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


Ligand Structure Quality Assessment 


This is version 1.3 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 296: 100679-100679

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

  • 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cis-prenyltransferase MM_0014
A, B, C, D, E
A, B, C, D, E, F, G, H
224Methanosarcina mazei Go1Mutation(s): 0 
UniProt
Find proteins for A0A0F8R9A0 (Methanosarcina mazei)
Explore A0A0F8R9A0 
Go to UniProtKB:  A0A0F8R9A0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F8R9A0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FQ0 (Subject of Investigation/LOI)
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
DMA (Subject of Investigation/LOI)
Query on DMA

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
P [auth C]
Q [auth C]
S [auth D]
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
DPO (Subject of Investigation/LOI)
Query on DPO

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
EA [auth G]
FA [auth G]
JA [auth H]
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
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth G]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth G]
HA [auth H]
K [auth A]
L [auth B]
R [auth C]
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
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



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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
  • Version 1.2: 2021-07-14
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description