3PHM | pdb_00003phm

REDUCED (CU+) PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM)

• PDB DOI: https://doi.org/10.2210/pdb3PHM/pdb

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


• Deposited: 1999-05-25 Released: 1999-09-29 
• Deposition Author(s): Prigge, S.T., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.257 (Depositor) 
• R-Value Work: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Substrate-mediated electron transfer in peptidylglycine alpha-hydroxylating monooxygenase.

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

(1999) Nat Struct Biol 6: 976-983

• PubMed: 10504734 
• DOI: https://doi.org/10.1038/13351
• Primary Citation Related Structures: 
  1OPM, 3PHM


• PubMed Abstract: 
  

  Peptide amidation is a ubiquitous posttranslational modification of bioactive peptides. Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3), the enzyme that catalyzes the first step of this reaction, is composed of two domains, each of which binds one copper atom. The coppers are held 11 A apart on either side of a solvent-filled interdomain cleft, and the PHM reaction requires electron transfer between these sites. A plausible mechanism for electron transfer might involve interdomain motion to decrease the distance between the copper atoms. Our experiments show that PHM catalytic core (PHMcc) is enzymatically active in the crystal phase, where interdomain motion is not possible. Instead, structures of two states relevant to catalysis indicate that water, substrate and active site residues may provide an electron transfer pathway that exists only during the PHM catalytic cycle.

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Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.27 kDa 
• Atom Count: 2,622 
• Modeled Residue Count: 310 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NI	E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
AZI	C [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.257 (Depositor) 
• R-Value Work:  0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.519	α = 90
b = 68.77	β = 90
c = 82.417	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-09-29 
Deposition Author(s): Prigge, S.T., Amzel, L.M.

Revision History  

• Version 1.0: 1999-09-29
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary