1SDW

Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase with bound peptide and dioxygen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex.

Prigge, S.T.Eipper, B.A.Mains, R.E.Amzel, L.M.

(2004) Science 304: 864-867

  • DOI: 10.1126/science.1094583

  • PubMed Abstract: 
  • Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow subst ...

    Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.


    Organizational Affiliation

    Department of Microbiology and Molecular Immunology, The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-glycine alpha-amidating monooxygenase
A
314Rattus norvegicusGene Names: Pam
EC: 4.3.2.5, 1.14.17.3
Find proteins for P14925 (Rattus norvegicus)
Go to UniProtKB:  P14925
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

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A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
IYT
Query on IYT

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A
N-ALPHA-ACETYL-3,5-DIIODOTYROSYL-D-THREONINE
THREONINE DERIVATIVE
C15 H18 I2 N2 O6
TWMKRGDZEJLDDH-LKXWSVAYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.478α = 90.00
b = 68.979β = 90.00
c = 82.108γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance