PDBsum entry 1v7u

Transferase

PDB id: 1v7u

Contents

Protein chains

227 a.a. *

Ligands

FPP ×3

Waters ×456

* Residue conservation analysis

PDB id:

1v7u

Name:

Transferase

Title:

Crystal structure of undecaprenyl pyrophosphate synthase with farnesyl pyrophosphate

Structure:

Undecaprenyl pyrophosphate synthetase. Chain: a, b. Synonym: upp synthetase, di-trans-poly-cis-decaprenylcistransferase, undecaprenyl diphosphate synthase, uds. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: bos-12. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.35Å R-factor: 0.173 R-free: 0.254

Authors:

S.-Y.Chang,T.-P.Ko,A.P.-C.Chen,A.H.-J.Wang,P.-H.Liang

Key ref:

S.Y.Chang et al. (2004). Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies. Protein Sci, 13, 971-978. PubMed id: 15044730 DOI: 10.1110/ps.03519904

Date:

24-Dec-03 Release date: 13-Jan-04

Protein chains

P60472  (UPPS_ECOLI) -  Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) from Escherichia coli (strain K12)

Seq: 253 a.a.

Struc: 227 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.31 - ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-
• Pathway: Polyprenol biosynthesis
• Reaction: 8 isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate = di-trans,octa- cis-undecaprenyl diphosphate + 8 diphosphate

8 × isopentenyl diphosphate (Bound ligand (Het Group name = FPP) corresponds exactly) + (2E,6E)-farnesyl diphosphate = di-trans,octa- cis-undecaprenyl diphosphate + 8 × diphosphate

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

reference

DOI no: 10.1110/ps.03519904

Protein Sci 13:971-978 (2004)

PubMed id: 15044730

Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies.

S.Y.Chang, T.P.Ko, A.P.Chen, A.H.Wang, P.H.Liang.

ABSTRACT

Undecaprenyl pyrophosphate synthase (UPPs) catalyzes eight consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to form a 55-carbon long-chain product. We previously reported the crystal structure of the apo-enzyme from Escherichia coli and the structure of UPPs in complex with sulfate ions (resembling pyrophosphate of substrate), Mg(2+), and two Triton molecules (product-like). In the present study, FPP substrate was soaked into the UPPs crystals, and the complex structure was solved. Based on the crystal structure, the pyrophosphate head group of FPP is bound to the backbone NHs of Gly29 and Arg30 as well as the side chains of Asn28, Arg30, and Arg39 through hydrogen bonds. His43 is close to the C2 carbon of FPP and may stabilize the farnesyl cation intermediate during catalysis. The hydrocarbon moiety of FPP is bound with hydrophobic amino acids including Leu85, Leu88, and Phe89, located on the alpha3 helix. The binding mode of FPP in cis-type UPPs is apparently different from that of trans-type and many other prenyltransferases which utilize Asprich motifs for substrate binding via Mg(2+). The new structure provides a plausible mechanism for the catalysis of UPPs.

Selected figure(s)

Figure 2.
Figure 2. Interactions between FPP pyrophosphate head group and the nearby amino acids in the active side. In A, the pyrophosphate of FPP (F1) is hydrogen-bound to the backbone NH and side chain of R30, and backbone NH of G29 as well as the side chains of R39 and N28. Oxygen and nitrogen atoms are shown as red and blue dots, respectively. All of the distances of possible hydrogen bonds are indicated in Å, shown with red dotted lines. In B, side chain of D26 forms hydrogen bonds with the backbone NH of Gly27 and the side chain of R194 with the distances indicated in Å. Moreover, R194 interacts with R200, which is hydrogen-bound to E198. The segments of UPPs containing residues 23-43 and 192-205 are represented by the red ribbon. (C) Superimposition of the A strand and three -helices ( 1, 2, and 3) in the active-site area from the closed and open conformations of UPPs. The 2 helix is shown in red in the closed conformer and purple in the open conformer. Several amino acids including L85, L88, F89, and W91 on this helix become closer to the bound FPP compared to their positions (L85', L88', F89', and W91') in the open form. In D, the Mg2+ (shown in yellow) near IPP is coordinated with H199 from A subunit, E213 from B subunit, and four waters. The hydrocarbon parts of FPP and hypothetical IPP are represented by ball-and-stick in yellow and black, respectively. The oxygen and phosphate atoms in the pyrophosphate moiety are shown in red and purple, respectively. The segments of A subunit of UPPs 23-43 and 192-205 are represented by red ribbon, and segments of B subunit of apo-UPPs 210-215 by cyan ribbon.

Figure 4.
Figure 4. The proposed reaction mechanism of UPPs. Based on the present crystal structure, Asp26 serves as a general base to subtract a proton from IPP. This essential active-site amino acid is near the proton at C2 carbon of IPP and ready to remove it. The remaining electrons after deprotonation shift to form a cis-double bond, and the carbanion intermediate attacks the C1 carbocation of FPP to form a condensation product. Eight cycles total of IPP condensation generate the UPP product.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 971-978) copyright 2004.

Figures were selected by an automated process.