7Q4F | pdb_00007q4f

Structure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coproheme

PDB DOI: https://doi.org/10.2210/pdb7Q4F/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-10-30 Released: 2022-02-23
Deposition Author(s): Michlits, H., Valente, N., Mlynek, G., Hofbauer, S.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.182 (Depositor), 0.179 (DCC)
R-Value Work:
0.140 (Depositor), 0.144 (DCC)
R-Value Observed:
0.142 (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

Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes.

Michlits, H., Valente, N., Mlynek, G., Hofbauer, S.

(2021) Front Bioeng Biotechnol 9: 807678-807678

PubMed: 35141216 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fbioe.2021.807678
Primary Citation Related Structures:
7Q4F, 7Q4G

PubMed Abstract:
The oxidative decarboxylation of coproheme to form heme b by coproheme decarboxylase is a stereospecific two-step reaction. In the first step, the propionate at position two (p2) is cleaved off the pyrrole ring A to form a vinyl group at this position. Subsequently, the propionate at position four (p4) on pyrrole ring B is cleaved off and heme b is formed. In this study, we attempted to engineer coproheme decarboxylase from Corynebacterium diphtheriae to alter the stereospecificity of this reaction. By introducing a tyrosine residue in proximity to the propionate at position 4, we were able to create a new radical center in the active site. However, the artificial Tyr183 ^• radical could not be shown to catalyze any decarboxylation.

Organizational Affiliation

Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.

Macromolecule Content

Total Structure Weight: 140.23 kDa
Atom Count: 10,323
Modeled Residue Count: 1,150
Deposited Residue Count: 1,185
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coproheme	A, B, C, D, E	237	Corynebacterium diphtheriae	Mutation(s): 1 Gene Names: BT093_04375 EC: 1.3.98.5
UniProt
Find proteins for Q6NGV6 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGV6 Go to UniProtKB: Q6NGV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NGV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FEC (Subject of Investigation/LOI) Query on FEC Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], K [auth D], L [auth E]	1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX C₃₆ H₃₆ Fe N₄ O₈ FEDZMOFKVKOYTI-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain I [auth B] MOL2 format, chain M [auth E] MOL2 format, chain I [auth B] mmCIF format, chain M [auth E] mmCIF format, chain I [auth B]	I [auth B], M [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain M [auth E] Interactions & Density Focus chain I [auth B] Focus chain M [auth E]