5O1L

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

PDB DOI: https://doi.org/10.2210/pdb5O1L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces sp. K30
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-05-18 Released: 2017-08-02
Deposition Author(s): Ilcu, L., Roether, W., Birke, J., Brausemann, A., Einsle, O., Jendrossek, D.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.189
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 28733658 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-017-05268-2
Primary Citation of Related Structures:
5O1L, 5O1M

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 (Lcp _K30) is a b-type cytochrome and acts as an endo-type dioxygenase producing C ₂₀ and higher oligo-isoprenoids that differ in the number of isoprene units but have the same terminal functions, CHO-CH ₂- and -CH ₂-COCH ₃. Our analysis of the Lcp _K30 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 Lcp _K30 is ligated to the polypeptide by a proximal histidine (His198) and by a lysine residue (Lys167) as the distal axial ligand. The comparison of Lcp _K30 structures in a closed and in an open state as well as spectroscopic and biochemical analysis of wild type and Lcp _K30 muteins provided insights into the action of the enzyme during catalysis.

Organizational Affiliation

Institute for Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 89.92 kDa
Atom Count: 6,352
Modelled Residue Count: 748
Deposited Residue Count: 814
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubber oxygenase	A, B	407	Streptomyces sp. K30	Mutation(s): 0 Gene Names: lcp EC: 1.13
UniProt
Find proteins for Q3L8N0 (Streptomyces sp. (strain K30)) Explore Q3L8N0 Go to UniProtKB: Q3L8N0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3L8N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
BU3 Query on BU3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B]	F [auth A], K [auth B]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	D [auth A], E [auth A], I [auth B], J [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]