2C1H

The X-ray Structure of Chlorobium vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2C1H/pdb

• Classification: LYASE
• Organism(s): Prosthecochloris vibrioformis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-14 Released: 2005-12-02 
• Deposition Author(s): Coates, L., Beaven, G., Erskine, P.T., Beale, S., Wood, S.P., Shoolingin-Jordan, P.M., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.320 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 

Literature

Structure of Chlorobium Vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor.

Coates, L., Beaven, G., Erskine, P.T., Beale, S., Wood, S.P., Shoolingin-Jordan, P.M., Cooper, J.B.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1594

• PubMed: 16304458 
• DOI: https://doi.org/10.1107/S0907444905030350
• Primary Citation of Related Structures:  
  2C1H


• PubMed Abstract: 
  

  The structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase (ALAD) complexed with the irreversible inhibitor 4,7-dioxosebacic acid has been solved. The inhibitor binds by forming Schiff-base linkages with lysines 200 and 253 at the active site. The structure reported here provides a definition of the interactions made by both of the substrate molecules (A-side and P-side substrates) with the C. vibrioforme ALAD and is compared and contrasted with structures of the same inhibitor bound to Escherichia coli and yeast ALAD. The structure suggests why 4,7-dioxosebacic acid is a better inhibitor of the zinc-dependent ALADs than of the zinc-independent ALADs.

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Organizational Affiliation: 

Bioscience Division, Los Alamos National Laboratory, NM 87545, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 73.38 kDa 
• Atom Count: 5,246 
• Modelled Residue Count: 638 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA-AMINOLEVULINIC ACID DEHYDRATASE	A, B	328	Prosthecochloris vibrioformis	Mutation(s): 0  EC: 4.2.1.24
UniProt
Find proteins for Q59334 (Chlorobaculum parvum (strain DSM 263 / NCIMB 8327)) Explore Q59334  Go to UniProtKB:  Q59334

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DSB	D [auth A], F [auth B]	4,7-DIOXOSEBACIC ACID C10 H14 O6 DUAWJQCMZICMIK-UHFFFAOYSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.320 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.48	α = 90
b = 126.48	β = 90
c = 81.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-02 
Deposition Author(s): Coates, L., Beaven, G., Erskine, P.T., Beale, S., Wood, S.P., Shoolingin-Jordan, P.M., Cooper, J.B.

Revision History  

• Version 1.0: 2005-12-02
  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: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description