7BK7 | pdb_00007bk7

PfCopC mutant - D83N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.268 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.211 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BK7

This is version 1.1 of the entry. See complete history

Literature

Copper binding and reactivity at the histidine brace motif: insights from mutational analysis of the Pseudomonas fluorescens copper chaperone CopC.

Ipsen, J.O.Hernandez-Rollan, C.Muderspach, S.J.Brander, S.Bertelsen, A.B.Jensen, P.E.Norholm, M.H.H.Lo Leggio, L.Johansen, K.S.

(2021) FEBS Lett 595: 1708-1720

  • DOI: https://doi.org/10.1002/1873-3468.14092
  • Primary Citation Related Structures: 
    7BK5, 7BK6, 7BK7

  • PubMed Abstract: 

    The histidine brace (His-brace) is a copper-binding motif that is associated with both oxidative enzymes and proteinaceous copper chaperones. Here, we used biochemical and structural methods to characterize mutants of a His-brace-containing copper chaperone from Pseudomonas fluorescens (PfCopC). A total of 15 amino acid variants in primary and second-sphere residues were produced and characterized in terms of their copper binding and redox properties. PfCopC has a very high affinity for Cu(II) and also binds Cu(I). A high reorganization barrier likely prevents redox cycling and, thus, catalysis. In contrast, mutations in the conserved second-sphere Glu27 enable slow oxidation of ascorbate. The crystal structure of the variant E27A confirmed copper binding at the His-brace. Unexpectedly, Asp83 at the equatorial position was shown to be indispensable for Cu(II) binding in the His-brace of PfCopC. A PfCopC mutant that was designed to mimic the His-brace from lytic polysaccharide monooxygenase-like family X325 did not bind Cu(II), but was still able to bind Cu(I). These results highlight the importance of the proteinaceous environment around the copper His-brace for reactivity and, thus, the difference between enzyme and chaperone.


  • Organizational Affiliation
    • Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark.

Macromolecule Content 

  • Total Structure Weight: 20.6 kDa 
  • Atom Count: 1,574 
  • Modeled Residue Count: 190 
  • Deposited Residue Count: 194 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative copper resistance proteinA [auth AAA],
B [auth BBB]
97Pseudomonas [fluorescens] SBW25Mutation(s): 1 
Gene Names: PFLU_3946
UniProt
Find proteins for C3JYL7 (Pseudomonas fluorescens (strain SBW25))
Explore C3JYL7 
Go to UniProtKB:  C3JYL7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3JYL7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth AAA]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
D [auth AAA]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth AAA],
H [auth BBB]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth AAA],
F [auth AAA],
I [auth BBB]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.268 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.3α = 90
b = 80.3β = 90
c = 89.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF17SA0027704

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description