6W2L

Crystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 

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This is version 1.3 of the entry. See complete history


Literature

Structural elucidation of thecis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation.

Edani, B.H.Grabinska, K.A.Zhang, R.Park, E.J.Siciliano, B.Surmacz, L.Ha, Y.Sessa, W.C.

(2020) Proc Natl Acad Sci U S A 117: 20794-20802

  • DOI: https://doi.org/10.1073/pnas.2008381117
  • Primary Citation of Related Structures:  
    6W2L

  • PubMed Abstract: 

    Cis- prenyltransferase ( cis- PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis -PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis -PTase activity. Comparison of NgBR/DHDDS with homodimeric cis -PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis -PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.


  • Organizational Affiliation

    Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrodolichyl diphosphate synthase complex subunit DHDDS330Homo sapiensMutation(s): 1 
Gene Names: DHDDSHDS
EC: 2.5.1.87
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SQ9 (Homo sapiens)
Explore Q86SQ9 
Go to UniProtKB:  Q86SQ9
PHAROS:  Q86SQ9
GTEx:  ENSG00000117682 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86SQ9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrodolichyl diphosphate synthase complex subunit NUS1214Homo sapiensMutation(s): 0 
Gene Names: NUS1C6orf68NGBR
EC: 2.5.1.87
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E22 (Homo sapiens)
Explore Q96E22 
Go to UniProtKB:  Q96E22
PHAROS:  Q96E22
GTEx:  ENSG00000153989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96E22
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.67α = 90
b = 185.67β = 90
c = 113.351γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States2P01 HLHL107205-06A1
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States5R35 HL139945-03

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-09-09
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description