1OHL

YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION INTERMEDIATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1042/BJ20030513

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DELTA-AMINOLEVULINIC ACID DEHYDRATASE
A
342Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: HEM2
EC: 4.2.1.24
Find proteins for P05373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05373
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PBG
Query on PBG

Download SDF File 
Download CCD File 
A
3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID
2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID; PORPHOBILINOGEN; 5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROLE-3-PROPANOIC ACID
C10 H14 N2 O4
QSHWIQZFGQKFMA-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.200α = 90.00
b = 103.200β = 90.00
c = 167.700γ = 90.00
Software Package:
Software NamePurpose
CCP4refinement
MOSFLMdata reduction
CCP4phasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance