7ZZL | pdb_00007zzl

Crystal structure of CYP106A1

PDB DOI: https://doi.org/10.2210/pdb7ZZL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium DSM 319
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-25 Released: 2023-04-12
Deposition Author(s): Carius, Y., Kiss, F., Hutter, M., Bernhardt, R., Lancaster, C.R.D.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.206 (Depositor), 0.216 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural comparison of the cytochrome P450 enzymes CYP106A1 and CYP106A2 provides insight into their differences in steroid conversion.

Carius, Y., Hutter, M., Kiss, F., Bernhardt, R., Lancaster, C.R.D.

(2022) FEBS Lett 596: 3133-3144

PubMed: 36151590 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14502
Primary Citation Related Structures:
7Q9E, 7ZZL

PubMed Abstract:
Understanding the structural basis of the selectivity of steroid hydroxylation requires detailed structural and functional investigations on various steroid hydroxylases with different selectivities, such as the bacterial cytochrome P450 enzymes. Here, the crystal structure of the cytochrome P450 CYP106A1 from Priestia megaterium was solved. CYP106A1 exhibits a rare additional structural motif of a cytochrome P450, a sixth β-sheet. The protein was found in different unusual conformations corresponding to both open and closed forms even when crystallized without any known substrate. The structural comparison of CYP106A1 with the previously investigated CYP106A2, including docking studies for both isoforms with the substrate cortisol, reveals a completely different orientation of the steroid molecule in the active sites. This distinction convincingly explains the experimentally observed differences in substrate conversion and product formation by the two enzymes.

Organizational Affiliation

Department of Structural Biology, Faculty of Medicine, Center of Human and Molecular Biology (ZHMB), Saarland University, Homburg, Germany.

Macromolecule Content

Total Structure Weight: 198.51 kDa
Atom Count: 14,013
Modeled Residue Count: 1,558
Deposited Residue Count: 1,664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B, C, D	416	Priestia megaterium DSM 319	Mutation(s): 0 Gene Names: BMD_1855 EC: 1.14.14
UniProt
Find proteins for D5DF35 (Priestia megaterium (strain DSM 319 / IMG 1521)) Explore D5DF35 Go to UniProtKB: D5DF35
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5DF35
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain L [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D]	DA [auth D], E [auth A], L [auth B], V [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain V [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Q [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B]	Q [auth B], Z [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain Q [auth B] Focus chain Z [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] EA [auth D] F [auth A] FA [auth D] AA [auth C], BA [auth C], EA [auth D], F [auth A], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], P [auth B], T [auth B], U [auth B], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain GA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain GA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain GA [auth D]	GA [auth D], R [auth B], S [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain GA [auth D] Focus chain R [auth B] Focus chain S [auth B]
OXY Query on OXY 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]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Interactions & Density Focus chain CA [auth C]