2QIE

Staphylococcus aureus molybdopterin synthase in complex with precursor Z


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Molybdopterin-converting factor subunit 2A, G [auth E], C [auth H], E [auth K]148Staphylococcus aureusMutation(s): 0 
Gene Names: moaE
EC: 2.8.1.12
UniProt
Find proteins for P65401 (Staphylococcus aureus (strain N315))
Explore P65401 
Go to UniProtKB:  P65401
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Molybdopterin synthase small subunitB, H [auth D], D [auth G], F [auth J]77Staphylococcus aureusMutation(s): 0 
Gene Names: moaD
UniProt
Find proteins for Q7A441 (Staphylococcus aureus (strain N315))
Explore Q7A441 
Go to UniProtKB:  Q7A441
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8CS
Query on 8CS

Download Ideal Coordinates CCD File 
I [auth A], J [auth H], K, L [auth E](2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE
C10 H12 N5 O7 P
PWFXLXMPGSLEOZ-RNCCKPSGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.639α = 90
b = 58.1β = 90
c = 331.817γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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