5WJA

Crystal structure of H107A peptidylglycine alpha-hydroxylating monooxygenase (PHM) in complex with citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Effects of copper occupancy on the conformational landscape of peptidylglycine alpha-hydroxylating monooxygenase.

Maheshwari, S.Shimokawa, C.Rudzka, K.Kline, C.D.Eipper, B.A.Mains, R.E.Gabelli, S.B.Blackburn, N.Amzel, L.M.

(2018) Commun Biol 1: 74-74

  • DOI: 10.1038/s42003-018-0082-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of metalloproteins that use redox-active metals for catalysis are usually exquisitely folded in a way that they are prearranged to accept their metal cofactors. Peptidylglycine α-hydroxylating monooxygenase (PHM) is a dicopper enzyme t ...

    The structures of metalloproteins that use redox-active metals for catalysis are usually exquisitely folded in a way that they are prearranged to accept their metal cofactors. Peptidylglycine α-hydroxylating monooxygenase (PHM) is a dicopper enzyme that catalyzes hydroxylation of the α-carbon of glycine-extended peptides for the formation of des-glycine amidated peptides. Here, we present the structures of apo-PHM and of mutants of one of the copper sites (H107A, H108A, and H172A) determined in the presence and absence of citrate. Together, these structures show that the absence of one copper changes the conformational landscape of PHM. In one of these structures, a large interdomain rearrangement brings residues from both copper sites to coordinate a single copper (closed conformation) indicating that full copper occupancy is necessary for locking the catalytically competent conformation (open). These data suggest that in addition to their required participation in catalysis, the redox-active metals play an important structural role.


    Organizational Affiliation

    6Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA.,3Division of Environmental and Biomolecular Systems, School of Medicine, Oregon Health and Sciences University, Portland, OR 97239 USA.,5Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,4Department of Neuroscience, University of Connecticut, Farmington, CT 06030 USA.,2Department of Chemistry, Kurume University School of Medicine, Kurume, Fukuoka 830-0011 Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-glycine alpha-amidating monooxygenase
A, D
312Rattus norvegicusMutation(s): 1 
Gene Names: Pam
Find proteins for P14925 (Rattus norvegicus)
Go to UniProtKB:  P14925
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
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, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

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Download CCD File 
D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.544α = 90.00
b = 100.613β = 90.00
c = 101.582γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
HKL-2000data reduction
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1517522

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references
  • Version 1.2: 2019-11-27
    Type: Author supporting evidence