PDBsum entry 7cpm

Transferase

PDB id: 7cpm

Contents

Protein chains

(+ 0 more) 244 a.a.

Waters ×191

PDB id:

7cpm

Name:

Transferase

Title:

Crystal structure of dodecaprenyl diphosphate synthase from thermobifida fusca

Structure:

Trans,polycis-polyprenyl diphosphate synthase ((2z,6e)- farnesyl diphosphate specific). Chain: a, b, c, d, e, f. Synonym: cis-prenyltransferase,dodecaprenyl diphosphate synthase. Engineered: yes

Source:

Thermobifida fusca (strain yx). Organism_taxid: 269800. Strain: yx. Gene: tfu_0853. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.189 R-free: 0.234

Authors:

H.Kurokawa,T.Ambo,S.Takahashi,T.Koyama

Key ref:

H.Kurokawa et al. (2020). Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Biochem Biophys Res Commun, 532, 459-465. PubMed id: 32892948 DOI: 10.1016/j.bbrc.2020.08.062

Date:

07-Aug-20 Release date: 14-Oct-20

Protein chains

Q47RM6  (DPDP_THEFY) -  Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific) from Thermobifida fusca (strain YX)

Seq: 282 a.a.

Struc: 244 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.88 - trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl
• Reaction:
  1. (2Z,6E)-farnesyl diphosphate + 9 isopentenyl diphosphate = di-trans,nona-cis-dodecaprenyl diphosphate + 9 diphosphate
  2. (2Z,6E)-farnesyl diphosphate + 10 isopentenyl diphosphate = di-trans,deca-cis-tridecaprenyl diphosphate + 10 diphosphate
  3. (2Z,6E)-farnesyl diphosphate + 11 isopentenyl diphosphate = di-trans,undeca-cis-tetradecaprenyl diphosphate + 11 diphosphate

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

reference

DOI no: 10.1016/j.bbrc.2020.08.062

Biochem Biophys Res Commun 532:459-465 (2020)

PubMed id: 32892948

Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity.

H.Kurokawa, T.Ambo, S.Takahashi, T.Koyama.

ABSTRACT

cis-Prenyltransferases (cis-PTs) catalyze consecutive condensations of isopentenyl diphosphate to an allylic diphosphate acceptor to produce a linear polyprenyl diphosphate of designated length. Dimer formation is a prerequisite for cis-PTs to catalyze all cis-prenyl condensation reactions. The structure-function relationship of a conserved C-terminal RXG motif in cis-PTs that forms inter-subunit interactions and has a role in catalytic activity has attracted much attention. Here, we solved the crystal structure of a medium-chain cis-PT from Thermobifida fusca that produces dodecaprenyl diphosphate as a polyprenoid glycan carrier for cell wall synthesis. The structure revealed a characteristic dimeric architecture of cis-PTs in which a rigidified RXG motif of one monomer formed inter-subunit hydrogen bonds with the catalytic site of the other monomer, while the RXG motif of the latter remained flexible. Careful analyses suggested the existence of a possible long-range negative cooperativity between the two catalytic sites on the two monomeric subunits that allowed the binding of one subunit to stabilize the formation of the enzyme-substrate ternary complex and facilitated the release of Mg-PPi and subsequent intra-molecular translocation at the counter subunit so that the condensation reaction could occur in consecutive cycles. The current structure reveals the dynamic nature of the RXG motif and provides a rationale for pursuing further investigations to elucidate the inter-subunit cooperativity of cis-PTs.