7CC3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.196 

Starting Model: experimental
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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
FV3 (Subject of Investigation/LOI)
Query on FV3

Download Ideal Coordinates CCD File 
BA [auth E]
FA [auth F]
JA [auth G]
L [auth A]
NA [auth H]
BA [auth E],
FA [auth F],
JA [auth G],
L [auth A],
NA [auth H],
P [auth B],
T [auth C],
X [auth D]
(2S)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol
C18 H32 O3
VGIZXGYRSPTVQF-RNKQFFRGSA-N
FQF (Subject of Investigation/LOI)
Query on FQF

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
IA [auth G]
K [auth A]
MA [auth H]
AA [auth E],
EA [auth F],
IA [auth G],
K [auth A],
MA [auth H],
O [auth B],
S [auth C],
W [auth D]
(2R)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol
C18 H32 O3
VGIZXGYRSPTVQF-LEAVJPGDSA-N
FQ0 (Subject of Investigation/LOI)
Query on FQ0

Download Ideal Coordinates CCD File 
DA [auth F]
HA [auth G]
J [auth A]
LA [auth H]
N [auth B]
DA [auth F],
HA [auth G],
J [auth A],
LA [auth H],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,3-diol
C18 H32 O3
CANVIAXUPVPMNA-BTMZFSHUSA-N
DPO (Subject of Investigation/LOI)
Query on DPO

Download Ideal Coordinates CCD File 
GA [auth G],
M [auth B],
Y [auth E]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth F],
I [auth A],
KA [auth H],
Q [auth C],
U [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.048α = 90
b = 99.221β = 90
c = 193.876γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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