1H7O | pdb_00001h7o

SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 5-AMINOLAEVULINIC ACID AT 1.7 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.353 (Depositor) 
  • R-Value Work: 
    0.221 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Substrate and Three Inhibitors

Erskine, P.T.Newbold, R.Brindley, A.A.Wood, S.P.Shoolingin-Jordan, P.M.Warren, M.J.Cooper, J.B.

(2001) J Mol Biology 312: 133

  • DOI: https://doi.org/10.1006/jmbi.2001.4947
  • Primary Citation Related Structures: 
    1H7N, 1H7O, 1H7P, 1H7R

  • PubMed Abstract: 

    The structures of 5-aminolaevulinic acid dehydratase (ALAD) complexed with substrate (5-aminolaevulinic acid) and three inhibitors: laevulinic acid, succinylacetone and 4-keto-5-aminolaevulinic acid, have been solved at high resolution. The ligands all bind by forming a covalent link with Lys263 at the active site. The structures define the interactions made by one of the two substrate moieties that bind to the enzyme during catalysis. All of the inhibitors induce a significant ordering of the flap covering the active site. Succinylacetone appears to be unique by inducing a number of conformational changes in loops covering the active site, which may be important for understanding the co-operative properties of ALAD enzymes. Succinylacetone is produced in large amounts by patients suffering from the hereditary disease type I tyrosinaemia and its potent inhibition of ALAD also has implications for the pathology of this disease. The most intriguing result is that obtained with 4-keto-5-amino-hexanoic acid, which seems to form a stable carbinolamine intermediate with Lys263. It appears that we have defined the structure of an intermediate of Schiff base formation that the substrate forms upon binding to the P-site of the enzyme.


  • Organizational Affiliation
    • Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.

Macromolecule Content 

  • Total Structure Weight: 37.85 kDa 
  • Atom Count: 3,110 
  • Modeled Residue Count: 341 
  • Deposited Residue Count: 341 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-AMINOLAEVULINIC ACID DEHYDRATASE341Saccharomyces cerevisiaeMutation(s): 0 
EC: 4.2.1.24
UniProt
Find proteins for P05373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05373 
Go to UniProtKB:  P05373
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05373
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.353 (Depositor) 
  • R-Value Work:  0.221 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.8α = 90
b = 102.8β = 90
c = 168.3γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
MOSFLMdata reduction
Agrovatadata scaling
SCALAdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other
  • Version 2.1: 2023-12-13
    Changes: Refinement description
  • Version 2.2: 2024-11-20
    Changes: Structure summary