PDBsum entry 2fp1

Isomerase

PDB id: 2fp1

Contents

Protein chains

165 a.a. *

Metals

_PB ×2

Waters ×427

* Residue conservation analysis

PDB id:

2fp1

Name:

Isomerase

Title:

Secreted chorismate mutase from mycobacterium tuberculosis

Structure:

Chorismate mutase. Chain: a, b. Fragment: residues 34-199. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.176 R-free: 0.211

Authors:

M.Okvist,R.Dey,S.Sasso,E.Grahn,P.Kast,U.Krengel

Key ref:

M.Okvist et al. (2006). 1.6 A crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: novel fold topology revealed. J Mol Biol, 357, 1483-1499. PubMed id: 16499927 DOI: 10.1016/j.jmb.2006.01.069

Date:

15-Jan-06 Release date: 28-Mar-06

Protein chains

P9WIB9  (SCMU_MYCTU) -  Secreted chorismate mutase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 199 a.a.

Struc: 165 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.99.5 - chorismate mutase.
• Pathway: Phenylalanine and Tyrosine Biosynthesis
• Reaction: chorismate = prephenate

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

Added reference

DOI no: 10.1016/j.jmb.2006.01.069

J Mol Biol 357:1483-1499 (2006)

PubMed id: 16499927

1.6 A crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: novel fold topology revealed.

M.Okvist, R.Dey, S.Sasso, E.Grahn, P.Kast, U.Krengel.

ABSTRACT

The presence of exported chorismate mutases produced by certain organisms such as Mycobacterium tuberculosis has been shown to correlate with their pathogenicity. As such, these proteins comprise a new group of promising selective drug targets. Here, we report the high-resolution crystal structure of the secreted dimeric chorismate mutase from M. tuberculosis (*MtCM; encoded by Rv1885c), which represents the first 3D-structure of a member of this chorismate mutase family, termed the AroQ(gamma) subclass. Structures are presented both for the unliganded enzyme and for a complex with a transition state analog. The protomer fold resembles the structurally characterized (dimeric) Escherichia coli chorismate mutase domain, but exhibits a new topology, with helix H4 of *MtCM carrying the catalytic site residue missing in the shortened helix H1. Furthermore, the structure of each *MtCM protomer is significantly more compact and only harbors one active site pocket, which is formed entirely by one polypeptide chain. Apart from the structural model, we present evidence as to how the substrate may enter the active site.

Selected figure(s)

Figure 4.
Figure 4. Proposed AroQ subclasses. The upper panels show cylinder representations of the folds of (a) EcCM (PDB entry 1ECM; representative of the AroQ[a] subclass), (b) the ScCM protomer (PDB entry 4CSM; representative of the AroQ[b] subclass), and (c) the *MtCM protomer (PDB entry 2FP2; representative of the AroQ[g] subclass). Termini and prominent helices are labeled. The lower panels show the superimpositions (ribbon representations) of (d) *MtCM (yellow) and EcCM (red/blue; two protomers), (e) *MtCM (yellow) and ScCM (green), and (f) *MtCM (yellow) and EcCM (blue; second protomer). Superimpositions are with respect to the *MtCM structure. The disulfide bond in *MtCM is highlighted by colored spheres. Note that the active site is composed primarily of helices from the N-terminal half in *MtCM, but from the C-terminal half in ScCM. All structures are complexes with the transition state analog inhibitor 1 (shown as stick model).

Figure 6.
Figure 6. Active sites of *MtCM (a) and (d), EcCM (b) and ScCM (c). In the schematic representation (a) of the *MtCM active site, *MtCM residue labels are boxed and accompanied by colored labels identifying the corresponding amino acid residues of EcCM (blue/red; upper labels) and ScCM (green; lower labels). The homolog of Arg72 in ScCM, Val197 (see Figure 3(a)), forms part of a wall of the active site pocket, but does not seem to interact directly with 1 and was therefore omitted. Residues denoted with an asterisk are functional analogs but not sequence homologs of Glu106. The transition state analog inhibitor 1 is highlighted with heavy lines in (a), with yellow carbon atoms in (b) and (c), and with orange carbon atoms in (d). Hydrogen bonds are indicated by dotted lines. Note that in *MtCM, the carboxylate oxygen O2 from inhibitor 1 has three possible hydrogen bonding partners (with equally favorable geometries): Arg49, Gln76 and a structural water molecule. This water molecule, which simultaneously binds to the two carboxylate groups of inhibitor 1, is tightly coordinated by Arg72 of *MtCM and Arg51 of EcCM (residue shown only in Figure 6 and Figure 7, due to crowding in the other pictures; the arginine side-chains align in an antiparallel fashion with Arg134 and Arg11' of *MtCM and EcCM, respectively). For *MtCM, the electron density is shown in stereo representation (s[A]-weighted 2F[o] -F[c] map, at 1s) (d). (e) and (f) give stereo views of superimpositions of the three active sites from *MtCM (yellow carbon atoms), EcCM (red/blue, for the two protomers) and ScCM (green). The view in (f) is flipped along the horizontal axis of the paper plane, with respect to the view in (e). Note the differential positioning (leading to a swap of function) of the residues corresponding to Val73/Glu106 of *MtCM (Glu52/Val85 in EcCM and Glu198/Lys243 in ScCM, respectively), which are behind inhibitor 1 in (e) and above the plane in (f).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 1483-1499) copyright 2006.

Figures were selected by the author.