase

Title:

Crystal structure of n-acyl-d-glucosamine 2-epimerase from porcine kidney

Structure:

N-acyl-d-glucosamine 2-epimerase. Chain: a, b. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Tissue: kidney. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.169 R-free: 0.244

Authors:

T.Itoh,B.Mikami,I.Maru,Y.Ohta,W.Hashimoto,K.Murata

Key ref:

T.Itoh et al. (2000). Crystal structure of N-acyl-D-glucosamine 2-epimerase from porcine kidney at 2.0 A resolution. J Mol Biol, 303, 733-744. PubMed id: 11061972 DOI: 10.1006/jmbi.2000.4188

Date:

30-Aug-00 Release date: 22-Nov-00

Protein chains

P17560  (RENBP_PIG) -  N-acylglucosamine 2-epimerase from Sus scrofa

Seq: 402 a.a.

Struc: 402 a.a.

Enzyme reactions

• Enzyme class: E.C.5.1.3.8 - N-acylglucosamine 2-epimerase.
• Reaction: an N-acyl-D-glucosamine = an N-acyl-D-mannosamine

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

Added reference

DOI no: 10.1006/jmbi.2000.4188

J Mol Biol 303:733-744 (2000)

PubMed id: 11061972

Crystal structure of N-acyl-D-glucosamine 2-epimerase from porcine kidney at 2.0 A resolution.

T.Itoh, B.Mikami, I.Maru, Y.Ohta, W.Hashimoto, K.Murata.

ABSTRACT

The X-ray crystallographic structure of N-acyl-d-glucosamine 2-epimerase (AGE) from porcine kidney, which has been identified to be a renin-binding protein (RnBP), was determined by the multiple isomorphous replacement method and refined at 2.0 A resolution with a final R-factor of 16.9 % for 15 to 2.0 A resolution data. The refined structure of AGE comprised 804 amino acid residues (one dimer) and 145 water molecules. The dimer of AGE had an asymmetric unit with approximate dimensions 46 Ax48 Ax96 A. The AGE monomer is composed of an alpha(6)/alpha(6)-barrel, the structure of which is found in glucoamylase and cellulase. One side of the AGE alpha(6)/alpha(6)-barrel structure comprises long loops containing five short beta-sheets, and contributes to the formation of a deep cleft shaped like a funnel. The putative active-site pocket and a possible binding site for the substrate N-acetyl-d-glucosamine (GlcNAc) were found in the cleft. The other side of the alpha(6)/alpha(6)-barrel comprises short loops and contributes to the dimer formation. At the dimer interface, which is composed of the short loops and alpha-helices of the subunits, five strong ion-pair interactions were observed, which play a major role in the dimer assembly. This completely ruled out the previously accepted hypothesis that the formation of the RnBP homodimer and RnBP-renin heterodimer requires the leucine zipper motif present in RnBP.

Selected figure(s)

Figure 6.
Figure 6. Interface of the AGE dimer. The structure is represented as a pink and cyan molecular tube model of AGE subunits A and B, respectively. Residues buried in the dimer interface are presented in red (subunit A) and blue (subunit B). The side-chains of residues forming hydrogen bonds or van der Waals contacts are also colored. The broken line in the Figure is the non-crystallographic 2-fold axis of the AGE dimer. The Figure was drawn using the program GRASP [Nicholls et al 1991].

Figure 7.
Figure 7. Structural comparison of a-helices within the a/a-barrel structures of AGE (red), glucoamylase (cyan), cellulase (yellow), and alginate lyase A1-III (green). The superimposed results are shown as a schematic view in C^a-traces of the a-helices. The coordinates of glucoamylase (1DOG), cellulase (1CEM), and alginate lyase A1-III (1QAZ) were taken from the RCSB Protein Data Bank [Berman et al 2000]. The Figure was prepared using MOLSCRIPT [Kraulis 1991] and RASTER3D [Merrit and Murphy 1994].

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 733-744) copyright 2000.

Figures were selected by an automated process.