Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.86 kDa 
• Atom Count: 7289 
• Modelled Residue Count: 797 
• Deposited Residue Count: 822 
• Unique protein chains: 1

1KYQ

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

• PDB DOI: 10.2210/pdb1KYQ/pdb

• Classification: OXIDOREDUCTASE, LYASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-02-05 Released: 2002-05-08 
• Deposition Author(s): Schubert, H.L., Raux, E., Brindley, A.A., Wilson, K.S., Hill, C.P., Warren, M.J.

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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 

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

• PubMed: 11980703 
• 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. 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.

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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

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Organizational Affiliation: 

Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Siroheme biosynthesis protein MET8	A, B, C	274	Saccharomyces cerevisiae	Mutation(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)
UniProt
Find proteins for P15807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15807  Go to UniProtKB:  P15807

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], E [auth B], F [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 156.988	α = 90
b = 80.856	β = 121.88
c = 103.975	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-05 
• Released Date: 2002-05-08 
Deposition Author(s): Schubert, H.L., Raux, E., Brindley, A.A., Wilson, K.S., Hill, C.P., Warren, M.J.

Revision History  

• 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