5ZIS

Crystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3

PDB DOI: https://doi.org/10.2210/pdb5ZIS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-17 Released: 2018-08-15
Deposition Author(s): Omura, K., Aiba, Y., Onoda, H., Sugimoto, H., Shoji, O., Watanabe, Y.
Funding Organization(s): Japan Science and Technology, Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.258 (Depositor), 0.260 (DCC)
R-Value Observed:
0.259 (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

Reconstitution of full-length P450BM3 with an artificial metal complex by utilising the transpeptidase Sortase A.

Omura, K., Aiba, Y., Onoda, H., Stanfield, J.K., Ariyasu, S., Sugimoto, H., Shiro, Y., Shoji, O., Watanabe, Y.

(2018) Chem Commun (Camb) 54: 7892-7895

PubMed: 29845154 Search on PubMed
DOI: https://doi.org/10.1039/c8cc02760a
Primary Citation of Related Structures:
5ZIS, 5ZLH

PubMed Abstract:
Haem substitution is an effective approach to tweak the function of haemoproteins. Herein, we report a facile haem substitution method for self-sufficient cytochrome P450BM3 (CYP102A1) from Bacillus megaterium utilising the transpeptidase Sortase A from Staphylococcus aureus. We successfully constructed Mn-substituted BM3 and investigated its catalytic activity.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan. shoji.osami@a.mbox.nagoya-u.ac.jp.

Macromolecule Content

Total Structure Weight: 211.14 kDa
Atom Count: 14,722
Modelled Residue Count: 1,804
Deposited Residue Count: 1,820
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B, C, D	455	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 0 Gene Names: cyp102A1, cyp102, BG04_163 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MNH Query on MNH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE PROTOPORPHYRIN IX C₃₄ H₃₂ Mn N₄ O₄ UIBYYPDLEONCGQ-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]