4US5 | pdb_00004us5

Crystal Structure of apo-MsnO8

PDB DOI: https://doi.org/10.2210/pdb4US5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces bottropensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-03 Released: 2014-07-16
Deposition Author(s): Maier, S., Pflueger, T., Loesgen, S., Asmus, K., Broetz, E., Paululat, T., Zeeck, A., Andrade, S., Bechthold, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.216 (Depositor), 0.228 (DCC)
R-Value Work:
0.188 (Depositor), 0.201 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Insights Into the Bioactivity of Mensacarcin and Epoxide Formation by Msno8.

Maier, S., Pflueger, T., Loesgen, S., Asmus, K., Broetz, E., Paululat, T., Zeeck, A., Andrade, S., Bechthold, A.

(2014) Chembiochem 15: 749

PubMed: 24554499 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201300704
Primary Citation Related Structures:
4US5

PubMed Abstract:
Mensacarcin, a potential antitumour drug, is produced by Streptomyces bottropensis. The structure consists of a three-membered ring system with many oxygen atoms. Of vital importance in this context is an epoxy moiety in the side chain of mensacarcin. Our studies with different mensacarcin derivatives have demonstrated that this epoxy group is primarily responsible for the cytotoxic effect of mensacarcin. In order to obtain further information about this epoxy moiety, inactivation experiments in the gene cluster were carried out to identify the epoxy-forming enzyme. Therefore the cosmid cos2, which covers almost the complete type II polyketide synthase (PKS) gene cluster, was heterologously expressed in Streptomyces albus. This led to production of didesmethylmensacarcin, due to the fact that methyltransferase genes are missing in the cosmid. Further gene inactivation experiments on this cosmid showed that MsnO8, a luciferase-like monooxygenase, introduces the epoxy group at the end of the biosynthesis of mensacarcin. In addition, the protein MsnO8 was purified, and its crystal structure was determined to a resolution of 1.80 Å.

Organizational Affiliation

Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany).

Macromolecule Content

Total Structure Weight: 152.96 kDa
Atom Count: 11,466
Modeled Residue Count: 1,323
Deposited Residue Count: 1,352
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LUCIFERASE-LIKE MONOOXYGENASE	A, B, C	338	Streptomyces bottropensis	Mutation(s): 0
UniProt
Find proteins for W8QCH3 (Streptomyces bottropensis) Explore W8QCH3 Go to UniProtKB: W8QCH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8QCH3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LUCIFERASE-LIKE MONOOXYGENASE	D	338	Streptomyces bottropensis	Mutation(s): 0
UniProt
Find proteins for W8QCH3 (Streptomyces bottropensis) Explore W8QCH3 Go to UniProtKB: W8QCH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8QCH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain S [auth B]	BA [auth C], K [auth A], LA [auth D], S [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain K [auth A] Focus chain LA [auth D] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain K [auth A] Focus chain LA [auth D] Focus chain S [auth B]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain CA [auth C]	CA [auth C]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain CA [auth C] Interactions & Density Focus chain CA [auth C]
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain MA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain MA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain MA [auth D]	DA [auth C], EA [auth C], MA [auth D]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain MA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain MA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain AA [auth C]	AA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Interactions & Density Focus chain AA [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	E [auth A] F [auth A] FA [auth D] G [auth A] GA [auth D] E [auth A], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], KA [auth D], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216 (Depositor), 0.228 (DCC)
R-Value Work: 0.188 (Depositor), 0.201 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.005	α = 90
b = 102.902	β = 90
c = 160.697	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary