2VOX

An oxidized tryptophan facilitates copper-binding in Methylococcus capsulatus secreted protein MopE. The structure of mercury soaked MopE to 1.9AA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Oxidized Tryptophan Facilitates Copper Binding in Methylococcus Capsulatus-Secreted Protein Mope.

Helland, R.Fjellbirkeland, A.Karlsen, O.A.Ve, T.Lillehaug, J.R.Jensen, H.B.

(2008) J.Biol.Chem. 283: 13897

  • DOI: 10.1074/jbc.M800340200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins can coordinate metal ions with endogenous nitrogen and oxygen ligands through backbone amino and carbonyl groups, but the amino acid side chains coordinating metals do not include tryptophan. Here we show for the first time the involvement o ...

    Proteins can coordinate metal ions with endogenous nitrogen and oxygen ligands through backbone amino and carbonyl groups, but the amino acid side chains coordinating metals do not include tryptophan. Here we show for the first time the involvement of the tryptophan metabolite kynurenine in a protein metal-binding site. The crystal structure to 1.35 angstroms of MopE* from the methane-oxidizing Methylococcus capsulatus (Bath) provided detailed information about its structure and mononuclear copper-binding site. MopE* contains a novel protein fold of which only one-third of the structure displays similarities to other known folds. The geometry around the copper ion is distorted tetrahedral with one oxygen ligand from a water molecule, two histidine imidazoles (His-132 and His-203), and at the fourth distorted tetrahedral position, the N1 atom of the kynurenine, an oxidation product of Trp-130. Trp-130 was not oxidized to kynurenine in MopE* heterologously expressed in Escherichia coli, nor did this protein bind copper. Our findings indicate that the modification of tryptophan to kynurenine and its involvement in copper binding is an innate property of M. capsulatus MopE*.


    Organizational Affiliation

    Norwegian Structural Biology Centre, Faculty of Science, University of Tromso, N-9073 Tromso, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SURFACE-ASSOCIATED PROTEIN
A
336Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Mutation(s): 0 
Gene Names: mopE
Find proteins for G1UBC6 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  G1UBC6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KYN
Query on KYN
A
L-PEPTIDE LINKINGC10 H12 N2 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.939α = 90.00
b = 101.282β = 98.32
c = 54.816γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
SHELXphasing
MOSFLMdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance