1OPM

OXIDIZED (CU2+) PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM) WITH BOUND SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/13351
  • Primary Citation of Related Structures:  
    3PHM, 1OPM

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE)A310Rattus norvegicusMutation(s): 0 
Gene Names: Pam
EC: 1.14.17.3 (PDB Primary Data), 4.3.2.5 (UniProt)
Find proteins for P14925 (Rattus norvegicus)
Explore P14925 
Go to UniProtKB:  P14925
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IYG
Query on IYG

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]N-ALPHA-ACETYL-3,5-DIIODOTYROSYLGLYCINE
C13 H14 I2 N2 O5
SXRYVFRVDCDPKH-JTQLQIEISA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A], D [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download Ideal Coordinates CCD File 
C [auth A]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.399α = 90
b = 68.84β = 90
c = 81.047γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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