7S7G | pdb_00007s7g

Crystal Structure Analysis of Human VLCAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 
    0.169 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S7G

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural basis for defective membrane targeting of mutant enzyme in human VLCAD deficiency.

Prew, M.S.Camara, C.M.Botzanowski, T.Moroco, J.A.Bloch, N.B.Levy, H.R.Seo, H.S.Dhe-Paganon, S.Bird, G.H.Herce, H.D.Gygi, M.A.Escudero, S.Wales, T.E.Engen, J.R.Walensky, L.D.

(2022) Nat Commun 13: 3669-3669

  • DOI: https://doi.org/10.1038/s41467-022-31466-2
  • Primary Citation Related Structures: 
    7S7G

  • PubMed Abstract: 

    Very long-chain acyl-CoA dehydrogenase (VLCAD) is an inner mitochondrial membrane enzyme that catalyzes the first and rate-limiting step of long-chain fatty acid oxidation. Point mutations in human VLCAD can produce an inborn error of metabolism called VLCAD deficiency that can lead to severe pathophysiologic consequences, including cardiomyopathy, hypoglycemia, and rhabdomyolysis. Discrete mutations in a structurally-uncharacterized C-terminal domain region of VLCAD cause enzymatic deficiency by an incompletely defined mechanism. Here, we conducted a structure-function study, incorporating X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, computational modeling, and biochemical analyses, to characterize a specific membrane interaction defect of full-length, human VLCAD bearing the clinically-observed mutations, A450P or L462P. By disrupting a predicted α-helical hairpin, these mutations either partially or completely impair direct interaction with the membrane itself. Thus, our data support a structural basis for VLCAD deficiency in patients with discrete mutations in an α-helical membrane-binding motif, resulting in pathologic enzyme mislocalization.


  • Organizational Affiliation
    • Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 67.61 kDa 
  • Atom Count: 4,985 
  • Modeled Residue Count: 571 
  • Deposited Residue Count: 617 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Very long-chain specific acyl-CoA dehydrogenase, mitochondrial617Homo sapiensMutation(s): 0 
Gene Names: ACADVLVLCAD
EC: 1.3.8.9 (PDB Primary Data), 1.3.8.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49748 (Homo sapiens)
Explore P49748 
Go to UniProtKB:  P49748
PHAROS:  P49748
GTEx:  ENSG00000072778 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49748
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free:  0.169 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.26α = 90
b = 108.27β = 90
c = 149.65γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-29
    Changes: Database references