2UX6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    2UX6, 2UX7, 2UXF, 2UXG

  • 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 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PSEUDOAZURINA122Achromobacter cycloclastesMutation(s): 0 
Gene Names: bcp
UniProt
Find proteins for P19567 (Achromobacter cycloclastes)
Explore P19567 
Go to UniProtKB:  P19567
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19567
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.627α = 90
b = 105.626β = 90
c = 57.925γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other