1KYQ

Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase.

Schubert, H.L.Raux, E.Brindley, A.A.Leech, H.K.Wilson, K.S.Hill, C.P.Warren, M.J.

(2002) EMBO J 21: 2068-2075

  • DOI: 10.1093/emboj/21.9.2068
  • Primary Citation of Related Structures:  
    1KYQ

  • PubMed Abstract: 
  • Sirohaem is a tetrapyrrole-derived prosthetic group that is required for the essential assimilation of sulfur and nitrogen into all living systems as part of the sulfite and nitrite reductase systems. The final two steps in the biosynthesis of sirohaem involve a beta-NAD(+)-dependent dehydrogenation of precorrin-2 to generate sirohydrochlorin followed by ferrochelation to yield sirohaem ...

    Sirohaem is a tetrapyrrole-derived prosthetic group that is required for the essential assimilation of sulfur and nitrogen into all living systems as part of the sulfite and nitrite reductase systems. The final two steps in the biosynthesis of sirohaem involve a beta-NAD(+)-dependent dehydrogenation of precorrin-2 to generate sirohydrochlorin followed by ferrochelation to yield sirohaem. In Saccharomyces cerevisiae, Met8p is a bifunctional enzyme that carries out both of these reactions. Here, we report the 2.2 A resolution crystal structure of Met8p, which adopts a novel fold that bears no resemblance to the previously determined structures of cobalt- or ferro-chelatases. Analysis of mutant proteins suggests that both catalytic activities share a single active site, and that Asp141 plays an essential role in both dehydrogenase and chelatase processes.


    Related Citations: 
    • The Role of Saccharomyces cerevisiae Met1p and Met8p in Sirohaem and Cobalamin Biosynthesis
      Raux, E., McVeigh, T., Peters, S.E., Leustek, T., Warren, M.J.
      (1999) Biophys J 338: 701

    Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA. heidi@biochem.utah.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Siroheme biosynthesis protein MET8A, B, C274Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: MET8
EC: 1 (PDB Primary Data), 4.99.1.1 (PDB Primary Data), 1.3.1.76 (UniProt), 4.99.1.4 (UniProt)
Find proteins for P15807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15807 
Go to UniProtKB:  P15807
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.988α = 90
b = 80.856β = 121.88
c = 103.975γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance