7CAQ

Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: substrate-free)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.248 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLMClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view details

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
224Methanosarcina mazei Go1Mutation(s): 0 
Gene Names: MM_0014
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.248 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.019α = 90
b = 100.439β = 90
c = 130.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLMClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view details

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, Refinement description