2FT6

Structure of Cu(II)azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPM"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Basic requirements for a metal-binding site in a protein: The influence of loop shortening on the cupredoxin azurin.

Li, C.Yanagisawa, S.Martins, B.M.Messerschmidt, A.Banfield, M.J.Dennison, C.

(2006) Proc.Natl.Acad.Sci.Usa 103: 7258-7263

  • DOI: 10.1073/pnas.0600774103
  • Primary Citation of Related Structures:  
  • Also Cited By: 2HXA, 2HX9, 2HX8, 2HX7

  • PubMed Abstract: 
  • The main active-site loop of the copper-binding protein azurin (a cupredoxin) has been shortened from C(112)TFPGH(117)SALM(121) to C(112)TPH(115)PFM(118) (the native loop from the cupredoxin amicyanin) and also to C(112)TPH(115)PM(117). The Cu(II) si ...

    The main active-site loop of the copper-binding protein azurin (a cupredoxin) has been shortened from C(112)TFPGH(117)SALM(121) to C(112)TPH(115)PFM(118) (the native loop from the cupredoxin amicyanin) and also to C(112)TPH(115)PM(117). The Cu(II) site structure is almost unaffected by shortening, as is that of the Cu(I) center at alkaline pH in the variant with the C(112)TPH(115)PM(117) loop sequence. Subtle spectroscopic differences due to alterations in the spin density distribution at the Cu(II) site can be attributed mainly to changes in the hydrogen-bonding pattern. Electron transfer is almost unaffected by the introduction of the C(112)TPH(115)PFM(118) loop, but removal of the Phe residue has a sizable effect on reactivity, probably because of diminished homodimer formation. At mildly acidic pH values, the His-115 ligand protonates and dissociates from the cuprous ion, an effect that has a dramatic influence on the reactivity of cupredoxins. These studies demonstrate that the amicyanin loop adopts a conformation identical to that found in the native protein when introduced into azurin, that a shorter than naturally occurring C-terminal active-site loop can support a functional T1 copper site, that CTPHPM is the minimal loop length required for binding this ubiquitous electron transfer center, and that the length and sequence of a metal-binding loop regulates a range of structural and functional features of the active site of a metalloprotein.


    Related Citations: 
    • Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip
      Nar, H.,Messerschmidt, A.,Huber, R.,van de Kamp, M.,Canters, G.W.
      (1991) J.Mol.Biol. 221: 765
    • Crystal structure analysis and refinement at 2.15 A resolution of amicyanin, a type I blue copper PROTEIN, FROM THIOBACILLUS VERSUTUS
      Romero, A.,Nar, H.,Huber, R.,Messerschmidt, A.,Kalverda, A.P.,Canters, G.W.,Durley, R.,Mathews, F.S.
      (1994) J.Mol.Biol. 236: 1196
    • Loop-contraction mutagenesis of type 1 copper sites
      Yanagisawa, S.,Dennison, C.
      (2004) J.Am.Chem.Soc. 126: 15711


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Azurin
A
124Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: azu
Find proteins for P00282 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P00282
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.25 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.127 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.788α = 90.00
b = 51.788β = 90.00
c = 75.553γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-01-24 
  • Released Date: 2006-04-11 
  • Deposition Author(s): Banfield, M.J.

Revision History 

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection