2BYD | pdb_00002byd

Structure of aminoadipate-semialdehyde dehydrogenase- phosphopantetheinyl transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.242 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2BYD

This is version 1.4 of the entry. See complete history

Literature

Mechanism and substrate recognition of human holo ACP synthase.

Bunkoczi, G.Pasta, S.Joshi, A.Wu, X.Kavanagh, K.L.Smith, S.Oppermann, U.

(2007) Chem Biol 14: 1243-1253

  • DOI: https://doi.org/10.1016/j.chembiol.2007.10.013
  • Primary Citation Related Structures: 
    2BYD, 2C43, 2CG5

  • PubMed Abstract: 

    Mammals utilize a single phosphopantetheinyl transferase for the posttranslational modification of at least three different apoproteins: the carrier protein components of cytosolic and mitochondrial fatty acid synthases and the aminoadipate semialdehyde reductase involved in lysine degradation. We determined the crystal structure of the human phosphopantetheinyl transferase, a eukaryotic phosphopantetheinyl transferase characterized, complexed with CoA and Mg(2+), and in ternary complex with CoA and ACP. The involvement of key residues in ligand binding and catalysis was confirmed by mutagenesis and kinetic analysis. Human phosphopantetheinyl transferase exhibits an alpha/beta fold and 2-fold pseudosymmetry similar to the Sfp phosphopantetheinyl transferase from Bacillus subtilis. Although the bound ACP exhibits a typical four-helix structure, its binding is unusual in that it is facilitated predominantly by hydrophobic interactions. A detailed mechanism is proposed describing the substrate binding and catalytic process.


  • Organizational Affiliation
    • Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, UK.

Macromolecule Content 

  • Total Structure Weight: 38.16 kDa 
  • Atom Count: 2,513 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 323 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HSPC223323Homo sapiensMutation(s): 0 
EC: 1.2.1.31 (PDB Primary Data), 2.7.8.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRN7 (Homo sapiens)
Explore Q9NRN7 
Go to UniProtKB:  Q9NRN7
PHAROS:  Q9NRN7
GTEx:  ENSG00000149313 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRN7
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on BR



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.242 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.78α = 90
b = 69.948β = 90
c = 71.239γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Other