5LIV

Crystal structure of myxobacterial CYP260A1

PDB DOI: https://doi.org/10.2210/pdb5LIV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sorangium cellulosum So ce56
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-07-15 Released: 2016-11-23
Deposition Author(s): Carius, Y., Khatri, Y., Bernhardt, R., Lancaster, C.R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.223
R-Value Work: 0.187
R-Value Observed: 0.189

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural characterization of CYP260A1 from Sorangium cellulosum to investigate the 1 alpha-hydroxylation of a mineralocorticoid.

Khatri, Y., Carius, Y., Ringle, M., Lancaster, C.R., Bernhardt, R.

(2016) FEBS Lett 590: 4638-4648

PubMed: 27878817 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12479
Primary Citation of Related Structures:
5LIV

PubMed Abstract:
In this study, we report the crystal structure of the cytochrome P450 CYP260A1 (PDB 5LIV) from the myxobacterium Sorangium cellulosum So ce56. In addition, we investigated the hydroxylation of 11-deoxycorticosterone by CYP260A1 by reconstituting the enzyme with the surrogate redox partners adrenodoxin and adrenodoxin reductase. The major product of this steroid conversion was identified as 1α-hydroxy-11-deoxycorticosterone, a novel Δ4 C-21 steroidal derivative. Furthermore, we docked the substrate into the crystal structure and replaced Ser326, the residue responsible for substrate orientation, with asparagine and observed that the mutant S326N displayed higher activity and selectivity for the formation of 1α-hydroxy-11-deoxycorticosterone compared to the wild-type CYP260A1. Thus, our findings highlight the usefulness of the obtained crystal structure of CYP260A1 in identifying biotechnologically more efficient reactions.

Organizational Affiliation

Institute of Biochemistry, Saarland University, Saarbrücken, Germany.

Macromolecule Content

Total Structure Weight: 205.04 kDa
Atom Count: 12,879
Modelled Residue Count: 1,570
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 CYP260A1,Cytochrome P450 CYP260A1	A, B, C, D	450	Sorangium cellulosum So ce56	Mutation(s): 0 Gene Names: sce1588 EC: 1.14 (PDB Primary Data), 1.14.15.19 (UniProt)
UniProt
Find proteins for A9FDB7 (Sorangium cellulosum (strain So ce56)) Explore A9FDB7 Go to UniProtKB: A9FDB7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9FDB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth D] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	E [auth A], FA [auth D], P [auth B], W [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain FA [auth D] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain FA [auth D] Focus chain P [auth B] Focus chain W [auth C]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	DA [auth C] EA [auth C] K [auth A] L [auth A] MA [auth D] DA [auth C], EA [auth C], K [auth A], L [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], PA [auth D], Q [auth B], QA [auth D], R [auth B], U [auth B], V [auth B], X [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain LA [auth D] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] F [auth A] G [auth A] GA [auth D] AA [auth C], BA [auth C], F [auth A], G [auth A], GA [auth D], H [auth A], J [auth A], JA [auth D], LA [auth D], S [auth B], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain S [auth B] Focus chain Z [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain KA [auth D] SDF format, chain T [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain T [auth B]	CA [auth C] HA [auth D] I [auth A] IA [auth D] KA [auth D] CA [auth C], HA [auth D], I [auth A], IA [auth D], KA [auth D], T [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain T [auth B] Interactions & Density Focus chain CA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.223
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 234.56	α = 90
b = 234.56	β = 90
c = 96.43	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2016-12-07
Changes: Database references
Version 1.2: 2017-01-11
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description