Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.48 kDa 
• Atom Count: 1918 
• Residue Count: 214 
• Unique protein chains: 2

2Q5W

The X-ray Crystal Structure of Molybdopterin Synthase from Staphylococcus aureus

• DOI: 10.2210/pdb2Q5W/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-06-03 Released: 2008-02-19 
• Deposition Author(s): Daniels, J.N., Schindelin, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.193 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency.

Daniels, J.N., Wuebbens, M.M., Rajagopalan, K.V., Schindelin, H.

(2008) Biochemistry 47: 615-626

• PubMed: 18092812 
• DOI: 10.1021/bi701734g
• Primary Citation of Related Structures:  
  2Q5W, 2QIE, 3BII


• PubMed Abstract: 
  

In almost all biological life forms, molybdenum and tungsten are coordinated by molybdopterin (MPT), a tricyclic pyranopterin containing a cis-dithiolene group. Together, the metal and the pterin moiety form the redox reactive molybdenum cofactor (Moco). Mutations in patients with deficiencies in Moco biosynthesis usually occur in the enzymes catalyzing the first and second steps of biosynthesis, leading to the formation of precursor Z and MPT, respectively. The second step is catalyzed by the heterotetrameric MPT synthase protein consisting of two large (MoaE) and two small (MoaD) subunits with the MoaD subunits located at opposite ends of a central MoaE dimer. Previous studies have determined that the conversion of the sulfur- and metal-free precursor Z to MPT by MPT synthase involves the transfer of sulfur atoms from a C-terminal MoaD thiocarboxylate to the C-1' and C-2' positions of precursor Z. Here, we present the crystal structures of non-thiocarboxylated MPT synthase from Staphylococcus aureus in its apo form and in complex with precursor Z. A comparison of the two structures reveals conformational changes in a loop that participates in interactions with precursor Z. In the complex, precursor Z is bound by strictly conserved residues in a pocket at the MoaE dimer interface in close proximity of the C-terminal glycine of MoaD. Biochemical evidence indicates that the first dithiolene sulfur is added at the C-2' position.

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Organizational Affiliation: 

Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin-converting factor subunit 2	E	149	Staphylococcus aureus	Mutation(s): 0  Gene Names: moaE EC: 2.8.1.12
Find proteins for P65401 (Staphylococcus aureus (strain N315)) Explore P65401  Go to UniProtKB:  P65401

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin converting factor, subunit 1	D	77	Staphylococcus aureus	Mutation(s): 0  Gene Names: moaD
Find proteins for Q7A441 (Staphylococcus aureus (strain N315)) Explore Q7A441  Go to UniProtKB:  Q7A441

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.193 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.922	α = 90
b = 45.754	β = 93.36
c = 41.772	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-06-03 
• Released Date: 2008-02-19 
Deposition Author(s): Daniels, J.N., Schindelin, H.

Revision History 

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description