PDBsum entry 1v4k

Transferase

PDB id: 1v4k

Contents

Protein chain

277 a.a. *

Ligands

SO4 ×6

Waters ×337

* Residue conservation analysis

PDB id:

1v4k

Name:

Transferase

Title:

Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic thermotoga maritima s77f mutant

Structure:

Octoprenyl-diphosphate synthase. Chain: a. Synonym: octaprenyl pyrophosphate synthase. Engineered: yes. Mutation: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Octamer (from PDB file)

Resolution:

2.45Å R-factor: 0.211 R-free: 0.280

Authors:

R.T.Guo,C.J.Kuo,C.C.Chou,T.P.Ko,H.L.Shr,P.H.Liang,A.H.-J.Wang

Key ref:

R.T.Guo et al. (2004). Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination. J Biol Chem, 279, 4903-4912. PubMed id: 14617622 DOI: 10.1074/jbc.M310161200

Date:

14-Nov-03 Release date: 02-Mar-04

Protein chain

Q9X1M1  (Q9X1M1_THEMA) -  Octoprenyl-diphosphate synthase, putative from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 299 a.a.

Struc: 277 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.11 - Transferred entry: 2.5.1.84 and 2.5.1.85.
• Pathway: Terpenoid biosynthesis
• Reaction: All-trans-octaprenyl diphosphate + isopentenyl diphosphate = diphosphate + all-trans-nonaprenyl diphosphate

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

reference

DOI no: 10.1074/jbc.M310161200

J Biol Chem 279:4903-4912 (2004)

PubMed id: 14617622

Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination.

R.T.Guo, C.J.Kuo, C.C.Chou, T.P.Ko, H.L.Shr, P.H.Liang, A.H.Wang.

ABSTRACT

Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to generate C40 octaprenyl pyrophosphate (OPP), which constitutes the side chain of bacterial ubiquinone or menaquinone. In this study, the first structure of long chain C40-OPPs from Thermotoga maritima has been determined to 2.28-A resolution. OPPs is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity. An elongated hydrophobic tunnel between D and F alpha-helices contains two DDXXD motifs on the top for substrate binding and is occupied at the bottom with two large residues Phe-52 and Phe-132. The products of the mutant F132A OPPs are predominantly C50, longer than the C40 synthesized by the wild-type and F52A mutant OPPs, suggesting that Phe-132 is the key residue for determining the product chain length. Ala-76 and Ser-77 located close to the FPP binding site and Val-73 positioned further down the tunnel were individually mutated to larger amino acids. A76Y and S77F mainly produce C20 indicating that the mutated large residues in the vicinity of the FPP site limit the substrate chain elongation. Ala-76 is the fifth amino acid upstream from the first DDXXD motif on helix D of OPPs, and its corresponding amino acid in FPPs is Tyr. In contrast, V73Y mutation led to additional accumulation of C30 intermediate. The new structure of the trans-type OPPs, together with the recently determined cis-type UPPs, significantly extends our understanding on the biosynthesis of long chain polyprenyl molecules.

Selected figure(s)

Figure 3.
FIG. 3. OPPs active site structure and reaction mechanism. In A, the surface of active site is color coded from red to blue according to charge potential from -15 to 15 k[B]T. This figure was generated using GRASP (30). In B, two sulfate ions in the active site of totally six sulfates of OPPs F132A mutant are shown (these sulfate ions are more obvious than other data sets). Along with two sulfate ions, amino acids Lys-41, Arg-44, His-74, Asp-81, Asp-82, Asp-85, Arg-90, Arg-91, Asp-204, Asp-205, and Asp-208 are shown in ball-and-stick model. S1 containing the first DDXXD motif is responsible for binding with FPP, and S2 located downstream the FPP binding site functions to stabilize the PP[i] leaving group. This is illustrated in C that Arg-90 and Arg-91 are important in FPP binding, and AArg-44, Lys-41, and His-74 surround another sulfate ion to grasp the leaving group of FPP while reaction occurs.

Figure 8.
FIG. 8. Proposed mechanism for chain length determination catalyzed by OPPs. The first DDXXD motif attached to helix D represents the FPP binding site. Ser-77 and Ala-76 are located in immediate proximity of FPP, and V73Y is further down. The substitution of Ser-77 and Ala-76 with larger residues led to the formation of C[20], a single condensation between the bound FPP and IPP. V73Y mutation results in temporary accumulation of C[30]. Phe-132 located on the bottom of helix D blocks further chain elongation of OPP and determines the ultimate product chain length.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 4903-4912) copyright 2004.

Figures were selected by an automated process.