8HJX | pdb_00008hjx

Crystal structure of a cupin protein (tm1459, H52A/H58E mutant) in copper (Cu) substituted form

PDB DOI: https://doi.org/10.2210/pdb8HJX/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-11-24 Released: 2023-06-14
Deposition Author(s): Matsumoto, R., Kurisu, G., Fujieda, N.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

An artificial metallolyase with pliable 2-His-1-carboxylate facial triad for stereoselective Michael addition.

Matsumoto, R., Yoshioka, S., Yuasa, M., Morita, Y., Kurisu, G., Fujieda, N.

(2023) Chem Sci 14: 3932-3937

PubMed: 37035687 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d2sc06809e
Primary Citation of Related Structures:
8HJX, 8HJY, 8HJZ

PubMed Abstract:
We repurposed the metal-binding site of a cupin superfamily protein into the 2-His-1-carboxylate facial triad, which is one of the common motifs in natural non-heme enzymes, to construct artificial metalloenzymes that can catalyze new-to-nature reactions. The Cu ²⁺-H52A/H58E variant catalyzed the stereoselective Michael addition reaction and was found to bear a flexible metal-binding site in the high-resolution crystal structure. Furthermore, the H52A/H58E/F104W mutant accommodated a water molecule, which was supported by Glu58 and Trp104 residues via hydrogen bonding, presumably leading to high stereoselectivity. Thus, the 2-His-1-carboxylate facial triad was confirmed to be a versatile and promising metal-binding motif for abiological and canonical biological reactions.

Organizational Affiliation

Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku Sakai-shi Osaka 599-8531 Japan fujieda@omu.ac.jp.

Macromolecule Content

Total Structure Weight: 26.96 kDa
Atom Count: 2,196
Modelled Residue Count: 233
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin_2 domain-containing protein	A, B	118	Thermotoga maritima MSB8	Mutation(s): 2 Gene Names: TM_1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H0 Go to UniProtKB: Q9X1H0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1H0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]