6W2L | pdb_00006w2l

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

PDB DOI: https://doi.org/10.2210/pdb6W2L/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2020-03-06 Released: 2020-08-19
Deposition Author(s): Edani, B.H., Ha, Y., Sessa, W.C.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.255 (Depositor), 0.258 (DCC)
R-Value Work:
0.212 (Depositor), 0.216 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 32817466 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2008381117
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 63.06 kDa
Atom Count: 4,036
Modeled Residue Count: 523
Deposited Residue Count: 544
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrodolichyl diphosphate synthase complex subunit DHDDS	A	330	Homo sapiens	Mutation(s): 1 Gene Names: DHDDS, HDS 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86SQ9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrodolichyl diphosphate synthase complex subunit NUS1	B	214	Homo sapiens	Mutation(s): 0 Gene Names: NUS1, C6orf68, NGBR 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96E22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPE Query on IPE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C₅ H₁₂ O₇ P₂ NUHSROFQTUXZQQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.255 (Depositor), 0.258 (DCC)
R-Value Work: 0.212 (Depositor), 0.216 (DCC)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.67	α = 90
b = 185.67	β = 90
c = 113.351	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-19

Deposition Author(s):

Edani, B.H.

Ha, Y.

Sessa, W.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	2P01 HLHL107205-06A1
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	5R35 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