2UX6

Pseudoazurin with engineered amicyanin ligand loop, oxidized form, pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Influence of Loop Shortening on the Metal Binding Site of Cupredoxin Pseudoazurin.

Velarde, M.Huber, R.Yanagisawa, S.Dennison, C.Messerschmidt, A.

(2007) Biochemistry 46: 9981

  • DOI: 10.1021/bi701113w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Atomic resolution structures of the pseudoazurin (PAZ) variant into which the shorter ligand-containing loop of amicyanin (AMI) is introduced have been determined. The mutated loop adopts a different conformation in PAZAMI than in AMI. The copper sit ...

    Atomic resolution structures of the pseudoazurin (PAZ) variant into which the shorter ligand-containing loop of amicyanin (AMI) is introduced have been determined. The mutated loop adopts a different conformation in PAZAMI than in AMI. The copper site structure is affected, with the major influence being an increased axial interaction resulting in the shortest Cu(II)-S(Met) bond observed for the cupredoxin family of electron-transfer proteins. This is accompanied by a lengthening of the important Cu-S(Cys) bond and enhanced tetragonal distortion, consistent with the influence of the PAZAMI loop contraction on the UV/vis spectrum. The change in active site geometry is the major cause of the 50 mV decrease in reduction potential. The copper site structure changes very little upon reduction, consistent with the distorted site still possessing the properties required to facilitate rapid electron transfer. The exposed His ligand on the loop protonates in the reduced protein and reasons for the increased pKa compared to that of PAZ are discussed. The area surrounding the His ligand is more hydrophobic in PAZAMI than in PAZ, while electron self-exchange, which involves homodimer formation via this surface patch, is decreased. The nature of the side chains in this region, as dictated by the sequence of the ligand-containing loop, is a more significant factor than hydrophobicity for facilitating transient protein interactions in PAZ. The structure of PAZAMI demonstrates the importance of loop-scaffold interactions for metal sites in proteins.


    Organizational Affiliation

    Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PSEUDOAZURIN
A
122Achromobacter cycloclastesMutation(s): 0 
Gene Names: bcp
Find proteins for P19567 (Achromobacter cycloclastes)
Go to UniProtKB:  P19567
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 105.627α = 90.00
b = 105.626β = 90.00
c = 57.925γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance