7CAV

Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG+DMAPP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations.

Okada, M.Unno, H.Emi, K.I.Matsumoto, M.Hemmi, H.

(2021) J Biol Chem : 100679-100679

  • DOI: 10.1016/j.jbc.2021.100679
  • Primary Citation of Related Structures:  
    7CAS, 7CAQ, 7CAR, 7CC3, 7CAV

  • PubMed Abstract: 
  • Polyprenyl groups, products of isoprenoid metabolism, are utilized in peptidoglycan biosynthesis, protein N-glycosylation, and other processes. These groups are formed by cis-prenyltransferases, which use allylic prenyl pyrophosphates as prenyl-donors to catalyze the C-prenylation of the general acceptor substrate, isopentenyl pyrophosphate ...

    Polyprenyl groups, products of isoprenoid metabolism, are utilized in peptidoglycan biosynthesis, protein N-glycosylation, and other processes. These groups are formed by cis-prenyltransferases, which use allylic prenyl pyrophosphates as prenyl-donors to catalyze the C-prenylation of the general acceptor substrate, isopentenyl pyrophosphate. Repetition of this reaction forms (Z,E-mixed)-polyprenyl pyrophosphates, which are converted later into glycosyl carrier lipids, such as undecaprenyl phosphate and dolichyl phosphate. MM_0014 from the methanogenic archaeon Methanosarcina mazei is known as a versatile cis-prenyltransferase that accepts both isopentenyl pyrophosphate and dimethylallyl pyrophosphate as acceptor substrates. To learn more about this enzyme's catalytic activity, we determined the X-ray crystal structures of MM_0014 in the presence or absence of these substrates. Surprisingly, one structure revealed a complex with O-prenylglycerol, suggesting that the enzyme catalyzed the prenylation of glycerol contained in the crystallization buffer. Further analyses confirmed that the enzyme could catalyze the O-prenylation of small alcohols, such as 2-propanol, expanding our understanding of the catalytic ability of cis-prenyltransferases.


    Organizational Affiliation

    Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan. Electronic address: hhemmi@agr.nagoya-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cis-prenyltransferase MM_0014A, B, C, D, E, F, G, H224Methanosarcina mazei Go1Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FQ0
Query on FQ0

Download Ideal Coordinates CCD File 
DA [auth G], IA [auth H], M [auth B], Z [auth F]2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,3-diol
C18 H32 O3
CANVIAXUPVPMNA-BTMZFSHUSA-N
 Ligand Interaction
DMA
Query on DMA

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], P [auth C], Q [auth C], S [auth D], T [auth D], V [auth E], W [auth E]DIMETHYLALLYL DIPHOSPHATE
C5 H12 O7 P2
CBIDRCWHNCKSTO-UHFFFAOYSA-N
 Ligand Interaction
DPO
Query on DPO

Download Ideal Coordinates CCD File 
AA [auth F], BA [auth F], EA [auth G], FA [auth G], JA [auth H], N [auth B], O [auth B]DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth G]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth G], HA [auth H], K [auth A], L [auth B], R [auth C], U [auth D], X [auth E], Y [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.853α = 90
b = 98.91β = 90
c = 193.853γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-06-10 
  • Released Date: 2021-04-28 
  • Deposition Author(s): Unno, H., Hemmi, H.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17H05437
Japan Society for the Promotion of Science (JSPS)Japan19H04651

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references