9EP0 | pdb_00009ep0

Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.301 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystallographic data for Pyrococcus furiosus dolichylphosphate mannose synthase suggest that the enzyme could flip its glycolipid product.

Gandini, R.Keskitalo, M.M.Reichenbach, T.Kalyani, D.C.Divne, C.

(2026) Sci Rep 16

  • DOI: https://doi.org/10.1038/s41598-026-44343-5
  • Primary Citation Related Structures: 
    9EP0

  • PubMed Abstract: 

    Dolichylphosphate mannose synthase (DPMS) performs an essential function by synthesizing the activated lipid-linked mannose intermediate used in protein glycosylation pathways. In eukaryotes and archaea, DPMS catalyzes the transfer of mannose from GDP-mannose to dolichylphosphate to generate dolichylphosphate mannose (Dol-P-Man). Type-III DPMS from Pyrococcus furiosus (PfDPMS) has a catalytic domain attached to a GtrA-like transmembrane (TM) domain with an unusual topology. Here, we present crystallographic data from a crystal complex determined from an enzymatic reaction mixture that provides detailed information about donor- and acceptor binding in the active site prior to mannosyl transfer. We also present a new, unexpected structural state for the TM domain in which a Dol-P-Man molecule is bound "upside-down" with its mannosylphosphate headgroup positioned in a polar pocket between the TM helices. By generating a panel of TM-domain mutants, we confirm that the TM domain does not participate directly in the catalysis of mannosyl transfer and discuss the possibility of this domain providing moonlighting function to PfDPMS by translocating the Dol-P-Man product to the cell exterior.


  • Organizational Affiliation
    • Department of Industrial Biotechnology, School of Engineering Science in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichol monophosphate mannose synthase374Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0058
EC: 2.4.1.83
Membrane Entity: Yes 
UniProt
Find proteins for Q8U4M3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U4M3 
Go to UniProtKB:  Q8U4M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U4M3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MJC (Subject of Investigation/LOI)
Query on MJC

Download Ideal Coordinates CCD File 
E [auth A]dolichyl phosphate mannose
C61 H103 O9 P
FVCCNKBLEFCPJO-ALFQADJPSA-N
GDD (Subject of Investigation/LOI)
Query on GDD

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
EFS (Subject of Investigation/LOI)
Query on EFS

Download Ideal Coordinates CCD File 
D [auth A]ETHYL DIHYDROGEN PHOSPHATE
C2 H7 O4 P
ZJXZSIYSNXKHEA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.301 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.8α = 90
b = 145.25β = 90
c = 99.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-03877
Swedish Research CouncilSweden2013-5717

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Database references