1NVI

Orthorhombic Crystal Form of Molybdopterin Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Studies of Molybdopterin Synthase Provide Insights into its Catalytic Mechanism

Rudolph, M.J.Wuebbens, M.M.Turque, O.Rajagopalan, K.V.Schindelin, H.

(2003) J.Biol.Chem. 278: 14514-14522

  • DOI: 10.1074/jbc.M300449200
  • Primary Citation of Related Structures:  
  • Also Cited By: 3BII

  • PubMed Abstract: 
  • Molybdenum cofactor biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes, including humans. Genetic deficiencies of enzymes involved in cofactor biosynthesis in humans lead to a severe and usually fatal d ...

    Molybdenum cofactor biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes, including humans. Genetic deficiencies of enzymes involved in cofactor biosynthesis in humans lead to a severe and usually fatal disease. The molybdenum cofactor contains a tricyclic pyranopterin, termed molybdopterin, that bears the cis-dithiolene group responsible for molybdenum ligation. The dithiolene group of molybdopterin is generated by molybdopterin synthase, which consists of a large (MoaE) and small (MoaD) subunit. The crystal structure of molybdopterin synthase revealed a heterotetrameric enzyme in which the C terminus of each MoaD subunit is deeply inserted into a MoaE subunit to form the active site. In the activated form of the enzyme, the MoaD C terminus is present as a thiocarboxylate. The present study identified the position of the thiocarboxylate sulfur by exploiting the anomalous signal originating from the sulfur atom. The structure of molybdopterin synthase in a novel crystal form revealed a binding pocket for the terminal phosphate of molybdopterin, the product of the enzyme, and suggested a binding site for the pterin moiety present in precursor Z and molybdopterin. Finally, the crystal structure of the MoaE homodimer provides insights into the conformational changes accompanying binding of the MoaD subunit.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdopterin converting factor subunit 1
D
81Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: moaD (chlA4, chlM)
Find proteins for P30748 (Escherichia coli (strain K12))
Go to UniProtKB:  P30748
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Molybdopterin converting factor subunit 2
E
150Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: moaE (chlA5)
EC: 2.8.1.12
Find proteins for P30749 (Escherichia coli (strain K12))
Go to UniProtKB:  P30749
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.578α = 90.00
b = 94.860β = 90.00
c = 137.440γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance