PDBsum entry 1v0j

Isomerase

PDB id: 1v0j

Contents

Protein chains

388 a.a. *

Ligands

FAD ×4

BCN

Waters ×1021

* Residue conservation analysis

PDB id:

1v0j

Name:

Isomerase

Title:

Udp-galactopyranose mutase from mycobacterium tuberculosis

Structure:

Udp-galactopyranose mutase. Chain: a, b, c, d. Synonym: udp-galp mutase, NAD+-flavin adenine dinucleotide-requiring enzyme. Engineered: yes. Other_details: fad cofactor and bicine

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.25Å R-factor: 0.227 R-free: 0.266

Authors:

K.Beis,J.H.Naismith

Key ref:

K.Beis et al. (2005). Crystal structures of Mycobacteria tuberculosis and Klebsiella pneumoniae UDP-galactopyranose mutase in the oxidised state and Klebsiella pneumoniae UDP-galactopyranose mutase in the (active) reduced state. J Mol Biol, 348, 971-982. PubMed id: 15843027 DOI: 10.1016/j.jmb.2005.02.057

Date:

30-Mar-04 Release date: 26-Jan-05

Protein chains

P9WIQ1  (GLF_MYCTU) -  UDP-galactopyranose mutase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 399 a.a.

Struc: 388 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.99.9 - UDP-galactopyranose mutase.
• Pathway: UDP-glucose, UDP-galactose and UDP-glucuronate Biosynthesis
• Reaction: UDP-alpha-D-galactose = UDP-alpha-D-galactofuranose

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

Added reference

DOI no: 10.1016/j.jmb.2005.02.057

J Mol Biol 348:971-982 (2005)

PubMed id: 15843027

Crystal structures of Mycobacteria tuberculosis and Klebsiella pneumoniae UDP-galactopyranose mutase in the oxidised state and Klebsiella pneumoniae UDP-galactopyranose mutase in the (active) reduced state.

K.Beis, V.Srikannathasan, H.Liu, S.W.Fullerton, V.A.Bamford, D.A.Sanders, C.Whitfield, M.R.McNeil, J.H.Naismith.

ABSTRACT

Uridine diphosphogalactofuranose (UDP-Galf) is the precursor of the d-galactofuranose sugar found in bacterial and parasitic cell walls, including those of many pathogens. UDP-Galf is made from UDP-galactopyranose by the enzyme UDP-galactopyranose mutase. The enzyme requires the reduced FADH- co-factor for activity. The structure of the Mycobacterium tuberculosis mutase with FAD has been determined to 2.25 A. The structures of Klebsiella pneumoniae mutase with FAD and with FADH- bound have been determined to 2.2 A and 2.35 A resolution, respectively. This is the first report of the FADH(-)-containing structure. Two flavin-dependent mechanisms for the enzyme have been proposed, one, which involves a covalent adduct being formed at the flavin and the other based on electron transfer. Using our structural data, we have examined the two mechanisms. The electron transfer mechanism is consistent with the structural data, not surprisingly, since it makes fewer demands on the precise positioning of atoms. A model based on a covalent adduct FAD requires repositioning of the enzyme active site and would appear to require the isoalloxazine ring of FADH- to buckle in a particular way. However, the FADH- structure reveals that the isoalloxazine ring buckles in the opposite sense, this apparently requires the covalent adduct to trigger profound conformational changes in the protein or to buckle the FADH- opposite to that seen in the apo structure.

Selected figure(s)

Figure 1.
Figure 1. The mutase enzyme function and structure. (a) The chemical reaction catalysed by the mutase enzyme. The co-factor FAD and FADH - are shown. Ring positions numbers are referred to in the text. (b) The bicyclic mechanism, which does not require direct involvement of the FAD.8 (c) The redox mechanism, in which one electron is transferred to the substrate.11 The electron is transferred from FADH - to create a radical that then re-arranges to give product. (d) The covalent intermediate mechanism, in this N5 attacks C1 in a nucleophilic manner. The covalent intermediate then re-arranges to give product. The presence of the covalent intermediate was detected by mass specotrometry.12

Figure 3.
Figure 3. Stereo images of models of substrate with mutase. (a) The initial complex between UDP-galactose of the active reduced form of the K. pneumoniae enzyme. This complex is predicted to occur in a mechanism involving electron transfer or a covalent intermediate. No significant re-arrangements are required to accommodate the substrate. The structurally diverse loop 5 is shown in pink. (b) A model of the covalent adduct with the re-face buckle of isoalloxazine ring. The re-face buckled isoalloxazine ring is taken from a thioredoxin structure.17 This model allows interactions with key conserved residues. The model would require conformation changes in side-chain positions only to avoid steric clashes. (c) The covalent adduct based on the experimental K. pneumoniae FADH - structure. The sugar is interpenetrating with the protein structure. Either FADH - adopts a different buckle in the presence of substrate or the protein undergoes a profound conformation change. His63 has been omitted for clarity and Pro59 has been added to this Figure.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 971-982) copyright 2005.

Figures were selected by an automated process.