1OHL

YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION INTERMEDIATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 

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This is version 1.4 of the entry. See complete history


Literature

X-Ray Structure of a Putative Reaction Intermediateof 5-Aminolaevulinic Acid Dehydratase

Erskine, P.T.Coates, L.Butler, D.Youell, J.H.Brindley, A.A.Wood, S.P.Warren, M.J.Shoolingin-Jordan, P.M.Cooper, J.B.

(2003) Biochem J 373: 733

  • DOI: https://doi.org/10.1042/BJ20030513
  • Primary Citation of Related Structures:  
    1OHL

  • PubMed Abstract: 

    The X-ray structure of yeast 5-aminolaevulinic acid dehydratase, in which the catalytic site of the enzyme is complexed with a putative cyclic intermediate composed of both substrate moieties, has been solved at 0.16 nm (1.6 A) resolution. The cyclic intermediate is bound covalently to Lys(263) with the amino group of the aminomethyl side chain ligated to the active-site zinc ion in a position normally occupied by a catalytic hydroxide ion. The cyclic intermediate is catalytically competent, as shown by its turnover in the presence of added substrate to form porphobilinogen. The findings, combined with those of previous studies, are consistent with a catalytic mechanism in which the C-C bond linking both substrates in the intermediate is formed before the C-N bond.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DELTA-AMINOLEVULINIC ACID DEHYDRATASE342Saccharomyces 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PBG
Query on PBG

Download Ideal Coordinates CCD File 
D [auth A]3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID
C10 H14 N2 O4
QSHWIQZFGQKFMA-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
C [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.2α = 90
b = 103.2β = 90
c = 167.7γ = 90
Software Package:
Software NamePurpose
CCP4refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-02
    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: 2019-05-22
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description