1PHM

PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM) FROM RAT

• PDB DOI: https://doi.org/10.2210/pdb1PHM/pdb

• Classification: MONOOXYGENASE
• Organism(s): Rattus norvegicus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 1997-10-10 Released: 1998-11-11 
• Deposition Author(s): Prigge, S.T., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Amidation of bioactive peptides: the structure of peptidylglycine alpha-hydroxylating monooxygenase.

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

(1997) Science 278: 1300-1305

• PubMed: 9360928 
• DOI: https://doi.org/10.1126/science.278.5341.1300
• Primary Citation of Related Structures:  
  1PHM


• PubMed Abstract: 
  

  Many neuropeptides and peptide hormones require amidation at the carboxyl terminus for activity. Peptidylglycine alpha-amidating monooxygenase (PAM) catalyzes the amidation of these diverse physiological regulators. The amino-terminal domain of the bifunctional PAM protein is a peptidylglycine alpha-hydroxylating monooxygenase (PHM) with two coppers that cycle through cupric and cuprous oxidation states. The anomalous signal of the endogenous coppers was used to determine the structure of the catalytic core of oxidized rat PHM with and without bound peptide substrate. These structures strongly suggest that the PHM reaction proceeds via activation of substrate by a copper-bound oxygen species. The mechanistic and structural insight gained from the PHM structures can be directly extended to dopamine beta-monooxygenase.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.18 kDa 
• Atom Count: 2,633 
• Modelled Residue Count: 305 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE	A	310	Rattus norvegicus	Mutation(s): 0  EC: 1.14.17.3 (PDB Primary Data), 4.3.2.5 (UniProt)
UniProt
Find proteins for P14925 (Rattus norvegicus) Explore P14925  Go to UniProtKB:  P14925

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth A], C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
AZI	E [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.4	α = 90
b = 68.66	β = 90
c = 81.38	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MADSYS	phasing
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-11 
Deposition Author(s): Prigge, S.T., Amzel, L.M.

Revision History  

• Version 1.0: 1998-11-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary