1KYQ | pdb_00001kyq

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 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

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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: https://doi.org/10.1093/emboj/21.9.2068
  • Primary Citation 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. 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.

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

Macromolecule Content 

  • Total Structure Weight: 98.86 kDa 
  • Atom Count: 7,289 
  • Modeled Residue Count: 797 
  • Deposited Residue Count: 822 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Siroheme biosynthesis protein MET8
A, B, C
274Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: Met8
EC: 1 (PDB Primary Data), 4.99.1.1 (PDB Primary Data), 4.99.1.4 (UniProt), 1.3.1.76 (UniProt)
UniProt
Find proteins for P15807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15807 
Go to UniProtKB:  P15807
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15807
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.283 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
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

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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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary