8P2J | pdb_00008p2j

Imine Reductase from Ajellomyces dermatitidis in space group C21

PDB DOI: https://doi.org/10.2210/pdb8P2J/pdb

Classification: OXIDOREDUCTASE
Organism(s): Blastomyces dermatitidis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-16 Released: 2023-08-30
Deposition Author(s): Sharma, M., Grogan, G.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.193 (Depositor), 0.203 (DCC)
R-Value Work:
0.166 (Depositor), 0.178 (DCC)
R-Value Observed:
0.168 (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

Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms.

Sharma, M., Cuetos, A., Willliams, A., Gonzalez-Martinez, D., Grogan, G.

(2023) Acta Crystallogr F Struct Biol Commun 79: 224-230

PubMed: 37581897 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X23006672
Primary Citation Related Structures:
8OZV, 8OZW, 8P2J

PubMed Abstract:
The NADPH-dependent imine reductase from Ajellomyces dermatitidis (AdRedAm) catalyzes the reductive amination of certain ketones with amine donors supplied in an equimolar ratio. The structure of AdRedAm has been determined in three forms. The first form, which belongs to space group P3 ₁21 and was refined to 2.01 Å resolution, features two molecules (one dimer) in the asymmetric unit in complex with the redox-inactive cofactor NADPH ₄. The second form, which belongs to space group C2 ₁ and was refined to 1.73 Å resolution, has nine molecules (four and a half dimers) in the asymmetric unit, each complexed with NADP ⁺. The third form, which belongs to space group P3 ₁21 and was refined to 1.52 Å resolution, has one molecule (one half-dimer) in the asymmetric unit. This structure was again complexed with NADP ⁺ and also with the substrate 2,2-difluoroacetophenone. The different data sets permit the analysis of AdRedAm in different conformational states and also reveal the molecular basis of stereoselectivity in the transformation of fluorinated acetophenone substrates by the enzyme.

Organizational Affiliation

Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom.

Macromolecule Content

Total Structure Weight: 283.39 kDa
Atom Count: 21,304
Modeled Residue Count: 2,599
Deposited Residue Count: 2,646
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B, C, D, E A, B, C, D, E, F, G, H, I	294	Blastomyces dermatitidis	Mutation(s): 1 Gene Names: BDBG_03427
UniProt
Find proteins for A0A179UH34 (Blastomyces gilchristii (strain SLH14081)) Explore A0A179UH34 Go to UniProtKB: A0A179UH34
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A179UH34
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain R [auth I] SDF format, chain Q [auth H] SDF format, chain P [auth G] SDF format, chain M [auth D] SDF format, chain K [auth B] SDF format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain R [auth I] MOL2 format, chain Q [auth H] MOL2 format, chain P [auth G] MOL2 format, chain M [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain R [auth I] mmCIF format, chain Q [auth H] mmCIF format, chain P [auth G] mmCIF format, chain M [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A]	J [auth A] K [auth B] L [auth C] M [auth D] N [auth E] J [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth G], Q [auth H], R [auth I]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth I] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth I]