PDBsum entry 2vg3

Transferase

PDB id: 2vg3

Contents

Protein chains

284 a.a. *

Ligands

GPP ×4

PO4 ×3

SO4

GOL

Metals

_CL ×2

_MG ×4

Waters ×427

* Residue conservation analysis

PDB id:

2vg3

Name:

Transferase

Title:

Rv2361 with citronellyl pyrophosphate

Structure:

Undecaprenyl pyrophosphate synthetase. Chain: a, b, c, d. Fragment: residues 13-296. Synonym: upp synthetase, undecaprenyl diphosphate synthase, di-trans poly-cis-decaprenylcistransferase, uds, rv2361. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.204 R-free: 0.231

Authors:

J.H.Naismith,W.Wang,C.Dong

Key ref:

W.Wang et al. (2008). The structural basis of chain length control in Rv1086. J Mol Biol, 381, 129-140. PubMed id: 18597781 DOI: 10.1016/j.jmb.2008.05.060

Date:

08-Nov-07 Release date: 06-May-08

Protein chains

P9WFF7  (DPDS_MYCTU) -  Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 296 a.a.

Struc: 284 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.5.1.86 - trans,polycis-decaprenyl diphosphate synthase.
• Reaction: (2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate + 7 diphosphate

(2Z,6E)-farnesyl diphosphate (Bound ligand (Het Group name = GPP) matches with 79.17% similarity) + 7 × isopentenyl diphosphate = (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate + 7 × diphosphate

• Enzyme class 2: E.C.2.5.1.87 - ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl
• Reaction: n isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate = a di-trans,poly-cis-polyprenyl diphosphate + n diphosphate

n isopentenyl diphosphate (Bound ligand (Het Group name = GPP) matches with 79.17% similarity) + 7 × (2E,6E)-farnesyl diphosphate = di-trans,poly-cis-polyprenyl diphosphate + n diphosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.jmb.2008.05.060

J Mol Biol 381:129-140 (2008)

PubMed id: 18597781

The structural basis of chain length control in Rv1086.

W.Wang, C.Dong, M.McNeil, D.Kaur, S.Mahapatra, D.C.Crick, J.H.Naismith.

ABSTRACT

In Mycobacterium tuberculosis, two related Z-prenyl diphosphate synthases, E,Z-farnesyl diphosphate synthase (Rv1086) and decaprenyl diphosphate synthase (Rv2361c), work in series to synthesize decaprenyl phosphate (C(50)) from isopentenyl diphosphate and E-geranyl diphosphate. Decaprenyl phosphate plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan; thus, its synthesis has attracted considerable interest as a potential therapeutic target. Rv1086 is a unique prenyl diphosphate synthase in that it adds only one isoprene unit to geranyl diphosphate, generating the 15-carbon product (E,Z-farnesyl diphosphate). Rv2361c then adds a further seven isoprene units to E,Z-farnesyl diphosphate in a processive manner to generate the 50-carbon prenyl diphosphate, which is then dephosphorylated to generate a carrier for activated sugars. The molecular basis for chain-length discrimination by Rv1086 during synthesis is unknown. We also report the structure of apo Rv1086 with citronellyl diphosphate bound and with the product mimic E,E-farnesyl diphosphate bound. We report the structures of Rv2361c in the apo form, with isopentenyl diphosphate bound and with a substrate analogue, citronellyl diphosphate. The structures confirm the enzymes are very closely related. Detailed comparison reveals structural differences that account for chain-length control in Rv1086. We have tested this hypothesis and have identified a double mutant of Rv1086 that makes a range of longer lipid chains.

Selected figure(s)

Figure 1.
Fig. 1. Rv1086 and Rv2361c with the reactions they catalyze. (a) Multiple sequence alignment of open reading frames Rv1086 and Rv2361c from M. tuberculosis H37Rv with UDPS from M. luteus (SWISS-PROT O82827) and E. coli (SWISS-PROT Q47675). The alignment was generated using the Multalin interface. The N-terminal extension of 2361c is evident. (b) The molecules discussed in the paper. The product of Rv1086, EZ-FPP, is the preferred substrate for Rv2361c; we employed EE-FPP in our crystallographic studies to mimic this molecule. CITPP is an inhibitor of both enzymes and is a mimic of prenyl diphosphates. The phosphates are labeled as α and β to distinguish them. (c) Schematic diagram of the reaction catalyzed by Z-prenyl synthases. In Rv1086, the reaction is not processive as it stops after one cycle; in Rv2361c, the reaction continues for a further seven cycles to make a 50-carbon product.

Figure 3.
Fig. 3. The crucial role of L84 in limiting chain length in Rv1086. (a) Superposition of the active site of EE-FPP Rv1086 complex (protein carbon atoms are white; all other atoms are colored as in Fig. 2b) and Rv2361c (protein carbon atoms are colored salmon). The double mutant Rv1086[L84A, L85F] can be expressed in a soluble (folded) form. L85 in Rv1086 points away from product. We suggest the L85F mutation role assists only in folding protein. (b) Space-filling view of the side chains that limit the growing polymer in Rv1086. EE-FPP is shown as yellow space-filling spheres. It can be seen that the side chain of L84 covers the polymer. Carbon atoms are in grey for the protein and yellow for the ligand.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 129-140) copyright 2008.

Figures were selected by an automated process.