8PUN | pdb_00008pun

Old Yellow Enzyme from the thermophilic Ferrovum sp. JA12

PDB DOI: https://doi.org/10.2210/pdb8PUN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ferrovum sp. JA12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-07-17 Released: 2023-08-02
Deposition Author(s): Polidori, N., Gruber, K.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.205 (Depositor), 0.209 (DCC)
R-Value Work:
0.180 (Depositor), 0.184 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme.

Polidori, N., Babin, P., Daniel, B., Gruber, K.

(2025) Proteins 93: 1181-1188

PubMed: 39840754 Search on PubMed
DOI: https://doi.org/10.1002/prot.26800
Primary Citation Related Structures:
8PUN

PubMed Abstract:
The Old Yellow Enzyme from Ferrovum sp. JA12 (FOYE) displays an unusual thermal stability for an enzyme isolated from a mesophilic organism. We determined the crystal structure of this enzyme and performed bioinformatic characterization to get insights into its thermal stability. The enzyme displays a tetrameric quaternary structure; however, unlike the other tetrameric homologs, it clusters in a separate phylogenetic group and possesses unique interactions that stabilize this oligomeric state. The thermal stability of this enzyme is mainly due to an unusually high number of intramolecular hydrogen bonds. Finally, this study provides a general analysis of the forces driving the oligomerization in Old Yellow Enzymes.

Organizational Affiliation

Institute of Molecular Biosciences, University of Graz, Graz, Austria.

Macromolecule Content

Total Structure Weight: 166.83 kDa
Atom Count: 11,933
Modeled Residue Count: 1,424
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase	A, B, C, D	373	Ferrovum sp. JA12	Mutation(s): 0 Gene Names: namA EC: 1.6.99.1
UniProt
Find proteins for A0ACD6B9Y1 (Ferrovum sp. JA12) Explore A0ACD6B9Y1 Go to UniProtKB: A0ACD6B9Y1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9Y1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain Y [auth D] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C]	E [auth A], M [auth B], S [auth C], Y [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
9D2 Query on 9D2 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	G [auth A], O [auth B]	2-ethyl-2-(hydroxymethyl)propane-1,3-diol C₆ H₁₄ O₃ ZJCCRDAZUWHFQH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth A] SDF format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain V [auth C]	F [auth A], J [auth A], V [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain V [auth C]
YT3 Query on YT3 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain CA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain CA [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain CA [auth D]	AA [auth D] CA [auth D] H [auth A] I [auth A] P [auth B] AA [auth D], CA [auth D], H [auth A], I [auth A], P [auth B], Q [auth B], U [auth C]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain T [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	BA [auth D], T [auth C], W [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain T [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain T [auth C] Focus chain W [auth C] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain R [auth B] SDF format, chain X [auth C] SDF format, chain K [auth A] SDF format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth D]	DA [auth D], EA [auth D], K [auth A], R [auth B], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C]