4PYD

MoaC in complex with cPMP crystallized in space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.186 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis.

Hover, B.M.Tonthat, N.K.Schumacher, M.A.Yokoyama, K.

(2015) Proc.Natl.Acad.Sci.USA 112: 6347-6352

  • DOI: 10.1073/pnas.1500697112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The molybdenum cofactor (Moco) is essential for all kingdoms of life, plays central roles in various biological processes, and must be biosynthesized de novo. During Moco biosynthesis, the characteristic pyranopterin ring is constructed by a complex ...

    The molybdenum cofactor (Moco) is essential for all kingdoms of life, plays central roles in various biological processes, and must be biosynthesized de novo. During Moco biosynthesis, the characteristic pyranopterin ring is constructed by a complex rearrangement of guanosine 5'-triphosphate (GTP) into cyclic pyranopterin (cPMP) through the action of two enzymes, MoaA and MoaC (molybdenum cofactor biosynthesis protein A and C, respectively). Conventionally, MoaA was considered to catalyze the majority of this transformation, with MoaC playing little or no role in the pyranopterin formation. Recently, this view was challenged by the isolation of 3',8-cyclo-7,8-dihydro-guanosine 5'-triphosphate (3',8-cH2GTP) as the product of in vitro MoaA reactions. To elucidate the mechanism of formation of Moco pyranopterin backbone, we performed biochemical characterization of 3',8-cH2GTP and functional and X-ray crystallographic characterizations of MoaC. These studies revealed that 3',8-cH2GTP is the only product of MoaA that can be converted to cPMP by MoaC. Our structural studies captured the specific binding of 3',8-cH2GTP in the active site of MoaC. These observations provided strong evidence that the physiological function of MoaA is the conversion of GTP to 3',8-cH2GTP (GTP 3',8-cyclase), and that of MoaC is to catalyze the rearrangement of 3',8-cH2GTP into cPMP (cPMP synthase). Furthermore, our structure-guided studies suggest that MoaC catalysis involves the dynamic motions of enzyme active-site loops as a way to control the timing of interaction between the reaction intermediates and catalytically essential amino acid residues. Thus, these results reveal the previously unidentified mechanism behind Moco biosynthesis and provide mechanistic and structural insights into how enzymes catalyze complex rearrangement reactions.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdenum cofactor biosynthesis protein MoaC
A, B, C, D, E, F
161Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: moaC (chlA3)
EC: 4.6.1.17
Find proteins for P0A738 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A738
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8CS
Query on 8CS

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Download CCD File 
A, B, E, F
(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
GOL
Query on GOL

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Download CCD File 
C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

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Download CCD File 
D
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.186 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.594α = 90.00
b = 97.213β = 90.00
c = 165.331γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description