5O1L

Structure of Latex Clearing Protein LCP in the open state with bound imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and Functional Analysis of Latex Clearing Protein (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber.

Ilcu, L.Rother, W.Birke, J.Brausemann, A.Einsle, O.Jendrossek, D.

(2017) Sci Rep 7: 6179-6179

  • DOI: 10.1038/s41598-017-05268-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Latex clearing proteins (Lcps) are rubber oxygenases that catalyse the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria. Lcp of Streptomyces sp. K30 (LcpK30) is a b-type cytochrome and acts as an endo-type ...

    Latex clearing proteins (Lcps) are rubber oxygenases that catalyse the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria. Lcp of Streptomyces sp. K30 (LcpK30) is a b-type cytochrome and acts as an endo-type dioxygenase producing C20 and higher oligo-isoprenoids that differ in the number of isoprene units but have the same terminal functions, CHO-CH2- and -CH2-COCH3. Our analysis of the LcpK30 structure revealed a 3/3 globin fold with additional domains at the N- and C-termini and similarities to globin-coupled sensor proteins. The haem group of LcpK30 is ligated to the polypeptide by a proximal histidine (His198) and by a lysine residue (Lys167) as the distal axial ligand. The comparison of LcpK30 structures in a closed and in an open state as well as spectroscopic and biochemical analysis of wild type and LcpK30 muteins provided insights into the action of the enzyme during catalysis.


    Organizational Affiliation

    Institute for Biochemistry, Albert-Ludwigs-Universit├Ąt Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rubber oxygenase
A, B
407Streptomyces sp. (strain K30)Mutation(s): 0 
Gene Names: lcp
EC: 1.13.-.-
Find proteins for Q3L8N0 (Streptomyces sp. (strain K30))
Go to UniProtKB:  Q3L8N0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, B
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 56.758α = 85.43
b = 62.796β = 66.06
c = 64.416γ = 74.16
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEi-520/5
German Research FoundationGermanyJe-152/18

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release