7YXH | pdb_00007yxh

Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and succinate

PDB DOI: https://doi.org/10.2210/pdb7YXH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-16 Released: 2022-04-27
Deposition Author(s): Chowdhury, R., Schofield, C.J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.222 (DCC)
R-Value Work:
0.196 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans.

Chowdhury, R., Abboud, M.I., Wiley, J., Tumber, A., Markolovic, S., Schofield, C.J.

(2022) Sci Rep 12: 6065-6065

PubMed: 35410347 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-022-10028-y
Primary Citation Related Structures:
7YXG, 7YXH, 7YXI, 7YXJ, 7YXK, 7YXL

PubMed Abstract:
The JmjC family of 2-oxoglutarate dependent oxygenases catalyse a range of hydroxylation and demethylation reactions in humans and other animals. Jumonji domain-containing 7 (JMJD7) is a JmjC (3S)-lysyl-hydroxylase that catalyses the modification of Developmentally Regulated GTP Binding Proteins 1 and 2 (DRG1 and 2); JMJD7 has also been reported to have histone endopeptidase activity. Here we report biophysical and biochemical studies on JMJD7 from Drosophila melanogaster (dmJMJD7). Notably, crystallographic analyses reveal that the unusual dimerization mode of JMJD7, which involves interactions between both the N- and C-terminal regions of both dmJMJD7 monomers and disulfide formation, is conserved in human JMJD7 (hsJMJD7). The results further support the assignment of JMJD7 as a lysyl hydroxylase and will help enable the development of selective inhibitors for it and other JmjC oxygenases.

Organizational Affiliation

Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.

Macromolecule Content

Total Structure Weight: 73.77 kDa
Atom Count: 5,011
Modeled Residue Count: 613
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH14974p	A, B	322	Drosophila melanogaster	Mutation(s): 0 Gene Names: JMJD7, Dmel\CG10133, CG10133, Dmel_CG10133 EC: 1.14.11 (PDB Primary Data), 3.4 (UniProt), 1.14.11.63 (UniProt)
UniProt
Find proteins for Q9VU77 (Drosophila melanogaster) Explore Q9VU77 Go to UniProtKB: Q9VU77
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VU77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]