PDBsum entry 5e8h

Transferase

PDB id: 5e8h

Contents

Protein chains

278 a.a.

Waters ×259

PDB id:

5e8h

Name:

Transferase

Title:

Crystal structure of geranylfarnesyl pyrophosphate synthases 2 from arabidopsis thaliana

Structure:

Geranylgeranyl pyrophosphate synthase 3, chloroplastic. Chain: a, b. Synonym: ggps3,(2e,6e)-farnesyl diphosphate synthase 3, dimethylallyltranstransferase 3,farnesyl diphosphate synthase 3, farnesyltranstransferase 3,geranyltranstransferase 3. Ec: 2.5.1.-,2.5.1.1,2.5.1.29,2.5.1.10. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: ggpp3, at3g14550, mie1.5. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.208 R-free: 0.234

Authors:

C.Wang,Q.Chen,G.Wang,P.Zhang

Key ref:

C.Wang et al. (2016). Structural Analyses of Short-Chain Prenyltransferases Identify an Evolutionarily Conserved GFPPS Clade in Brassicaceae Plants. Mol Plant, 9, 195-204. PubMed id: 26537048 DOI: 10.1016/j.molp.2015.10.010

Date:

14-Oct-15 Release date: 11-Nov-15

Protein chains

Q9LUD9  (GGPP3_ARATH) -  Geranylgeranyl pyrophosphate synthase 3, chloroplastic from Arabidopsis thaliana

Seq: 360 a.a.

Struc: 278 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.5.1.- - ?????
• Enzyme class 2: E.C.2.5.1.1 - dimethylallyltranstransferase.

Pathway:

• Reaction: isopentenyl diphosphate + dimethylallyl diphosphate = (2E)- geranyl diphosphate + diphosphate
• Enzyme class 3: E.C.2.5.1.10 - (2E,6E)-farnesyl diphosphate synthase.

Pathway:

• Reaction: isopentenyl diphosphate + (2E)-geranyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate
• Enzyme class 4: E.C.2.5.1.29 - geranylgeranyl diphosphate synthase.

Pathway:

• Reaction: isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate = (2E,6E,10E)- geranylgeranyl diphosphate + 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.molp.2015.10.010

Mol Plant 9:195-204 (2016)

PubMed id: 26537048

Structural Analyses of Short-Chain Prenyltransferases Identify an Evolutionarily Conserved GFPPS Clade in Brassicaceae Plants.

C.Wang, Q.Chen, D.Fan, J.Li, G.Wang, P.Zhang.

ABSTRACT

Terpenoids are the largest and most diverse class of plant-specialized metabolites, which function in diverse physiological processes during plant development. In the biosynthesis of plant terpenoids, short-chain prenyltransferases (SC-PTs), together with terpene synthases (TPSs), play critical roles in determining terpenoid diversity. SC-PTs biosynthesize prenyl pyrophosphates with different chain lengths, and these compounds are the direct precursors of terpenoids. Arabidopsis thaliana possesses a subgroup of SC-PTs whose functions are not clearly known. In this study, we focus on 10 geranylgeranyl pyrophosphate synthase-like [GGPPSL] proteins, which are commonly thought to produce GGPP [C20]. We found that a subset of members of the Arabidopsis GGPPSL gene family have undergone neo-functionalization: GGPPSL6, 7, 9, and 10 mainly have geranylfarnesyl pyrophosphate synthase activity (C25; renamed AtGFPPS1, 2, 3, and 4), and GGPPSL8 produces even longer chain prenyl pyrophosphate (≥ C30; renamed polyprenyl pyrophosphate synthase 2, AtPPPS2). By solving the crystal structures of AtGFPPS2, AtPPPS2, and AtGGPPS11, we reveal the product chain-length determination mechanism of SC-PTs and interpret it as a "three floors" model. Using this model, we identified a novel GFPPS clade distributed in Brassicaceae plants and found that the GFPPS gene typically occurs in tandem with a gene encoding a TPS, forming a GFPPS-TPS gene cluster.